| 409 | 25 | 106 |
| 下载次数 | 被引频次 | 阅读次数 |
本研究利用NCBI上已公布的黄颡鱼全基因组测序结果,使用MISA软件对黄颡鱼全基因组的微卫星进行筛选并分析;结合MISA文件和基因组gff注释文件通过编写脚本定位微卫星在基因组的位置,并对外显子区含有微卫星的基因进行GO注释和KEGG富集。在黄颡鱼基因组713 810 725 bp序列中,共筛选出418 550个完整型的微卫星,其长度为12 974 321 bp,占基因组序列总长度的1.8%,相对丰度为586个/Mb。在1～6不同碱基重复类型微卫星中,二碱基重复数目最多,共173 177个,占微卫星总数的41.38%。然后依次是单碱基(40.26%)、四碱基(9.37%)、三碱基(7.63%)、五碱基(1.15%)和六碱基(0.21%)。基因组中重复数目最多的10种微卫星类别依次为T、A、AC、TG、GT、CA、TC、TA、AG和AT。同时通过对基因组微卫星进行定位,16 381个微卫星定位在基因外显子上,并分布在3 853个基因上。GO注释结果显示注释到分子功能的基因数目最多,富集前10的条目主要与电压门控钠通道复合物、电压门控钠通道活性和蛋白去磷酸化有关。KEGG富集分析显示共富集到21个通路,其中Hippo信号通路最为显著。研究结果为今后黄颡鱼微卫星标记的开发以及微卫星的定位功能等提供了一定的理论基础。
Abstract：The study used the published genome-wide sequencing results of the Pelteobagrus fulvidraco on NCBI to screen and analyze the microsatellites of the whole genome using MISA software.The MISA file and the genomic gff annotation file were combined to map the position of the microsatellites in the genome,and the gene containing the microsatellites in the exon region was subjected to GO annotation and KEGG enrichment.In the 713 810 725 bp long sequence of the Pelteobagrus fulvidraco genome,418 550 perfect microsatellites were screened with a length of12 974 321 bp,accounting for 1.8% of the total length of the genome sequence,and the relative abundance is 586 per Mb.Among the 1 to 6 different base repeat types of microsatellites,the number of two base repeats was the highest,reaching a total of 173 177,accounting for 41.38% of the total microsatellites.Then,it is followed by single base(40.26%),four bases(9.37%),three bases(7.63%),five bases(1.15%),and six bases(0.21%).T,A,AC,TG,GT,CA,TC,TA,AG and AT were the 10 microsatellite categories with the largest number of repeats in the genome.At the same time,by locating the genomic microsatellites,16 381 microsatellites were localized on the gene exons and distributed on 3 853 genes.The GO annotation results showed that the number of genes annotated to molecular function was the highest,and the top 10 entries were mainly related to voltage-gated sodium channel complexes,voltage-gated sodium channel activity,and protein dephosphorylation.KEGG enrichment analysis showed a total of21 pathways,of which Hippo signaling pathway was the most significant.The research results provide a theoretical basis for the development of microsatellite markers and the positioning function of microsatellites in the future.
Baxendale S.,Abdulla S.,Elgar G.,Buck D.,Berks M.,Micklem G.,Durbin R.,Bates G.,Brenner S.,and Beck S.,1995,Comparative sequence analysis of the human and pufferfish Huntington's disease genes,Nat.Genet.,,10(1):67-76
Conesa A.,Gotz S.,Garcia-Gomez J.M.,Terol J.,Talón M.,and Robles M.,2005,Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research,Bioinformatics,21(18):3674-3676
Cui J.Z.,Shen X.Y.,Yang G.P.,Gong Q.L.,and Gu Q.Q.,2006,The analysis of simple sequence repeats in Takifugu rubripes genome,Zhongguo Haiyang Daxue Xuebao (Periodical of Ocean University of China),36(2):249-254,272 (崔建洲,申雪艳,杨官品,宫庆礼,顾谦群,2006,红鳍东方鲀基因组微卫星特征分析,中国海洋大学学报,36(2):249-254,272)
Cui K.,and Yue B.S.,2018,Distribution patterns of microsatellites in the genome of Lophophorus lhuysii,Sichuan Dongwu(Sichuan Journal of Zoology),37(5):59-66 (崔凯,岳碧松,2018,绿尾虹雉全基因组微卫星分布规律研究,四川动物,37(5):59-66)
Du Y.R.,Tan C.M.,Xu Y.T.,Zhou Z.H.,Ma J.B.,and Guo S.C.,2016,Genome-wide Characterization and identification of microsatellites in Pantholops hodgsoni,Sichuan Dongwu(Sichuan Journal of Zoology),35(6):845-851 (都玉蓉,谭春敏,徐永涛,周智红,马建滨,郭松长,2016,藏羚羊基因组微卫星分析与初步验证,四川动物,35(6):845-851)
Edwards Y.J.K.,Elgar G.,Clark M.S.,and Bishop M.J.,1998,The identification and characterization of microsatellites in the compact genome of the japanese pufferfish,Fugu rubripes:perspectives in functional and comparative genomic analyses,J.Mol.Biol.,278(4):843-854
Gao H.,Liu P.,Meng X.H.,Wang W.J.,and Kong J.,2004,Analysis of microsatellite sequences in Chinese shrimp Fenneropenaeus chinensis genome,Haiyang yu Huzhao (Oceanologia et Limnologia Sinica),35(5):424-431 (高焕,刘萍,孟宪红,王伟继,孔杰,2004,中国对虾(Fenneropenaeus chinensis)基因组微卫星特征分析,海洋与湖沼,35(5):424-431)
Ge X.L.,Yin H.B.,Bi B.,and Sun Z.W.,2010,A preliminary research of genetic linkage map construction and QTL analysis for growth-related traits in yellow catfish (Pelteobagrus fulvidraco),Shuichan Xuebao (Journal of Fisheries of China),34(2):185-193 (葛学亮,尹洪滨,毕冰,孙中武,2010,黄颡鱼遗传图谱构建及生长相关性状的QTL定位,水产学报,34(2):185-193)
Huang J.,Du L.M.,Li Y.Z.,Li W.J.,Zhang X.Y.,and Yue B.S.,2012,Distribution regularities of microsatellites in the Gallus gallus genome,Sichuan Dongwu Xuebao (Sichuan Journal of Zoology),31(3):358-363 (黄杰,杜联明,李玉芝,李午佼,张修月,岳碧松,2012,红原鸡全基因组中微卫星分布规律研究,四川动物,31(3):358-363)
Huang J.,Yuan B.D.,and Yang C.Z.,2017,Distribution of microsatellites in genome of budgerigar (Melopsittacus undulatus),Yesheng Dongwu (Chinese Journal of Wildlife),38(3):422-426 (黄杰,原宝东,杨承忠,2017,虎皮鹦鹉全基因组中微卫星分布规律研究,野生动物学报,38(3):422-426)
Huang J.,Zhou Y.,Liu Y.Z.,Zhu D.,Song X.H.,Chen B.P.,Zhang X.Y.,and Yue B.S.,2015,Characteristics of microsatellites in Arborophila rufipectus genome sequences using454 GS FLX,Sichuan Dongwu (Sichuan Journal of Zoology),34(1):8-14 (黄杰,周瑜,刘与之,朱丹,宋旭颢,陈本平,张修月,岳碧松,2015,基于454 GS FLX高通量测序的四川山鹧鸪基因组微卫星特征分析,四川动物,34(1):8-14)
Hu G.F.,Liang H.W.,Li Z.,Wang C.Z.,Wu Q.C.,Liu X.J.,Luo X.Z.,and Zou G.W.,2009,Isolation and characterization of polymorphic microsatellite markers in the yellow catfish,Pelteobagrus fulvidraco,Conservation Genet.Resour.,1(1):63-66
Hulak M.,Kaspar V.,Kohlmann K.,Coward K.,Teitel J.,Rodina M.,Gela D.,Kocour M.,and Linhart O.,2010,Microsatellite-based genetic diversity and differentiation of foreign common carp (Cyprinus carpio) strains farmed in the Czech Republic,Aquaculture,298(3-4):194-201
Jiang P.,Yin H.B.,Zhang Y.,Li D.Y.,and Sun X.W.,2008,Analysis of parentage between male Pelteobagrus fulvidraco and guarded fertilized eggs,Dongwu Xuebao (Acta Zoologica Sinica),54(5):798-804 (蒋鹏,尹洪滨,张研,李大宇,孙效文,2008,雄性普通黄颡鱼与所保护受精卵间的亲缘关系分析,动物学报,54(5):798-804)
Jiang X.M.,Hu Y.Z.,Xiang X.S.,and Qi W.H.,2015,Statistics and bioinformatics analysis of microsatellite sequence in poplar whole genomes,Xinan Nongye Xuebao (Southwest China Journal of Agricultural Sciences),28(2):527-533 (蒋雪梅,胡廷章,向兴胜,戚文华,2015,杨树全基因组微卫星序列的统计及其生物信息学分析,西南农业学报,28(2):527-533)
Karaoglu H.,Lee C.M.Y.,and Meyer W.,2005,Survey of simple sequence repeats in completed fungal genomes,Mol.Biol.Evol.,22(3):639-649
Katti M.V.,Ranjekar P.K.,and Gupta V.S.,2001,Differential distribution of simple sequence repeats in eukaryotic genome sequences,Mol.Biol.Evol.,18(7):1161-1167
Kong Y.,Guo B.Y.,Xie C.X.,Fan Q.X.,He X.G.,Yang R.B.,and Shao J.,2009,The isolation via enrichment and characterization of 9 dinucleotide microsatellite markers in Pelteobagrus fulvidraco,Conservation Genet.Res.,1(1):353-355
Li M.F.,and Zheng X.Q.,2004,Research progress of methods of SSR primers development,Yichuan (Hereditas),26(5):769-776 (李明芳,郑学勤,2004,开发SSR引物方法之研究动态,遗传,26(5):769-776)
Li Y.C.,Korol A.B.,Fahima T.,Beiles A.,and Nevo E.,2010,Microsatellites:genomic distribution,putative functions and mutational mechanisms:a review,Mol.Ecol.,11 (12):2453-2465
Longshore J.W.,and Tarleton J.,1996,Dynamic mutations in human genes:a review of trinucleotide repeat diseases,J.Genet.,75(2):193-217Narasimhamoorthy B.,Saha M.C.,Swaller T.,and Bouton.J.H.,2008,Genetic diversity in switchgrass collections assessed by EST-SSR markers,Bio Energ.Res.,1(2):136-146
Ni S.S.,Yang Y.,Liu S.F.,and Zhuang Z.M.,2018,Microsatellite analysis of Patinopecten yessoensis using next-generation sequencing method,Yuye Kexue Jinzhan (Progress in Fishery Sciences),39(1):107-113 (倪守胜,杨钰,柳淑芳,庄志猛,2018,基于高通量测序的虾夷扇贝基因组微卫星特征分析,渔业科学进展,39(1):107-113)
Pearson C.E.,and Sinden R.R.,1998,Trinucleotide repeat DNAstructures:dynamic mutations from dynamic DNA,Curr.Opin.Struct.Biol.,8(3):321-330
Perutz M.F.,2001,Glutamine repeats and neurodegenerative diseases:molecular aspects,Hum.Genet.,109(1):125-125
Qi W.H.,Jiang X.M.,Xiao G.S.,Huang X.Y.,and Du L.M.,2013,Seeking and bioinformatics analysis of microsatellite sequence in the genomes of cow and sheep,Xumu Shouyi Xuebao (Acta Veterinaria Et Zootechnica Sinica),44(11):1724-1733 (戚文华,蒋雪梅,肖国生,黄小云,杜联明,2013,牛和绵羊全基因组微卫星序列的搜索及其生物信息学分析,畜牧兽医学报,44(11):1724-1733)
Qi W.H.,Jiang X.M.,Xiao G.S.,and Huang X.Y.,2014,Distribution regularities of microsatellites in the pig genome,Xumu Yu Shouyi (Animal Husbandry and Veterinary Medicine),46(8):9-13 (戚文华,蒋雪梅,肖国生,黄小云,2014,猪全基因组中微卫星分布规律,畜牧与兽医,46(8):9-13)
Schl觟tterer C.,and Tautz D.,1992,Slippage synthesis of simple sequence DNA,Nucleic Acids Res.,20(2):211-215
Schl觟tterer C.,1998,Genome evolution:are microsatellites really simple sequences?Curr.Biol.,8(4):132-134
Serbezov D.,Bernatchez L.,Olsen E.M.,and Villestad L.A.,2010,Mating system and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population,Conservation Genet.Res.,19(15):3193-3205
Shan Y.J.,Lu C.Y.,Li C.,Cheng L.,and Sun X.W.,2014,Isolation and characterization of 57 novel polynucleotide microsatellites from yellow catfish (Pelteobagrus fulvidraco) genome for genetic analysis,Mol.Ecol.,6(1):73-77
Shen X.Y.,Yang G.P.,Liu Y.J.,Liao M.J.,Wang X.C.,Zhu M.Z.,Song W.B.,Zou G.W.,Wei Q.W.,Wang D.Q.,and Chen D.Q.,2007,Construction of genetic linkage maps of guppy(Poecilia reticulata) based on AFLP and microsatellite DNAmarkers,Aquaculture,271(1-4):178-187
Song L.P.,Liu P.,Li J.,and Liu Z.H.,2008,Analysis of microsatellite sequences in genome of crab,Portunus trituberculatus,Zhongguo Shuichan Kexue (Journal of Fishery Sciences of China),15(5):738-744 (宋来鹏,刘萍,李健,刘振辉,2008,三疣梭子蟹基因组微卫星特征分析,中国水产科学,15(5):738-744)
Stallings R.L.,1992,Cp G suppression in vertebrate genomes does not account for the rarity of (Cp G)n microsatellite repeats,Genomics,13(3):890-891
Stott K.,Blackburn J.M.,Butler P.J.,and Perutz M.,1995,Incorporation of glutamine repeats makes protein oligomerize:implications for neurodegenerative diseases,Proc.Natl.Acad.Sci.USA,92(14):6509-6513
Subramanian S.,Mishra R.K.,and Singh L.,2003,Genome-wide analysis of microsatellite repeats in humans:their abundance and density in specific genomic regions,Genome Biol.,4(2):R13
Tautz D.,1989,Hypervariability of simple sequences as a general source for polymorphic DNA markers,Nucleic Acids Res.,17(16):6463-6471
Tautz D.,and Renz M.,1984,Simple sequences are ubiquitous repetitive components of eukaryotic genomes,Nucleic Acids Res.,12(10):4127-4138
Tong X.L.,Dai F.Y.,Li B.,Yu Q.Y.,Xia Q.Y.,and Lu C.,2006,Microsatellite repeats in mouse:abundance,distribution and density,Dongwu Xuebao (Acta Zoologica Sinica),52(1):138-152 (童晓玲,代方银,李斌,余泉友,夏庆友,鲁成,2006,小鼠基因组中的微卫星重复序列的数量、分布和密度,动物学报,52(1):138-152)
Toth G.,2000,Microsatellites in different eukaryotic genomes:survey and analysis,Genome Res.,10(7):967-981
Tu F.Y.,Liu X.H.,Du L.M.,Yan C.C.,and Huang X.F.,2015,Distribution characteristics of microsatellites in the rat genome,Jiangxi Nongye Daxue Xuebao (Acta Agriculturae Universitatis Jiangxiensis),(4):708-711 (涂飞云,刘晓华,杜联明,严超超,黄晓凤,2015,大鼠全基因组微卫星分布特征研究,江西农业大学学报,(4):708-711)
Van Belkum A.,Scherer S.,Van Alphen L.,and Verbrugh H.,1998,Short-sequence DNA repeats in prokaryotic genomes,Microbiol.Mol.Biol.Rev.,62(2):275-293
Wang X.T.,Zhang Y.J.,He X.,Mei T.,and Chen B.,2016,Identification,characteristics and distribution of microsatellites in the whole genome of Anopheles sinensis (Diptera:Culicidae),Kunchong Xuebao (Acta Entomologica Sinica),59(10):1058-1068 (王小婷,张玉娟,何秀,梅婷,陈斌,2016,中华按蚊全基因组微卫星的鉴定、特征及分布规律,昆虫学报,59(10):1058-1068)
Wei C.M.,Kong G.Y.,Lian Z.M.,Liu H.,Fan Y.W.,and Zhang H.,2007,Abundance and distribution of microsatellites in the entire Apis mellifera genome,Kunchong Zhishi (Chinese Bulletin of Entomology),44(4):501-504 (魏朝明,孔光耀,廉振民,刘慧,范永文,张慧,2007,蜜蜂全基因组中微卫星的丰度及其分布,昆虫知识,44(4):501-504)
Wierdl M.,Dominska M.,and Petes T.D.,1997,Microsatellite instability in yeast:dependence on the length of the microsatellite,Genetics,146(3):769-779
Wu Q.C.,Liang H.W.,Li Z.,Hu G.F.,Luo X.Z.,Shen Z.W.,and Zou G.W.,2010,Isolation of microsatellite makers in the yellow catfish and its application in genetic structure in three wild populations,Shengwu Jishu Tongbao (Biotechnology Bulletin),(3):154-159,163 (吴勤超,梁宏伟,李忠,呼光富,罗相忠,沈子伟,邹桂伟,2010,黄颡鱼微卫星标记的筛选及三个野生群体的遗传结构分析,生物技术通报,(3):154-159,163)
Xia J.H.,Liu F.,Zhu Z.Y.,Fu J.J.,Feng J.B.,Li J.L.,and Yue G.H.,2010,A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs,BMCGenomics,11:135-139
Xie C.,Mao X.Z.,Huang J.J.,Ding Y.,Wu J.M.,Dong S.,Kong L.,Gao G.,Li C.Y.,and Wei L.P.,2011,KOBAS 2.0:a web server for annotation and identification of enriched pathways and diseases,Nucleic Acids Res.,39(W):316-322
Yu Q.Y.,Li B.,Li G.R.,Fang S.M.,Yan H.,Tong X.L.,Qian J.F.,Xia Q.Y.,and Lu C.,2005,Abundance and distribution of microsatellites in the entire mosquito genome,Prog.Biochem.Biophys.,32(5):435-441
Zhang G.S.,Yin S.Y.,Wang Y.Y.,Li L.,Wang X.L.,Ding Y.D.,Zang X.,Zhang H.W.,Jia Y.H.,and Hu Y.L.,2016,The effects of water temperature and stocking density on survival,feeding and growth of the juveniles of the hybrid yellow catfish from Pelteobagrus fulvidraco (♀)×Pelteobagrus vachelli (♂),Aquac.Res.,47(9):2844-2850
Zhang J.J.,Li J.,Zhang G.S.,Wang T.,Yin S.W.,Tang Z.L.,Mao J.Q.,and Wang R.R.,2018,Microsatellite-based analysis of genetic diversity of parent and hybrid of yellow catfish Pelteobagrus fulvidraco (♀)×P.vachelli (♂),Shuichan Kexue (Fisheries Science),37(5):612-621 (张佳佳,李杰,张国松,王涛,尹绍武,唐忠林,茆健强,王若然,2018,杂交黄颡鱼(黄颡鱼♀×瓦氏黄颡鱼♂)及其双亲遗传多样性的微卫星分析,水产科学,37(5):612-621)
基本信息:
DOI：10.13417/j.gab.039.005488
中图分类号:S917.4
引用信息:
[1]徐杰杰,郑翔,李杰,等.黄颡鱼(Pelteobagrus fulvidraco)全基因组微卫星分布特征分析[J].基因组学与应用生物学,2020,39(12):5488-5498.DOI:10.13417/j.gab.039.005488.
基金信息:
江苏省重点研发计划(现代农业)重点项目(BE2017377);; 江苏省农业重大新品种创制项目(PZCZ201742);; 江苏省研究生科研与实践创新计划项目(SJCX18_0364)共同资助
2019-12-06
2019-12-06
2019-12-06