[1]梁 霞,王慧琪,马宇璇,等.鲤鱼(Cyprinus carpio)全基因组微卫星分布特征研究[J].南京师大学报(自然科学版),2021,44(03):103-111.[doi:10.3969/j.issn.1001-4616.2021.03.016]
　Liang Xia,Wang Huiqi,Ma Yuxuan,et al.Distribution Characteristics of Microsatellites in theWhole Genome of Cyprinus carpio,Linnaeus[J].Journal of Nanjing Normal University(Natural Science Edition),2021,44(03):103-111.[doi:10.3969/j.issn.1001-4616.2021.03.016]
点击复制

鲤鱼(Cyprinus carpio)全基因组微卫星分布特征研究()
分享到：

《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

卷:
第44卷
期数:
2021年03期
页码:
103-111
栏目:
·生物学·
出版日期:
2021-09-15

文章信息/Info

Title:
Distribution Characteristics of Microsatellites in theWhole Genome of Cyprinus carpio,Linnaeus
文章编号:
1001-4616(2021)03-0103-09
作者:
梁 霞; 王慧琪; 马宇璇; 宋 磊; 吴 超; 李亮徽; 张国松
菏泽学院生理生化及应用实验室,山东 菏泽 274000
Author(s):
Liang Xia; Wang Huiqi; Ma Yuxuan; Song Lei; Wu Chao; Li Lianghui; Zhang Guosong
Physiological,Biochemical and Applied Laboratory,Heze University,Heze 274000,China
关键词:
鲤鱼; 全基因组; 微卫星; 分布特征
Keywords:
Cyprinus carpio; genome; microsatellite; characteristics
分类号:
Q959.46+8
DOI:
10.3969/j.issn.1001-4616.2021.03.016
文献标志码:
A
摘要:
本研究利用微卫星搜索软件MISA,对鲤鱼全基因组中的完整型微卫星进行了搜索,并对其分布规律进行了分析,同时对微卫星定位在编码区域的基因进行了GO注释、富集和KEGG富集分析. 结果显示,在约1.7Gb鲤鱼全基因组中,共搜索出837 004个完整型微卫星,相对丰度为488个/Mb. 微卫星总长度为15 513 551 bp,占鲤鱼全基因组大小的0.91%,相对密度为9 051 bp/Mb. 在6种完整型微卫星中,单碱基微卫星数目最多,共有495 421个,在6种微卫星中占比59.19%; 其他依次是二碱基(26.79%)、三碱基(8.48%)、四碱基(4.21%)、五碱基(1.25%)和六碱基(0.07%)类型微卫星. 其中,A、AC、AT、AAT、AG、C、AAAT、AAC、AGAT、AAG依次为鲤鱼全基因组中出现次数最多的前十种微卫星类别,表现出明显的A/T碱基优势. 通过对全基因组微卫星进行定位,共24 222个微卫星定位在基因外显子上,并分布在3 853个基因上. GO功能注释的1 758个GO条目中,注释到生物学过程的条目数和基因数均最多,GO功能富集最为显著的条目是代谢过程的调节. KEGG富集表明,机体系统分支富集到的基因总数最多. 环境信息处理分支中的鞘脂信号通路基因富集最为显著. 分布到代谢分支的通路种类最为广泛. 分析结果推测,定位在基因编码区域的微卫星可能在细胞间信息交流、信号转导、细胞新陈代谢以及生物合成调控等方面发挥作用. 本研究为鲤鱼后续的种群遗传信息评估、微卫星引物的开发及功能鉴定等提供了数据支持.
Abstract:
In this study,the microsatellite search software MISA was used to search for the complete microsatellite in the whole genome of C.carpio,and its distribution pattern was analyzed. Meanwhile,GO annotation enrichment and KEGG enrichment analysis were conducted for the genes located in the coding region of the microsatellite. The results were as follows,837,004 complete microsatellites were searched in the whole genome of C.carpio with a relative abundance of 488/Mb and a total length of 15 513 551 bp,accounting for 0.91% of the whole genome size of C.carpio,with a relative density of 9 051 bp/Mb. Among the 6 complete microsatellites,the number of Mononucleotide was the largest(59.19%),followed by the Dinucleotide(26.79%),Trinucleotide(8.48%),Tetranucleotide(4.21%),Pentanucleotide(1.25%)and Hexanucleotide(0.07%). Among them,A,AC,AT,AAT,AG,C,AAAT,AAC,AGAT,AAG were the top ten microsatellite categories that appeared most frequently in the whole genome of C.carpio,showing obvious A/T base advantage. Through genome-wide microsatellite localization,a total of 24 222 microsatellites were located on gene exons and distributed on 3 853 genes. Among the 1 758 GO entries annotated by GO function,the number of entries and genes annotated by biological process were the most,and the most significant entry enriched by GO function was the regulation of metabolic process. KEGG enrichment showed that the total number of genes enriched in the branches of the organism system was the largest,the accumulation of sphinolipid signaling pathway genes was the most significant in the branches of environmental information processing,and the types of pathways distributed in the metabolic branches were the most extensive. The results suggest that microsatellites located in the gene coding region may play a role in intercellular information communication,signal transduction,cell metabolism and biosynthesis regulation. This study provides data support for the subsequent population genetic information assessment,development of microsatellite primers and functional identification of C.carpio.

参考文献/References:

[1] TAUTZ D,RENZ M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes[J]. Nucleic acids research,1984,12(10):4127-4138.
[2]周思倩,焦伟丽,彭珠黎,等. 埃博拉病毒基因组中微卫星序列的分布分析[J]. 基因组学与应用生物学,2019,38(3):1087-1095.
[3]SHEN X Y,YANG G P,LIU Y J,et al. Construction of genetic linkage maps of guppy(Poecilia reticulata)based on AFLP and microsatellite DNA markers[J]. Aquaculture,2007,271(1-4):178-187.
[4]NARASIMHAMOORTHY B,SAHA M C,SWALLER T,et al. Genetic diversity in switchgrass collections assessed by EST-SSR markers[J]. Bioenergy research,2008,1(2):136-146.
[5]HULAK M,KASPAR V,KOHLMANN K,et al. Microsatellite-based genetic diversity and differentiation of foreign common carp(Cyprinus carpio)strains farmed in the Czech Republic[J]. Aquaculture,2010,298(3/4):194-201.
[6]SERBEZOV D,BERNATCHEZ L,OLSEN E M,et al. Mating patterns and determinants of individual reproductive success in brown trout(Salmo trutta)revealed by parentage analysis of an entire stream living population[J]. Molecular ecology,2010,19(15):3193-3205.
[7]XIA J H,LIU F,ZHU Z Y,et al. A consensus linkage map of the grass carp(Ctenopharyngodon idella)based on microsatellites and SNPs[J]. BMC genomics,2010,11(1):135-150.
[8]XU P Z,XIAO F,WANG X M,et al. Genome sequence and genetic diversity of the common carp,Cyprinus carpio[J]. Nature genetics,2014,46(11):1212-1219.
[9]孙效文,梁利群. 鲤鱼的遗传连锁图谱[J]. 中国水产科学,2000,7(1):1-5.
[10]赵兰. 鲤遗传_物理整合图谱的构建及鲤与斑马鱼的比较作图[D]. 大连:大连海洋大学,2013.
[11]郑先虎,匡友谊,吕伟华,等. 基于整合图谱的鲤生长相关性状QTL的分布及变异规律[J]. 中国科学:生命科学,2013,43(2):159-167.
[12]吴明林,侯冠军,李海洋,等. 长江野鲤(Cyprinus carpio)及两种养殖鲤群体遗传多样性评估[J]. 基因组学与应用生物学,2020,39(1):70-78.
[13]XIONG L W,WANG Q,QIU G F. Large-scale isolation of microsatellites from Chinese mitten crab Eriocheir sinensis via a Solexa Genomic Survey[J]. International journal of molecular sciences,2012,13(12):16333-16345.
[14]魏东旺,楼允东,孙效文,等. 鲤鱼微卫星分子标记的筛选[J]. 动物学研究,2001,22(3):238-241.
[15]全迎春,孙效文,梁利群. 应用微卫星多态分析四个鲤鱼群体的遗传多样性[J]. 动物学研究,2005,26(6):595-602.
[16]孙效文,贾智英,魏东旺,等. 磁珠富集法与小片段克隆法筛选鲤微卫星的比较研究[J]. 中国水产科学,2005,12(2):126-132.
[17]Van BELKUM A,SCHERER S,Van ALPHEN L,et al. Short-sequence DNA repeats in prokaryotic genomes[J]. Microbiology and molecular biology reviews,1998,62(2):275-293.
[18]SUBRAMANIAN S,MISHRA R K,SINGH L. Genome-wide analysis of microsatellite repeats in humans:their abundance and density in specific genomic regions[J]. Genome biology,2003,4(2):1-10.
[19]KARAOGLU H,LEE C M Y,MEYER W. Survey of simple sequence repeats in completed fungal genomes[J]. Molecular biology and evolution,2004,22(3):639-649.
[20]王希,陈丽,赵春雷. 利用MISA工具对不同类型序列进行SSR标记位点挖掘的探讨[J]. 中国农学通报,2016,32(10):150-156.
[21]王耀嵘,杨尉,任席林,等. 金钱鱼基因组微卫星分布特征分析及多态性标记开发[J]. 广东海洋大学学报,2020,40(4):7-14.
[22]郭新颖,张健,李梦柔,等. 藏鸡基因组微卫星特征分析[J]. 中国家禽,2020,42(1):116-120.
[23]上官清,陈昆慈,刘海洋,等. 斑鳢基因组中微卫星分布特征及野生种群遗传结构分析[J]. 南方水产科学,2020,16(3):47-60.
[24]CONESA A,GOTZ S,GARCIA G J M,et al. Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research[J]. Bioinformatics,2005,21(18):3674-3676.
[25]XIE C,MAO X Z,HUANG J J,et al. KOBAS 2.0:a web server for annotation and identification of enriched pathways and diseases[J]. Nucleic acids research,2011,39(suppl):W316-W322.
[26]童晓玲,代方银,李斌,等. 小鼠基因组中的微卫星重复序列的数量、分布和密度[J]. 动物学报,2006,52(1):138-152.
[27]涂飞云,刘晓华,杜联明,等. 大鼠全基因组微卫星分布特征研究[J]. 江西农业大学学报,2015,37(4):708-711.
[28]徐杰杰,郑翔,张鑫宇,等. 2019,4种河鲀全基因组微卫星分布特征分析研究[J/OL]. 基因组学与应用生物学,2019. http://kns.cnki.net/kcms/detail/45.1369.q.20191126.1019.002.html.
[29]黄杰,杜联明,李玉芝,等. 红原鸡全基因组中微卫星分布规律研究[J]. 四川动物,2012,31(3):358-363.
[30]李午佼,李玉芝,杜联明,等. 大熊猫和北极熊基因组微卫星分布特征比较分析[J]. 四川动物,2014,33(6):874-878.
[31]涂飞云,刘俊,韩卫杰,等. 食蟹猴全基因组微卫星分布特征分析[J]. 野生动物学报,2018,39(2):400-404.
[32]高焕,刘萍,孟宪红,等. 中国对虾(Fenneropenaeus chinensis)基因组微卫星特征分析[J]. 海洋与湖沼,2004(5):424-431.
[33]宋来鹏,刘萍,李健,等. 三疣梭子蟹基因组微卫星特征分析[J]. 中国水产科学,2008,15(5):738-744.
[34]熊良伟,王帅兵,封琦,等. 基于高通量测序的中华鳑鲏基因组微卫星特征分析及标记开发[J]. 江苏农业科学,2018,46(18):164-168.
[35]TOTH G. Microsatellites in different eukaryotic genomes:survey and analysis[J]. Genome research,2000,10(7):967-981.
[36]徐杰杰,郑翔,李杰,等. 黄颡鱼(Pelteobagrus fulvidraco)全基因组微卫星分布特征研究[J/OL]. 基因组学与应用生物学,2019. http://kns.cnki.net/kcms/detail/45.1369.Q.20191204.1055.002.html.
[37]PEARSON C E,SINDEN R R. Trinucleotide repeat DNA structures:dynamic mutations from dynamic DNA[J]. Current opinion in structural biology,1998,8(3):321-330.
[38]黄杰,原宝东,杨承忠. 虎皮鹦鹉全基因组中微卫星分布规律研究[J]. 野生动物学报,2017,38(3):422-426.
[39]倪守胜,杨钰,柳淑芳,等. 基于高通量测序的虾夷扇贝基因组微卫星特征分析[J]. 渔业科学进展,2018,39(1):107-113.
[40]LAI Y,SUN F. The relationship between microsatellite slippage mutation rate and the number of repeat units[J]. Molecular biology and evolution,2003,20(12):2123-2131.
[41]WIERDL M,DOMINSKA M,PETES T D. Microsatellite instability in yeast:dependence on the length of the microsatellite[J]. Genetics,1997,146(3):769-779.
[42]CUI K,YUE B S. Distribution patterns of microsatellites in the genome of lophophorus lhuysii[J]. Sichuan journal of zoology,2018,37(5):59-66.

备注/Memo

备注/Memo:
收稿日期:2020-09-07.
基金项目:山东省自然科学基金项目(ZR2019QC002)、山东省高等学校青创科技支持计划和菏泽学院博士基金(XY18BS08).
通讯作者:张国松,博士,副教授,研究方向:鱼类遗传育种. E-mail:hzxyzgs@163.com
更新日期/Last Update: 2021-09-15