Wild soybean resources, which are progenitor of cultivated soybean with selected agronomic characters, have rich genetic diversity. Here we used genome re-sequencing technology to analyze genetic variations between th...Wild soybean resources, which are progenitor of cultivated soybean with selected agronomic characters, have rich genetic diversity. Here we used genome re-sequencing technology to analyze genetic variations between the wild soybean ＇ED059’ and cultivar ＇Tianlong 2＇. In genome level, 3,214,319 and 1,519,765 single nucleotide polymorphisms （SNPs）, 553,141 and 314,430 insertion/deletion polymorphisms （InDels）, and 471,063 and 334,412 structural variations （SVs） were identified between ＇ED0595＇ and ＇Tianlong 2＇ respec-tively based on soybean （Glycine max L. Merr） reference genome. Base on gene annotation of reference genome, 68,830 （2.14%） and 34,570 （2.27%） non-synonymous SNPs, 8,478 and 4,826 frameshift substitution were detected in CDS regions of ＇ED0595＇ and ＇Tianlong 2＇. ＇ED059’ harbored much more specific genetic variations of jasmonic acid （JA）, salicylic acid （SA） and ethylene （ET） biosynthesis and signal pathway genes than those in ＇Tianlong 2＇ indicating its unique strong insect defense activity. This work provides important information allowing better understanding of the soybean genome and being helpful for dissecting the genetic basis of important traits such as insect defense in soybean.展开更多
Soil salinization is detrimental to the growth and development of flax and ultimately leads to a decrease in yield.However,the molecular mechanism of linseed response to salt stress is still unclear.In this study,a sa...Soil salinization is detrimental to the growth and development of flax and ultimately leads to a decrease in yield.However,the molecular mechanism of linseed response to salt stress is still unclear.In this study,a salt-tolerant(ST)linseed variety STS and a salt-sensitive(SS)variety DYM were selected as experiment materials.Bulk segregation analysis and whole-genome resequencing technologies were performed to map salt tolerance quantitative trait loci(QTL).A total of 38,625 QTL loci were identified.Fifteen genes(which were not annotated in the reference genome)were identified within a 2.597 Mb region in chromosome 1.Two salt tolerance candidate genes Lus.o.m.scaffold91.141 and Lus.o.m.Scaffold1.14 encoding WD40 and cytochrome P450 were identified by predicting protein functions.Previous studies showed that WD40 and cytochrome P450 could significantly improve plant salt stress tolerance.In this paper,results showed that Lus.o.m.scaffold91.141 and Lus.o.m.Scaffold1.14 might be involved in response to salt stress in lineseed.The fine mapping and functional analysis of these genes provide a molecular breeding basis for the genetic improvement of high salt-tolerant linseed varieties.展开更多
Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 indivi...Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation.We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.展开更多
The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysac...The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.展开更多
Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(...Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.展开更多
The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main...The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.展开更多
In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA ...In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.展开更多
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformat...Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.展开更多
Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-thro...Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence,structure,and other characteristics of the P.atropurpurea chloroplast genome.The result showed that the chloroplast genome of P.atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure.The genome has annotated a total of 132 functional genes,including 43 tRNAs,8 rRNAs,76 protein-coding genes,and 5 pseudo-genes.In total,358 SSR loci were checked out,mainly composed of mononucleotide and trinucleotide repeat.There are three types of scattered repetitive sequences,totaling 4223,including 2452 forward repeats,1763 palindrome repeats,and eight reverse repeats.The optimal codon usage frequency is relatively high with AT usage preference in this genome.Chloroplast genome comparative analysis in the family Ericaceae shows that the overall sequence is more complex,and there are more variations in the gene interval region.The collinearity analysis indicated that there is a complex rearrangement of species between different genera in Ericaceae.The selection pressure analysis showed that the protein-encoding genes rpl33 and rps16 were positively selected among the seven medicinal plants in Ericaceae.The maximum likelihood tree shows that the genetic relationship among P.atropurpurea,Pyrola rotundifolia,and Chimaphila japonica is relatively close.Therefore,an important data basis was provided for species identification,genetic diversity,and phylogenetic studies of P.atropurpurea and even this genus of plants.展开更多
Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit...Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit plant growth and development,and reduce species richness comparing to tropical continental islands with mesophytic habitats(Li et al.,2024;Ren et al.,2017;Tu et al.,2022,2024).Coupled with global climate changes,these adverse conditions have been being exacerbated,leading to extensive degradation of ecosystems throughout the tropical coral islands(Li et al.,2021).Native insular plant resources provide enormous potentials in island greening and ecological restoration,since they have colonized and become well adapted to the specialized habitat on tropical coral islands,evolving a series of functional traits and molecular strategies to accommodate the abiotic stresses.Thus,understanding the genomic make-up of these plants will help uncover molecular mechanisms underlying adaptation to tropical coral islands.However,contrary to the numerous genomic studies done for other extreme habitats,such as deserts(Hu et al.,2021;Ma et al.,2013),alpine regions(Zhang et al.,2023),intertidal habitats(Feng et al.,2021;Hu et al.,2020;Natarajan et al.,2021),and karst caves(Feng et al.,2020),molecular adaptation of plants on the tropical coral islands remains to be elucidated.展开更多
Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such fu...Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.展开更多
Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bi...Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.展开更多
Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economica...Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economically important in eliminating poverty and protecting ecology in the Yangtze River Three Gorges Reservoir.However,rain-induced cracking(rain-cracking,literally skin cracking caused by rain)is a limitation to‘Wushancuili'fruit production and causes severe losses.This study reported a high-quality‘Wushancuili'genome assembly consisting of a 302.17-Mb sequence with eight pseudo-chromosomes and a contig N50 of 23.59 Mb through the combination of Illumina sequencing,Pacific Biosciences HiFiⅢsequencing,and high-throughput chromosome conformation capture technology.A total of 25109 protein-coding genes are predicted and 54.17%of the genome is composed of repetitive sequences.‘Wushancuili'underwent a remarkable orthoselection during evolution.Gene identification revealed that loss-of-function in four core MYB10 genes results in the anthocyanin deficiency and absence of red color,revealing the green coloration due to the residual high chlorophyll in fruit skin.Besides,the occurrence of cracking is assumed to be closely associated with cell wall modification and frequently rain-induced pathogen enrichment through transcriptomic analysis.The loss of MYB10 genes might render fruit more susceptible to pathogen-mediated cracking by weakening the epidermal strength and reactive oxygen species(ROS)scavenging.Our findings provided fundamental knowledge regarding fruit coloration and rain-cracking and will facilitate genetic improvement and cultivation management in Chinese plums.展开更多
Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study...Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.展开更多
Animal models are extensively used in all aspects of biomedical research,with substantial contributions to our understanding of diseases,the development of pharmaceuticals,and the exploration of gene functions.The fie...Animal models are extensively used in all aspects of biomedical research,with substantial contributions to our understanding of diseases,the development of pharmaceuticals,and the exploration of gene functions.The field of genome modification in rabbits has progressed slowly.However,recent advancements,particularly in CRISPR/Cas9-related technologies,have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases,including cardiovascular disorders,immunodeficiencies,agingrelated ailments,neurological diseases,and ophthalmic pathologies.These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice.This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine,underscoring their impact and future potential in translational medicine.展开更多
Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,...Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.展开更多
Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study ...Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.展开更多
Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associati...Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.展开更多
Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,th...Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,the classic morphological taxonomy of this family needs to be revised.In recent years,many genera of Scenedesmaceae have been established via the use of molecular methods.The phylogenetic relationships within Scenedesmaceae were analyzed using different molecular markers and morphological data,and the new freshwater genus Coccoidesmus Wang,Hou et Liu gen.nov.was described.Two new species in this genus were also described.Phylogenetic analysis based on tufA genes revealed that the new genus formed an independent clade closely related to Comasiella.However,these two genera are characterized by significant morphological differences in colony arrangement and cell shape.The chloroplast genome of the type species was assembled and annotated,and analyses of genome structure and sequences were conducted.More genome data could help clarify the phylogenetic relationships within this family.展开更多
As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level genome of green pri...As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level genome of green prickly ash which was widely cultivated in a major production area including Chongqing and Sichuan province, China. We generated 712 Gb (~112×) PacBio long reads and 511 Gb (~82×) Hi-C data, and yielded an assembly of 99 pseudochromosomes with total size of 5.32 Gb and contig N50 of 796 kb. The genomic analyses and cytogenetic experiments both indicated that the cultivarZhuye Huajiao’ was a triploid. We identified a Zanthoxylum-specific whole genome duplication event emerging about 24.8 million years ago (Mya). We also detected a transposition burst event (0.3-0.4 Mya) responsible for the large genome size of Z. armatum. Metabolomic analysis of the Zanthoxylum fruits during development stages revealed profiles of39 volatile aroma compounds and 528 secondary metabolites, from which six types of sanshools were identified. Based on metabolomic and transcriptomic network analysis, we screened candidate genes encoding long chain acyl-CoA synthetase, fatty acid desaturase,branched-chain amino acid aminotransferase involved in sanshool biosynthesis and three genes encoding terpene synthase during fruit development. The multi-omics data provide insights into the evolution of Zanthoxylum and molecular basis of numbing and aroma flavor of Sichuan pepper.展开更多
基金This work was supported by National Natural Science Foundation of China （31371654, 31522042, 31501655 and 31501334）, National Transgenic Proj-ect （grant 2014ZX08004003, 2015ZX08004003 and 2016ZX08004003）, Agricultural Science and Technology Innovation Program, Breeding Project （SQ2016ZY03002375） and Wuhan Chenguang Plan （2015070404010193）.
文摘Wild soybean resources, which are progenitor of cultivated soybean with selected agronomic characters, have rich genetic diversity. Here we used genome re-sequencing technology to analyze genetic variations between the wild soybean ＇ED059’ and cultivar ＇Tianlong 2＇. In genome level, 3,214,319 and 1,519,765 single nucleotide polymorphisms （SNPs）, 553,141 and 314,430 insertion/deletion polymorphisms （InDels）, and 471,063 and 334,412 structural variations （SVs） were identified between ＇ED0595＇ and ＇Tianlong 2＇ respec-tively based on soybean （Glycine max L. Merr） reference genome. Base on gene annotation of reference genome, 68,830 （2.14%） and 34,570 （2.27%） non-synonymous SNPs, 8,478 and 4,826 frameshift substitution were detected in CDS regions of ＇ED0595＇ and ＇Tianlong 2＇. ＇ED059’ harbored much more specific genetic variations of jasmonic acid （JA）, salicylic acid （SA） and ethylene （ET） biosynthesis and signal pathway genes than those in ＇Tianlong 2＇ indicating its unique strong insect defense activity. This work provides important information allowing better understanding of the soybean genome and being helpful for dissecting the genetic basis of important traits such as insect defense in soybean.
基金financially supported by grants from the National Natural Science Foundation of China (NSFC) (Grant no. 31560347, and 31760426)the China Agriculture Research System (CARS-14)
文摘Soil salinization is detrimental to the growth and development of flax and ultimately leads to a decrease in yield.However,the molecular mechanism of linseed response to salt stress is still unclear.In this study,a salt-tolerant(ST)linseed variety STS and a salt-sensitive(SS)variety DYM were selected as experiment materials.Bulk segregation analysis and whole-genome resequencing technologies were performed to map salt tolerance quantitative trait loci(QTL).A total of 38,625 QTL loci were identified.Fifteen genes(which were not annotated in the reference genome)were identified within a 2.597 Mb region in chromosome 1.Two salt tolerance candidate genes Lus.o.m.scaffold91.141 and Lus.o.m.Scaffold1.14 encoding WD40 and cytochrome P450 were identified by predicting protein functions.Previous studies showed that WD40 and cytochrome P450 could significantly improve plant salt stress tolerance.In this paper,results showed that Lus.o.m.scaffold91.141 and Lus.o.m.Scaffold1.14 might be involved in response to salt stress in lineseed.The fine mapping and functional analysis of these genes provide a molecular breeding basis for the genetic improvement of high salt-tolerant linseed varieties.
基金financially supported by National Natural Science Foundation of China (No. 31471899)the Knowledge Innovation Project of the Chinese Academy of Sciences (No. Y455421Z02)
文摘Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation.We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.
基金supported by the National Natural Science Foundation of China(32360058)the Central Government Guides Local Science and Technology Development Projects,China(2023ZYZX1224)Xinjiang University Excellent Doctoral Student Innovation Project(XJU2022BS051)。
文摘The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.
基金supported by grants from the National Natural Science Foundation of China(32170238,32400191)Guangdong Basic and Applied Basic Research Foundation(2023A1515111029)+2 种基金the Science,Technology and Innovation Commission of Shenzhen Municipality(RCYX20200714114538196)the Chinese Academy of Agricultural Sciences Elite Youth Program(grant 110243160001007)the Guangdong Pearl River Talent Program(2021QN02N792)。
文摘Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.
基金supported by NSFC(32070226,32360065)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2024QZKK0200)Yunnan Fundamental Research Projects(202101AS070032)the CAS“Light ofWest China”Program(xbzg-zdsys-202110)the Yunnan Innovation Team Project(202305AS350004,with LD/NY/SB/CJG/CJH as the core member).
文摘The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.
基金supported by the Natural Science Foundation of Guangdong Province(2022A1515012158)the National Science Foundation of China(41977138)+3 种基金the Construction Project of Teaching Quality and Teaching Reform in Guangdong Province(SJD202001)the General University Project of Guangdong Provincial Department of Education(2021KCXTD070 and 2021ZDZX4072)the Key Project of Social Welfare and Basic Research of Zhongshan City(2020B2010)the Start-up Fund from the Zhongshan Institute at the University of Electronic Science and Technology in China(419YKQN12)。
文摘In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.
基金supported by the National Natural Science Foundation of China Project(Grant No.32260097)the National Guidance Foundation for Local Science and Technology Development of China(Grant No.[2023]009)the Natural Science Foundation for Distinguished Young Scholars of Hebei(Grant No.C2022209010)。
文摘Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
基金supported by the Education Reform Program of Jiangxi Provincial Department of Education(JXJG-22-23-3,JXJG-23-23-5)the“Biology and Medicine”Discipline Construction Project of Nanchang NormalUniversity(100/20149)+2 种基金Jiangxi Province Key Laboratory of Oil Crops Biology(YLKFKT202203)the Education Reform Program of Nanchang Normal University(NSJG-21-25)Nanchang Key Laboratory of Comprehensive Research and Development of Brasenia schreberi(32060078).
文摘Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence,structure,and other characteristics of the P.atropurpurea chloroplast genome.The result showed that the chloroplast genome of P.atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure.The genome has annotated a total of 132 functional genes,including 43 tRNAs,8 rRNAs,76 protein-coding genes,and 5 pseudo-genes.In total,358 SSR loci were checked out,mainly composed of mononucleotide and trinucleotide repeat.There are three types of scattered repetitive sequences,totaling 4223,including 2452 forward repeats,1763 palindrome repeats,and eight reverse repeats.The optimal codon usage frequency is relatively high with AT usage preference in this genome.Chloroplast genome comparative analysis in the family Ericaceae shows that the overall sequence is more complex,and there are more variations in the gene interval region.The collinearity analysis indicated that there is a complex rearrangement of species between different genera in Ericaceae.The selection pressure analysis showed that the protein-encoding genes rpl33 and rps16 were positively selected among the seven medicinal plants in Ericaceae.The maximum likelihood tree shows that the genetic relationship among P.atropurpurea,Pyrola rotundifolia,and Chimaphila japonica is relatively close.Therefore,an important data basis was provided for species identification,genetic diversity,and phylogenetic studies of P.atropurpurea and even this genus of plants.
基金supported by the National Natural Science Foundation of China(32170232,32070222,32271613)the National Key R&D Programof China(Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs 2021-400)+1 种基金Guangdong Science and Technology Program(2024B1212050007)the National Key Research and Development Program of China(2021YFC3100405)。
文摘Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit plant growth and development,and reduce species richness comparing to tropical continental islands with mesophytic habitats(Li et al.,2024;Ren et al.,2017;Tu et al.,2022,2024).Coupled with global climate changes,these adverse conditions have been being exacerbated,leading to extensive degradation of ecosystems throughout the tropical coral islands(Li et al.,2021).Native insular plant resources provide enormous potentials in island greening and ecological restoration,since they have colonized and become well adapted to the specialized habitat on tropical coral islands,evolving a series of functional traits and molecular strategies to accommodate the abiotic stresses.Thus,understanding the genomic make-up of these plants will help uncover molecular mechanisms underlying adaptation to tropical coral islands.However,contrary to the numerous genomic studies done for other extreme habitats,such as deserts(Hu et al.,2021;Ma et al.,2013),alpine regions(Zhang et al.,2023),intertidal habitats(Feng et al.,2021;Hu et al.,2020;Natarajan et al.,2021),and karst caves(Feng et al.,2020),molecular adaptation of plants on the tropical coral islands remains to be elucidated.
基金funded by the National Natural Science Foundation of China(No.31270408)the National High Technology Research and Development Program(863 Program) of China(No.2014AA022001)
文摘Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.
基金supported by the Chinese Academy of Agricultural Sciences Innovation Project(Grant No.CAASASTIP-2013CNRRI)Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute(Grant No.CPSIBRF-CNRRI-202102)。
文摘Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.
基金financially supported by the Construction Program for Chongqing's Distinctive“Wushancuili”Industry(Grant No.4322200370)Strategic Cooperation Project of Chongqing Municipality and Chinese Academy of Agricultural Sciences(Grant No.4322300181)Fundamental Research Funds for Central Universities-Talent induction project(Grant Nos.SWU-KR22001,SWU-KQ22070)。
文摘Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economically important in eliminating poverty and protecting ecology in the Yangtze River Three Gorges Reservoir.However,rain-induced cracking(rain-cracking,literally skin cracking caused by rain)is a limitation to‘Wushancuili'fruit production and causes severe losses.This study reported a high-quality‘Wushancuili'genome assembly consisting of a 302.17-Mb sequence with eight pseudo-chromosomes and a contig N50 of 23.59 Mb through the combination of Illumina sequencing,Pacific Biosciences HiFiⅢsequencing,and high-throughput chromosome conformation capture technology.A total of 25109 protein-coding genes are predicted and 54.17%of the genome is composed of repetitive sequences.‘Wushancuili'underwent a remarkable orthoselection during evolution.Gene identification revealed that loss-of-function in four core MYB10 genes results in the anthocyanin deficiency and absence of red color,revealing the green coloration due to the residual high chlorophyll in fruit skin.Besides,the occurrence of cracking is assumed to be closely associated with cell wall modification and frequently rain-induced pathogen enrichment through transcriptomic analysis.The loss of MYB10 genes might render fruit more susceptible to pathogen-mediated cracking by weakening the epidermal strength and reactive oxygen species(ROS)scavenging.Our findings provided fundamental knowledge regarding fruit coloration and rain-cracking and will facilitate genetic improvement and cultivation management in Chinese plums.
基金financially supported by the National Natural Science Foundation of China(Grant No.31772338)the Basic Scientific Research Business Special Project of Jiangsu Academy of Agricultural Sciences(Grant No.0090756100ZX)。
文摘Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.
基金supported by the National Natural Science Foundation of China (31970574)。
文摘Animal models are extensively used in all aspects of biomedical research,with substantial contributions to our understanding of diseases,the development of pharmaceuticals,and the exploration of gene functions.The field of genome modification in rabbits has progressed slowly.However,recent advancements,particularly in CRISPR/Cas9-related technologies,have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases,including cardiovascular disorders,immunodeficiencies,agingrelated ailments,neurological diseases,and ophthalmic pathologies.These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice.This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine,underscoring their impact and future potential in translational medicine.
基金supported by the China Postdoctoral Science Foundation(2022M722020)to Z.L.Key Project of Scientific Research Program of Shaanxi Provincial Education Department(23JY020)to Z.L.+5 种基金Natural Science Basic Research Program of Shaanxi(2024JCYBMS-152)to Z.L.Key Projects of Shaanxi University of Technology(SLGKYXM2302)to Z.L.Opening Foundation of Shaanxi University of Technology(SLGPT2019KF02-02)to Z.L.Natural Science Basic Research Program of Shaanxi(2020JM-280)to G.L.Fundamental Research Funds for the Central Universities(GK201902008)to G.LNational Natural Science Foundation of China(31570378)to X.M.
文摘Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.
基金funded by the Jiangxi Provincial Natural Science Foundation,Grant Number 20232BAB216119.
文摘Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.
基金supported by the National Natural Science Foundation of China(31972558)the Agricultural Improved Seed Project of Shandong Province,China(2020LZGC014)。
文摘Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.
基金Supported by the National Natural Science Foundation of China(Nos.32000167,32370219)the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi(No.2020L0524)+1 种基金the Fundamental Research Program of Shanxi Province(No.20210302124302)the Shanxi Key Laboratory of Earth Surface Processes and Resource Ecological Security in Fenhe River Basin,Taiyuan Normal University。
文摘Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,the classic morphological taxonomy of this family needs to be revised.In recent years,many genera of Scenedesmaceae have been established via the use of molecular methods.The phylogenetic relationships within Scenedesmaceae were analyzed using different molecular markers and morphological data,and the new freshwater genus Coccoidesmus Wang,Hou et Liu gen.nov.was described.Two new species in this genus were also described.Phylogenetic analysis based on tufA genes revealed that the new genus formed an independent clade closely related to Comasiella.However,these two genera are characterized by significant morphological differences in colony arrangement and cell shape.The chloroplast genome of the type species was assembled and annotated,and analyses of genome structure and sequences were conducted.More genome data could help clarify the phylogenetic relationships within this family.
基金supported by the Projects for Innovative Research Groups of Chongqing Universities (Grant No.CXQT21028)Chongqing talent program for Zexiong Chen+2 种基金Scientific Technological Research Program of Chongqing Municipal Education Commission (Grant No.KJZD-K201901303)National Natural Science Foundation of China (Grant No.31925034)National Key Research and Development Project (Grant No.2019YFD1001200)。
文摘As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level genome of green prickly ash which was widely cultivated in a major production area including Chongqing and Sichuan province, China. We generated 712 Gb (~112×) PacBio long reads and 511 Gb (~82×) Hi-C data, and yielded an assembly of 99 pseudochromosomes with total size of 5.32 Gb and contig N50 of 796 kb. The genomic analyses and cytogenetic experiments both indicated that the cultivarZhuye Huajiao’ was a triploid. We identified a Zanthoxylum-specific whole genome duplication event emerging about 24.8 million years ago (Mya). We also detected a transposition burst event (0.3-0.4 Mya) responsible for the large genome size of Z. armatum. Metabolomic analysis of the Zanthoxylum fruits during development stages revealed profiles of39 volatile aroma compounds and 528 secondary metabolites, from which six types of sanshools were identified. Based on metabolomic and transcriptomic network analysis, we screened candidate genes encoding long chain acyl-CoA synthetase, fatty acid desaturase,branched-chain amino acid aminotransferase involved in sanshool biosynthesis and three genes encoding terpene synthase during fruit development. The multi-omics data provide insights into the evolution of Zanthoxylum and molecular basis of numbing and aroma flavor of Sichuan pepper.
