Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta ...Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.展开更多
Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase...Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.展开更多
The outermost layer epidermis of a plant stem plays an important role in protection and environment-sensing. The mechanisms of sensing and response to the environment through the stem epidermis remain unclear. Here we...The outermost layer epidermis of a plant stem plays an important role in protection and environment-sensing. The mechanisms of sensing and response to the environment through the stem epidermis remain unclear. Here we report enriched expression of genes involved in stress resistance and signal transduction functions in the stem epidermis of both D. purpureus and A. thaliana by cDNA cloning and QPCR in D. purpureus and by analysis using dataset from a genome-wide comparison with cDNAs differentially expressed between the epidermis and inner parts of top and base stem in A. thaliana. Among 188 cDNAs from the stem epidermis of D. purpureus, 13% and 17% were related to signal transduction and defense respectively. Most of them were up-regulated more in the stem epidermis than the inner stem, as well as in A. thaliana. Also, the distribution of the numbers and specificities of up-regulated genes related to signal transduction and regulatory networks in the epidermis and inner stem revealed the possibility of positional differences in regulation. The results revealed the importance of the epidermis in signal transduction and plant defence.展开更多
Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanism...Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs（mRNAs） are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAembryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.展开更多
As a carbon-storage compound and osmoprotectant in brown algae,mannitol is synthesized and then accumulated at high levels in Saccharina japonica(Sja);however,the underlying control mechanisms have not been studied.Ou...As a carbon-storage compound and osmoprotectant in brown algae,mannitol is synthesized and then accumulated at high levels in Saccharina japonica(Sja);however,the underlying control mechanisms have not been studied.Our analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps.A mannitol-1-phosphate dehydrogenase(M1 PDH2)and two mannitol-1-phosphatases(M1 Pase1 and MIPase2)work together or in combination to exhibit full enzymatic properties.Based on comprehensive transcriptomic data from different tissues,generations,and sexes as well as under different stress conditions,coupled with droplet digital PCR(dd PCR)and proteomic confirmation,we suggest that Sja M1 Pase1 plays a major role in mannitol biosynthesis and that the basic mannitol anabolism and the carbohydrate pool dynamics are responsible for carbon storage and anti-stress mechanism.Our proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in Sja.In addition,we discover that mannitol-metabolism-associated(MMA)genes show differential expression between the multicellular filamentous(gametophyte)and large parenchymal thallus(sporophyte)generations and respond differentially to environmental stresses,such as hyposaline and hyperthermia conditions.Our results indicate that the ecophysiological significance of such differentially expressed genes may be attributable to the evolution of heteromorphic generations(filamentous and thallus)and environmental adaptation of Laminariales.展开更多
Bacillus thuringiensis（B.thuringiensis） is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins（Cry） are commonly used as biological alternatives to pesticides.In a pangenomic study,we sequenced ...Bacillus thuringiensis（B.thuringiensis） is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins（Cry） are commonly used as biological alternatives to pesticides.In a pangenomic study,we sequenced seven B.thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform.The B.thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added.Compared to the pangenomes of its closely related species of the same genus,B.thuringiensis pangenome shows an open characteristic,similar to B.cereus but not to B.anthracis;the latter has a closed pangenome. We also found extensive divergence among the seven B.thuringiensis genome assemblies,which harbor ample repeats and single nucleotide polymorphisms（SNPs）.The identities among orthologous genes are greater than 84.5%and the hotspots for the genome variations were discovered in genomic regions of 2.3-2.8 Mb and 5.0-5.6 Mb.We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed,are very useful for pangenomic studies.展开更多
基金Supported by the Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)(No.2021CXGC011306)the MNR Key Laboratory of Eco-Environmental Science and Technology,China(No.MEEST-2021-05)+2 种基金the Natural Science Foundation of Shandong Province(No.ZR2020MD002)the Doctoral Science Research Foundation of Yantai University(Nos.SM15B01,SM19B70,SM19B28)the“Double-Hundred Action”of Yantai City(No.2320004-SM20RC02)。
文摘Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.
基金Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)under contract No.2021CXGC011306MNR Key Laboratory of Eco-Environmental Science and Technology,China under contract No.MEEST-2021-05+2 种基金Natural Science Foundation of Shandong Province under contract No.ZR2020MD002Doctoral Science Research Foundation of Yantai University under contract Nos SM15B01,SM19B70 and SM19B28Double-Hundred Action of Yantai City under contract No.2320004-SM20RC02。
文摘Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.
文摘The outermost layer epidermis of a plant stem plays an important role in protection and environment-sensing. The mechanisms of sensing and response to the environment through the stem epidermis remain unclear. Here we report enriched expression of genes involved in stress resistance and signal transduction functions in the stem epidermis of both D. purpureus and A. thaliana by cDNA cloning and QPCR in D. purpureus and by analysis using dataset from a genome-wide comparison with cDNAs differentially expressed between the epidermis and inner parts of top and base stem in A. thaliana. Among 188 cDNAs from the stem epidermis of D. purpureus, 13% and 17% were related to signal transduction and defense respectively. Most of them were up-regulated more in the stem epidermis than the inner stem, as well as in A. thaliana. Also, the distribution of the numbers and specificities of up-regulated genes related to signal transduction and regulatory networks in the epidermis and inner stem revealed the possibility of positional differences in regulation. The results revealed the importance of the epidermis in signal transduction and plant defence.
基金supported by the National Basic Research Program of China(Grant Nos.2011CB944100 and2011CB944101)the National Natural Science Foundation of China(Grant No.90919024)+1 种基金the Special Foundation Work Program(Grant No.2009FY120100)the National High Technology Research and Development Program of Ministry of Science and Technology of China(Grant No.2012AA020409)
文摘Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs（mRNAs） are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAembryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.
基金supported by the National Natural Science Foundation of China (Grant No. 41376143)the Leading Talents Program in Taishan Industry of Shandong Province+3 种基金the Leading Talents Program in Entrepreneurship and Innovation of Qingdaothe China-ASEAN Maritime Cooperation Fund “China-ASEAN Center for Joint Research and Promotion of Marine Aquaculture Technology”the China Agriculture Research System (Grant No. CARS-50)the Seed Industry Innovation and Industrialization Project of Fujian Province, China
文摘As a carbon-storage compound and osmoprotectant in brown algae,mannitol is synthesized and then accumulated at high levels in Saccharina japonica(Sja);however,the underlying control mechanisms have not been studied.Our analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps.A mannitol-1-phosphate dehydrogenase(M1 PDH2)and two mannitol-1-phosphatases(M1 Pase1 and MIPase2)work together or in combination to exhibit full enzymatic properties.Based on comprehensive transcriptomic data from different tissues,generations,and sexes as well as under different stress conditions,coupled with droplet digital PCR(dd PCR)and proteomic confirmation,we suggest that Sja M1 Pase1 plays a major role in mannitol biosynthesis and that the basic mannitol anabolism and the carbohydrate pool dynamics are responsible for carbon storage and anti-stress mechanism.Our proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in Sja.In addition,we discover that mannitol-metabolism-associated(MMA)genes show differential expression between the multicellular filamentous(gametophyte)and large parenchymal thallus(sporophyte)generations and respond differentially to environmental stresses,such as hyposaline and hyperthermia conditions.Our results indicate that the ecophysiological significance of such differentially expressed genes may be attributable to the evolution of heteromorphic generations(filamentous and thallus)and environmental adaptation of Laminariales.
基金supported by a grant from King Abdulaziz City for Science and Technology,Riyadh,Saudi Arabia(No. KACST 428-29)institutional grant from CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics, Chinese Academy of Sciences+2 种基金supported by the grants from the National Basic Research Program(973 Program)(No.2010CB126604)the Special Foundation Work Program(No.2009FY 120100)the Ministry of Science and Technology of the People's Republic of China and from the National Science Foundation of China(No. 31071163).
文摘Bacillus thuringiensis（B.thuringiensis） is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins（Cry） are commonly used as biological alternatives to pesticides.In a pangenomic study,we sequenced seven B.thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform.The B.thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added.Compared to the pangenomes of its closely related species of the same genus,B.thuringiensis pangenome shows an open characteristic,similar to B.cereus but not to B.anthracis;the latter has a closed pangenome. We also found extensive divergence among the seven B.thuringiensis genome assemblies,which harbor ample repeats and single nucleotide polymorphisms（SNPs）.The identities among orthologous genes are greater than 84.5%and the hotspots for the genome variations were discovered in genomic regions of 2.3-2.8 Mb and 5.0-5.6 Mb.We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed,are very useful for pangenomic studies.
