Ruminants(Ruminantia) are among the most successful herbivorous mammals, exhibiting wideranging morphological and ecological characteristics(such as headgear and multichambered stomach)and including various key livest...Ruminants(Ruminantia) are among the most successful herbivorous mammals, exhibiting wideranging morphological and ecological characteristics(such as headgear and multichambered stomach)and including various key livestock species(e. g.,cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.展开更多
Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this st...Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies （Lampyridae） （two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis） were estimated by propidium iodide （PI）-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg, a 3.1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.展开更多
DEAR EDITOR,The Atlantic sea nettle(Chrysaora quinquecirrha)has an important evolutionary position due to its high ecological value.However,due to limited sequencing technologies and complex jellyfish genomic sequence...DEAR EDITOR,The Atlantic sea nettle(Chrysaora quinquecirrha)has an important evolutionary position due to its high ecological value.However,due to limited sequencing technologies and complex jellyfish genomic sequences,the current C.quinquecirrha genome assembly is highly fragmented.Here,we used the most advanced high-throughput chromosome conformation capture(Hi-C)technology to obtain high-coverage sequencing data of the C.quinquecirrha genome.We then anchored these data to the previously published contig-level assembly to improve the genome.Finally,a high-continuity genome sequence of C.quinquecirrha was successfully assembled,which contained 1882 scaffolds with a N50 length of 3.83 Mb.The N50 length of the genome assembly was 5.23 times longer than the previously released one,and additional analysis revealed that it had a high degree of genomic continuity and accuracy.Acquisition of the high-continuity genome sequence of C.quinquecirrha not only provides a basis for the study of jellyfish evolution through comparative genomics but also provides an important resource for studies on jellyfish growth and development.展开更多
Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the g...Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.Here,we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group.We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method,i.e.,dynamic cross-tissue(DCT)network analysis.We used one of the candidate genes,Os SPL4,whose function was previously unknown,for gene editing experimental validation of the high yield,and confirmed that Os SPL4 significantly affects panicle branching and increases the rice yield.This study,which included extensive field phenotyping,cross-tissue systems biology analyses,and functional validation,uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice.The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample.DCT can be downloaded from https://github.com/ztpub/DCT.展开更多
The fall armyworm Spodoptera frugiperda recently invaded China,ravaging crops in many provinces.Deciphering the possible genetic basics for its successful invasion is critical for innovative and specific control for t...The fall armyworm Spodoptera frugiperda recently invaded China,ravaging crops in many provinces.Deciphering the possible genetic basics for its successful invasion is critical for innovative and specific control for this gluttonous pest.Here we generated comparative genomic analyses between S.frugiperda and its native relative,S.litura,which differs in host preference,locomotivity and production behavior.We demonstrated that S.frugiperda genes are enriched in taste sensory perception and nervous system,obv iously difTerent from those of S.litura.Potential host adaptation genes showed generally an elevated ratio of non-synonymous substitution rate to synonymous substitution rate,suggesting a faster evolution during the divergence of the two species.Focusing on these sets of genes,we identified 23 genes being under positive selection in S.frugiperda.Among them are two notable genes involved in sensory perception,gustatory receptor(GR)and an acetaldehyde oxidase,which are important for host detection in invasion and expansion processes.Another two genes are mitochondrial adenosine triphosphate synthase^subunit and ferritin heavy chain,which may be associated with the enhanced locomotivity and resistance,which fascinated long-distance migration needed for invasion and rapid expansion.Another interesting gene is chorion protein,in which positive selection sites in S.frugiperda were found and a replacement in one site is predicted to affect the protein function,which might be associated with competent reproductivity in S.frugiperda to ensure genetic resources for expansion.展开更多
We studied the electromagnetic form factors （EMFFs） of Ac and the contributions of the quark and diquark currents to the EMFFs of Ac in the space-like region in the Bethe-Salpeter equation approach with instantaneou...We studied the electromagnetic form factors （EMFFs） of Ac and the contributions of the quark and diquark currents to the EMFFs of Ac in the space-like region in the Bethe-Salpeter equation approach with instantaneous approximation. In this picture, baryon Ac can be regarded as a two-body c（ud） system. We found that for different values of parameters the contribution of quark and diquark currents to the EMFFs of Ac is very different, while their total contribution to the EMFFs of Ac is similar. The EMFFs of ∧c are similar to those of other baryons （proton,≡ , and ∑＋） with a peak at ω= 1, where ω=v＇.v is the velocity transfer between the initial state （with velocity v） and the final state （with velocity vr） of Ac.展开更多
A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model.In this study,we developed a tissue-based proteome map using...A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model.In this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein isoforms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome.These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues,further improving the genome annotation of the corresponding protein-coding genes.Combining the well-annotated genes that have parallel expression pattern and subcellular witness,we predicted the tissue-related subcellular locations and potential functions for these unknown proteins.Finally,we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species,referring to 68 KEGG pathways as well as 23 disease signaling pathways.These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology,as well as biomedical model application to human medicine.展开更多
The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into...The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.展开更多
In the framework of the QCD factorization approach,we study the localized CP violations of the B^(-)→K^(-)π^(+)(π)^(-)decay with and without the a_(0)^(0)(980)-f_(0)(980) mixing mechanism and observe that the local...In the framework of the QCD factorization approach,we study the localized CP violations of the B^(-)→K^(-)π^(+)(π)^(-)decay with and without the a_(0)^(0)(980)-f_(0)(980) mixing mechanism and observe that the localized CP violation can be enhanced by this mixing effect when the mass of the π^(+)(π)^(-)pair is in the vicinity of the f_(0)(980) resonance.The corresponding theoretical prediction results are A_(CP)(B^(-)→Kf_(0)→K^(-)π^(+)(π)^(-))=[0.126,0.338](0.232±0.106 with the central value form) and A_(CP)(B^(-)→K^(-)f_(0)(a_0)→K^(-)π^(+)(π)^(-))=[0.230,0.615](0.423±0.193 with the central value form),respectively.Meanwhile,we also calculate the branching fraction of the B^(-)→K^(-)f_(0)(980)→K^(-)π^(+)(π)^(-)decay,which is consistent with the experimental results.We suggest that the a_(0)^(0)(980)-f_(0)(980) mixing mechanism should be considered when theoretically and experimentally studying the CP violation of the B or D meson decays.展开更多
The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the orig...The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here,we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into Gen Origin(http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In Gen Origin, the information such as gene age estimates,annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.展开更多
基金supported by the Talents Team Construction Fund of Northwestern Polytechnical University(NWPU)Strategic Priority Research Program of CAS(XDB13000000)to W.W.State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences(GREKF19-11 to L.C.)
文摘Ruminants(Ruminantia) are among the most successful herbivorous mammals, exhibiting wideranging morphological and ecological characteristics(such as headgear and multichambered stomach)and including various key livestock species(e. g.,cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.
基金supported by grants from the National Natural Science Foundation of China(No.31472035)Yunnan Provincial Science and Technology Department(No.2014FB179)to LXY
文摘Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies （Lampyridae） （two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis） were estimated by propidium iodide （PI）-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg, a 3.1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.
基金This work was supported by the Province of China(202011840014)Shaanxi College Students’Innovation and Entrepreneurship Training Program(S202011840014)+5 种基金Xi’an Medical University College Students’Innovation and Entrepreneurship Training Program(121520014)National Natural Science Foundation of China(31760671Detail)Joint Special Project of Agricultural Basic Research in Yunnan Province(2018FG001-041)Yunnan Provincial Department of Education Research Fund(2020J0251)Scientific Research Fund of Shaanxi Provincial Education Department(20JS143)Natural Science Basic Research Plan in Shaanxi Province of China(2020JQ-876)。
文摘DEAR EDITOR,The Atlantic sea nettle(Chrysaora quinquecirrha)has an important evolutionary position due to its high ecological value.However,due to limited sequencing technologies and complex jellyfish genomic sequences,the current C.quinquecirrha genome assembly is highly fragmented.Here,we used the most advanced high-throughput chromosome conformation capture(Hi-C)technology to obtain high-coverage sequencing data of the C.quinquecirrha genome.We then anchored these data to the previously published contig-level assembly to improve the genome.Finally,a high-continuity genome sequence of C.quinquecirrha was successfully assembled,which contained 1882 scaffolds with a N50 length of 3.83 Mb.The N50 length of the genome assembly was 5.23 times longer than the previously released one,and additional analysis revealed that it had a high degree of genomic continuity and accuracy.Acquisition of the high-continuity genome sequence of C.quinquecirrha not only provides a basis for the study of jellyfish evolution through comparative genomics but also provides an important resource for studies on jellyfish growth and development.
基金the National Basic Research Program of China(Grant No.2013CB835200)the National Key R&D Program of China(Grant No.2017YFA0505500)+4 种基金the Key Grant of Yunnan Provincial Science and Technology Department(Grant No.2013GA004)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB13040700)the National Natural Science Foundation of China(Grant Nos.11871456 and 31771476)the Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01)the Open Research Fund of State Key Laboratory of Hybrid Rice(Wuhan University,Grant No.KF201806),China。
文摘Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.Here,we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group.We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method,i.e.,dynamic cross-tissue(DCT)network analysis.We used one of the candidate genes,Os SPL4,whose function was previously unknown,for gene editing experimental validation of the high yield,and confirmed that Os SPL4 significantly affects panicle branching and increases the rice yield.This study,which included extensive field phenotyping,cross-tissue systems biology analyses,and functional validation,uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice.The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample.DCT can be downloaded from https://github.com/ztpub/DCT.
文摘The fall armyworm Spodoptera frugiperda recently invaded China,ravaging crops in many provinces.Deciphering the possible genetic basics for its successful invasion is critical for innovative and specific control for this gluttonous pest.Here we generated comparative genomic analyses between S.frugiperda and its native relative,S.litura,which differs in host preference,locomotivity and production behavior.We demonstrated that S.frugiperda genes are enriched in taste sensory perception and nervous system,obv iously difTerent from those of S.litura.Potential host adaptation genes showed generally an elevated ratio of non-synonymous substitution rate to synonymous substitution rate,suggesting a faster evolution during the divergence of the two species.Focusing on these sets of genes,we identified 23 genes being under positive selection in S.frugiperda.Among them are two notable genes involved in sensory perception,gustatory receptor(GR)and an acetaldehyde oxidase,which are important for host detection in invasion and expansion processes.Another two genes are mitochondrial adenosine triphosphate synthase^subunit and ferritin heavy chain,which may be associated with the enhanced locomotivity and resistance,which fascinated long-distance migration needed for invasion and rapid expansion.Another interesting gene is chorion protein,in which positive selection sites in S.frugiperda were found and a replacement in one site is predicted to affect the protein function,which might be associated with competent reproductivity in S.frugiperda to ensure genetic resources for expansion.
基金Supported by the Fundamental Research Funds for the Central Universities of China(31020170QD052)the Natural Science Basic Research Plan in Shaanxi Province of China(2018JQ1002)the National Natural Science Foundation of China(11775024,11575023)
文摘We studied the electromagnetic form factors （EMFFs） of Ac and the contributions of the quark and diquark currents to the EMFFs of Ac in the space-like region in the Bethe-Salpeter equation approach with instantaneous approximation. In this picture, baryon Ac can be regarded as a two-body c（ud） system. We found that for different values of parameters the contribution of quark and diquark currents to the EMFFs of Ac is very different, while their total contribution to the EMFFs of Ac is similar. The EMFFs of ∧c are similar to those of other baryons （proton,≡ , and ∑＋） with a peak at ω= 1, where ω=v＇.v is the velocity transfer between the initial state （with velocity v） and the final state （with velocity vr） of Ac.
基金financially supported by the National Natural Science Foundations of China (Grant No. 31661143013)the Jinxinnong Animal Science Development Foundation
文摘A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model.In this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein isoforms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome.These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues,further improving the genome annotation of the corresponding protein-coding genes.Combining the well-annotated genes that have parallel expression pattern and subcellular witness,we predicted the tissue-related subcellular locations and potential functions for these unknown proteins.Finally,we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species,referring to 68 KEGG pathways as well as 23 disease signaling pathways.These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology,as well as biomedical model application to human medicine.
基金supported by the National Key R&D Program of China(Grant No.2020YFA0712402)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDPB17)+3 种基金the CAS Project for Young Scientists in Basic Research(Grant No.YSBR-077)the National Natural Science Foundation of China(Grant Nos.12025107,11871463,11688101,and 61621003)the National Thousand Youth Talents Plan,and the CAS“Light of West China”Program(Grant No.xbzg-zdsys-201913)China.We thank High Performance Computing(HPC)of Northwest A&F University(NWAFU)for providing computing resources。
文摘The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
基金Supported by National Natural Science Foundation of China (12105149,11775024 and 11947001)Natural Science Foundation of Zhejiang Province(LQ21A050005)+1 种基金Ningbo Natural Science Foundation (2021J180)the Fundamental Research Funds for the Provincial Universities of Zhejiang Province。
文摘In the framework of the QCD factorization approach,we study the localized CP violations of the B^(-)→K^(-)π^(+)(π)^(-)decay with and without the a_(0)^(0)(980)-f_(0)(980) mixing mechanism and observe that the localized CP violation can be enhanced by this mixing effect when the mass of the π^(+)(π)^(-)pair is in the vicinity of the f_(0)(980) resonance.The corresponding theoretical prediction results are A_(CP)(B^(-)→Kf_(0)→K^(-)π^(+)(π)^(-))=[0.126,0.338](0.232±0.106 with the central value form) and A_(CP)(B^(-)→K^(-)f_(0)(a_0)→K^(-)π^(+)(π)^(-))=[0.230,0.615](0.423±0.193 with the central value form),respectively.Meanwhile,we also calculate the branching fraction of the B^(-)→K^(-)f_(0)(980)→K^(-)π^(+)(π)^(-)decay,which is consistent with the experimental results.We suggest that the a_(0)^(0)(980)-f_(0)(980) mixing mechanism should be considered when theoretically and experimentally studying the CP violation of the B or D meson decays.
基金supported by the National Natural Science Foundation of China(31871305)the Fundamental Research Funds for the Central Universities(2662019PY003,2662020PY001)+1 种基金HZAU-AGIS Cooperation Fund(SZYJY2021010)Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2016RC011)。
文摘The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here,we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into Gen Origin(http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In Gen Origin, the information such as gene age estimates,annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.
