Donkey(Equus asinus)is an important livestock animal in China because of its draft and medicinal value.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant....Donkey(Equus asinus)is an important livestock animal in China because of its draft and medicinal value.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant.We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds.According to population structure,most Chinese domestic donkeys showed a dominant ancestral type.However,the Chinese donkeys still represented a significant geographical distribution trend.In the selective sweep,gene annotation,functional enrichment,and differential expression analyses between large and small donkey groups,we identified selective signals,including NCAPG and LCORL,which are related to rapid growth and large body size.Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.展开更多
Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection.Howe...Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection.However,efficient storage,querying,and visualization of such large datasets remain challenging.Here,we developed a comprehensive database,the Bovine Genome Variation Database(BGVD).It provides six main functionalities:gene search,variation search,genomic signature search,Genome Browser,alignment search tools,and the genome coordinate conversion tool.BGVD contains information on genomic variations comprising^60.44 M SNPs,~6.86 M indels,76,634 CNV regions,and signatures of selective sweeps in 432 samples from modern cattle worldwide.Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map,using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes(ARS-UCD1.2,UMD3.1.1,and Btau5.0.1).Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks.To further investigate and visualize the relationships between variants and signatures of selection,the Genome Browser integrates all variations,selection data,and resources,from NCBI,the UCSC Genome Browser,and Animal QTLdb.Collectively,all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.展开更多
基金supported by the Key Research&Development Plan of Shaanxi Province of China(2020NY-002)Dong-E-E-Jiao Co.Ltd(20191001)the National Natural Science Foundation of China(81770514)。
文摘Donkey(Equus asinus)is an important livestock animal in China because of its draft and medicinal value.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant.We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds.According to population structure,most Chinese domestic donkeys showed a dominant ancestral type.However,the Chinese donkeys still represented a significant geographical distribution trend.In the selective sweep,gene annotation,functional enrichment,and differential expression analyses between large and small donkey groups,we identified selective signals,including NCAPG and LCORL,which are related to rapid growth and large body size.Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.
基金supported by the National Natural Science Foundation of China(Grant No.31822052)the National Thousand Youth Talents Plan,China(Grant No.2111021502)awarded to YJthe National Natural Science Foundation of China(Grant No.31872317)awarded to CL
文摘Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection.However,efficient storage,querying,and visualization of such large datasets remain challenging.Here,we developed a comprehensive database,the Bovine Genome Variation Database(BGVD).It provides six main functionalities:gene search,variation search,genomic signature search,Genome Browser,alignment search tools,and the genome coordinate conversion tool.BGVD contains information on genomic variations comprising^60.44 M SNPs,~6.86 M indels,76,634 CNV regions,and signatures of selective sweeps in 432 samples from modern cattle worldwide.Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map,using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes(ARS-UCD1.2,UMD3.1.1,and Btau5.0.1).Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks.To further investigate and visualize the relationships between variants and signatures of selection,the Genome Browser integrates all variations,selection data,and resources,from NCBI,the UCSC Genome Browser,and Animal QTLdb.Collectively,all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.
