为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国...为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国、加拿大、德国、中国等国家的发文量较高,国家之间的合作较密切;(3)该领域的高产研究机构为加拿大英属哥伦比亚大学、加州大学戴维斯分校、中国科学院等;(4)该领域的高产作者有bernatchez,louis,nosil,patrik,feder,jeffrey;(5)“物种适应与进化”“物种间相互作用”“基因组学方法在生态学领域的应用”以及“差异基因的表达研究”是该研究领域的热点方向;(6)生态基因组学研究经历了“模式生物适应进化和变异”“进化和生态功能基因组学”“新一代基因测序技术”这些发展过程,未来会关注“物种形成过程中的基因组差异”“基因组学工具”等方面。展开更多
Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecula...Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology,quantitative genetics and genomics. Therefore,it is extremely necessary to select several versatile,low-cost,efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study,we used Zhikong scallop(Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency,while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving,it is difficult to obtain a large number of microsatellite markers,mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study,we recommend two methods,microsatellite-enriched library construction method and FIASCO-colony hybridization method,for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.展开更多
DNA is the genetic material of various organisms. Extracellular DNA adsorbed or bound on surface-active particles in soils has been shown to persist for long periods against nucleases degradation and still retain the ...DNA is the genetic material of various organisms. Extracellular DNA adsorbed or bound on surface-active particles in soils has been shown to persist for long periods against nucleases degradation and still retain the ability to transform competent cells. This paper reviews some recent advances on the binding and transformation of extracellular DNA in soils, which is fundamental to understanding the nature of the soil, regulating biodiversity, and assessing the risk of releasing genetically engineered microo…展开更多
Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ...Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.展开更多
Ubiquitous on earth,bacteriophages are the most abundant entities in every ecosystem,but human knowledge about them is still limited compared with that about other forms of organisms.To enrich human knowledge and prom...Ubiquitous on earth,bacteriophages are the most abundant entities in every ecosystem,but human knowledge about them is still limited compared with that about other forms of organisms.To enrich human knowledge and promote the utilization of bacteriophages,it is necessary to isolate and characterize as many as possible different bacteriophages.Here we describe the isolation of a T4-like bacteriophage IME08 and a rapid method for its genetic characterization.With this method we easily cloned a few random fragments of the bacteriophage genome.Sequence analysis of these random clones showed that bacteriophage IME08 shared the highest sequence similarity with T4-like Enterobacteria phage T4（94%identity）,JS98（95% identity）,JS10（95%identity） and RB14（94%identity） respectively,which suggested that IME08 belonged to T4-like bacteriophage genus.展开更多
The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number...The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.展开更多
Nitrate assimilation is a process where bacteria utilize nitrate as a nitrogen source and synthesize it into organic nitrogen. We found that nitrate-assimilating bacteria(NAB) are widely distributed in various marine ...Nitrate assimilation is a process where bacteria utilize nitrate as a nitrogen source and synthesize it into organic nitrogen. We found that nitrate-assimilating bacteria(NAB) are widely distributed in various marine environments, from surface to the deep ocean and sediment, which indicates that NAB are significant to the oceanic nitrogen cycle. Comparative genomic analysis revealed nitrate-assimilating genes(nas A) in these marine heterotrophic NAB showed different gene arrangements and diverse regulation systems. Summary on recent findings will contribute to understanding the process of nitrate assimilation in NAB and their ecological significance in the nitrogen cycle. A systematic analysis of a number of studies on bacterial nitrate assimilation in marine ecological systems was conducted to clarify directions for future research.展开更多
Migratory birds are considered natural reservoirs of avian influenza A viruses(AIVs).To further our viral ecology knowledge and understand the subsequent risk posed by wild birds,we conducted a 4-year surveillance stu...Migratory birds are considered natural reservoirs of avian influenza A viruses(AIVs).To further our viral ecology knowledge and understand the subsequent risk posed by wild birds,we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River,China.We collected over8000 samples and isolated 122 AIV strains.Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases.The results showed that the Yangtze River wintering wetlands functioned as a mixing ground,where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences;moreover,a portion of AIV gene segments were persistent inter-seasonally.Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes.In addition,we observed that viral gene segments in wintering wetlands were closely related to known North American isolates,indicating that intercontinental gene flow occurred.Notably,highly pathogenic H5 and low pathogenic H9 viruses,which usually circulate in poultry,were found to have crossed the poultry/wild bird interface,with the viruses introduced to wintering birds.Overall,this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands.Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.展开更多
The quest for the origin of species has entered the genomics era. Despite decades of evidence confirming the role of the environment in ecological speciation, an understanding of the genomics of ecological speciation ...The quest for the origin of species has entered the genomics era. Despite decades of evidence confirming the role of the environment in ecological speciation, an understanding of the genomics of ecological speciation is still in its infancy. In this review, we explore the role of genomic architecture in ecological speciation in postglacial fishes. Growing evidence for the num- ber, location, effect size, and interactions among the genes underlying population persistence, adaptive trait divergence, and re- productive isolation in these fishes reinforces the importance of considering genomic architecture in studies of ecological speci- ation. Additionally, these populations likely adapt to new freshwater environments by selection on standing genetic variation, as de novo mutations are unlikely under such recent divergence times. We hypothesize that modular genomic architectures in post- glacial fish taxa may be associated with the probability of population persistence. Empirical studies have confirmed the genic na- ture of ecological speciation, implicating surprisingly extensive linkage disequilibrium across the genome. An understanding of these genomic mosaics and how they contribute to reproductive barriers remains unclear, but migration rates and the strength of selection at these loci is predicted to influence the likelihood of population divergence. Altogether, understanding the role of ge- nomic architecture is an important component of speciation research and postglacial fishes continue to provide excellent organ- isms to test these questions, both from the perspective of variation in architectures among taxa, and with respect to the distinct environments they have colonized. However, more empirical tests of ecological speciation predictions are needed [Current Zoo- logy 59 （1）： 53-71, 2013].展开更多
文摘为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国、加拿大、德国、中国等国家的发文量较高,国家之间的合作较密切;(3)该领域的高产研究机构为加拿大英属哥伦比亚大学、加州大学戴维斯分校、中国科学院等;(4)该领域的高产作者有bernatchez,louis,nosil,patrik,feder,jeffrey;(5)“物种适应与进化”“物种间相互作用”“基因组学方法在生态学领域的应用”以及“差异基因的表达研究”是该研究领域的热点方向;(6)生态基因组学研究经历了“模式生物适应进化和变异”“进化和生态功能基因组学”“新一代基因测序技术”这些发展过程,未来会关注“物种形成过程中的基因组差异”“基因组学工具”等方面。
基金supported by ‘863’ Program (2006AA10A408 and 2006AA10A411), NSFC30571417, NYHYZX07-047, 2005DKA30470, 2006BAD09A10 and NCET-06-0594.
文摘Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology,quantitative genetics and genomics. Therefore,it is extremely necessary to select several versatile,low-cost,efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study,we used Zhikong scallop(Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency,while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving,it is difficult to obtain a large number of microsatellite markers,mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study,we recommend two methods,microsatellite-enriched library construction method and FIASCO-colony hybridization method,for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.
文摘DNA is the genetic material of various organisms. Extracellular DNA adsorbed or bound on surface-active particles in soils has been shown to persist for long periods against nucleases degradation and still retain the ability to transform competent cells. This paper reviews some recent advances on the binding and transformation of extracellular DNA in soils, which is fundamental to understanding the nature of the soil, regulating biodiversity, and assessing the risk of releasing genetically engineered microo…
基金Supported by the Key Program of National Natural Science Foundation of China (No.30730071)the National High Technology R&D Program of China(863 Program)(No.2012AA10A404)the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700)
文摘Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
文摘Ubiquitous on earth,bacteriophages are the most abundant entities in every ecosystem,but human knowledge about them is still limited compared with that about other forms of organisms.To enrich human knowledge and promote the utilization of bacteriophages,it is necessary to isolate and characterize as many as possible different bacteriophages.Here we describe the isolation of a T4-like bacteriophage IME08 and a rapid method for its genetic characterization.With this method we easily cloned a few random fragments of the bacteriophage genome.Sequence analysis of these random clones showed that bacteriophage IME08 shared the highest sequence similarity with T4-like Enterobacteria phage T4（94%identity）,JS98（95% identity）,JS10（95%identity） and RB14（94%identity） respectively,which suggested that IME08 belonged to T4-like bacteriophage genus.
基金supported by the National Natural Science Foundation of China (Grant No. 30770298)
文摘The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.
基金National Key Basic Research Program of China (Grant No. 2013CB955700)
文摘Nitrate assimilation is a process where bacteria utilize nitrate as a nitrogen source and synthesize it into organic nitrogen. We found that nitrate-assimilating bacteria(NAB) are widely distributed in various marine environments, from surface to the deep ocean and sediment, which indicates that NAB are significant to the oceanic nitrogen cycle. Comparative genomic analysis revealed nitrate-assimilating genes(nas A) in these marine heterotrophic NAB showed different gene arrangements and diverse regulation systems. Summary on recent findings will contribute to understanding the process of nitrate assimilation in NAB and their ecological significance in the nitrogen cycle. A systematic analysis of a number of studies on bacterial nitrate assimilation in marine ecological systems was conducted to clarify directions for future research.
基金supported by the National Natural Science Foundation of China(81961138013,31570026,31970174,31970548,and 32061123001)the National Mega Project on Major Infectious Disease Prevention(2017ZX10103005-005)+1 种基金the Special Project of Ministry of Science and Technology(2013FY113500)the Russian Foundation for Basic Research—National Natural Science Foundation of China Collaboration Fund(19-54-55004)。
文摘Migratory birds are considered natural reservoirs of avian influenza A viruses(AIVs).To further our viral ecology knowledge and understand the subsequent risk posed by wild birds,we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River,China.We collected over8000 samples and isolated 122 AIV strains.Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases.The results showed that the Yangtze River wintering wetlands functioned as a mixing ground,where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences;moreover,a portion of AIV gene segments were persistent inter-seasonally.Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes.In addition,we observed that viral gene segments in wintering wetlands were closely related to known North American isolates,indicating that intercontinental gene flow occurred.Notably,highly pathogenic H5 and low pathogenic H9 viruses,which usually circulate in poultry,were found to have crossed the poultry/wild bird interface,with the viruses introduced to wintering birds.Overall,this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands.Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.
文摘The quest for the origin of species has entered the genomics era. Despite decades of evidence confirming the role of the environment in ecological speciation, an understanding of the genomics of ecological speciation is still in its infancy. In this review, we explore the role of genomic architecture in ecological speciation in postglacial fishes. Growing evidence for the num- ber, location, effect size, and interactions among the genes underlying population persistence, adaptive trait divergence, and re- productive isolation in these fishes reinforces the importance of considering genomic architecture in studies of ecological speci- ation. Additionally, these populations likely adapt to new freshwater environments by selection on standing genetic variation, as de novo mutations are unlikely under such recent divergence times. We hypothesize that modular genomic architectures in post- glacial fish taxa may be associated with the probability of population persistence. Empirical studies have confirmed the genic na- ture of ecological speciation, implicating surprisingly extensive linkage disequilibrium across the genome. An understanding of these genomic mosaics and how they contribute to reproductive barriers remains unclear, but migration rates and the strength of selection at these loci is predicted to influence the likelihood of population divergence. Altogether, understanding the role of ge- nomic architecture is an important component of speciation research and postglacial fishes continue to provide excellent organ- isms to test these questions, both from the perspective of variation in architectures among taxa, and with respect to the distinct environments they have colonized. However, more empirical tests of ecological speciation predictions are needed [Current Zoo- logy 59 （1）： 53-71, 2013].
