摘要
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713810725 bp序列中,共筛选出418550个完整型的微卫星,其长度为12974321 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173177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,16381个微卫星定位在基因外显子上,并分布在3853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。
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 713810725 bp long sequence of the Pelteobagrus fulvidraco genome,418550 perfect microsatellites were screened with a length of 12974321 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 173177,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,16381 microsatellites were localized on the gene exons and distributed on 3853 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 of 21 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.
作者
徐杰杰
郑翔
李杰
尹绍武
王涛
Xu Jiejie;Zheng Xiang;Li Jie;Yin Shaowu;Wang Tao(College of Marine Science and Engineering,Nanjing Normal University,Nanjing,210023)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2020年第12期5488-5498,共11页
Genomics and Applied Biology
基金
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(SJCX180364)共同资助。
关键词
黄颡鱼
基因组
微卫星
特征分析
Pelteobagrus fulvidraco
Genome
Microsatellite
Characteristics
