|Table of Contents|

Analysis of Microsatellite Distribution Characteristicsin the Whole Genome of Bagarius yarrelli(PDF)

南京师范大学学报（工程技术版）[ISSN:1006-6977/CN:61-1281/TN]

Issue:
2021年03期
Page:
62-68
Research Field:
农业工程
Publishing date:

Info

Title:
Analysis of Microsatellite Distribution Characteristicsin the Whole Genome of Bagarius yarrelli
Author(s):
Yang Wenshan1; 2; Tang Rongye1; 2; Su Mengyuan1; 2; Xu Jiejie1; 2; Wang Tao1; 2; Yin Shaowu1; 2
(1.School of Marine Science and Engineering,Nanjing Normal University,Nanjing 210023,China)(2.Jiangsu Province Engineering Research Center for Aquati Animals Breeding andGreen Efficient Aquacultural Technology,Nanjing 210023,China)
Keywords:
Bagarius yarrelli; genome; microsatellites; distribution characteristics
PACS:
S917
DOI:
10.3969/j.issn.1672-1292.2021.03.009
Abstract:
The study uses the published genome-wide sequencing results of the Bagarius yarrelli on NCBI to screen and analyze the number and distribution of the microsatellites of the whole genome using MISA software. In the 570 806 968 bp longsequence of the Bagarius yarrelli genome,360 235 perfect microsatellites are screened with a length of 6 998 449 bp,accounting for 1.23% of the total length of the genome sequence. Among the six types of microsatellites,mononucleotide is the most,accounting for 44.65% of the total,the other bases are dinucleotide(43.29%),trinucleotide(6.12%),tetranucleotide(4.80%),pentanucleotide(1.02%)and hexanucleotide(0.11%). The top 10 microsatellite copy types in the genome are:A,AC,AG,AT,AAT,C,ATAG,AAAT,ACT and ATC.

References:

[1] 田树魁,薛晨江,冷云,等. 巨魾的生物学特性初步研究[J]. 水生态学杂志,2009,2(3):115-117.
[2]刘跃天,田树魁,冷云,等. 野生巨魾生物学特性研究[J]. 现代农业科技,2010(18):302-303,307.
[3]薛晨江,张正雄,马建颜,等. 巨魾人工繁殖初报与胚胎发育观察[J]. 水生态学杂志,2012,33(5):54-56.
[4]KRISHNAN J,ATHAR F,RANI T S,et al. Simple sequence repeats showing‘length preference’have regulatory functions in humans[J]. Gene,2017,628:156-161.
[5]黄杰,周瑜,刘与之,等. 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[J]. 四川动物,2015,34(1):8-14.
[6]PAGE R B,SANKAMETHAWEE W,PIERCE A J,et al. High throughput sequencing enables discovery of microsatellites from the puff-throated bulbul(Alophoixus pallidus)and assessment of genetic diversity in Khao Yai National Park,Thailand[J]. Biochemical Systematics and Ecology,2014,55:176-183.
[7]孙效文,张晓锋,赵莹莹,等. 水产生物微卫星标记技术研究进展及其应用[J]. 中国水产科学,2008,15(4):689-703.
[8]武耀,贾智英,李池陶,等. 筛选杂交鲤亲子鉴定的微卫星标记(英文)[J]. 农业生物技术学报,2012,20(5):549-559.
[9]徐杰杰,郑翔,张鑫宇,等. 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:1-11[2021-03-20]. http://kns.cnki.net/kcms/detail/45.1369.q.20191126.1019.002.html.
[10]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):R13.
[11]涂飞云,李鹏,韩卫杰,等. 大鼠基因组微卫星分布特征分析[J]. 基因组学与应用生物学,2015,37(6):2374-2382.
[12]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(英文)[J]. 动物学报(英文版),2006,52(1):138-152.
[13]戚文华,蒋雪梅,肖国生,等. 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[J]. 畜牧兽医学报,2013,44(11):1724-1733.
[14]戚文华,蒋雪梅,杜联明,等. 牦牛和水牛全基因组微卫星分布规律及其比较分析[J]. 基因组学与应用生物学,2015,34(7):1406-1412.
[15]戚文华,严超超,肖国生,等. 山羊和藏羚羊全基因组微卫星分布规律及其生物信息学分析[J]. 四川大学学报(自然科学版),2016,53(4):937-944.
[16]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.
[17]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.
[18]段永楠,刘奕,胡隐昌,等. 美丽硬仆骨舌鱼全基因组微卫星分布规律特征[J]. 中国农学通报,2019,35(23):152-158.
[19]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/OL]. 南京师大学报(自然科学版):1-14[2021-03-18]. http://kns.cnki.net/kcms/detail/32.1239.N.20210113.1301.022.html.
[20]阮晓红. 大菱鲆(Turbot)微卫星标记的筛选与应用[D]. 青岛:中国海洋大学,2009.
[21]黄杰,杨波,贾银平,等. 白鹭基因组微卫星分布规律研究[J]. 重庆师范大学学报(自然科学版),2019,36(5):66-71.
[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]崔凯,岳碧松. 绿尾虹雉全基因组微卫星分布规律研究[J]. 四川动物,2018,37(5):533-540.
[24]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.
[25]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.
[26]戚文华,蒋雪梅,肖国生,等. 猪全基因组中微卫星分布规律[J]. 畜牧与兽医,2014,46(8):9-13.
[27]卢婷,王晨,杜超,等. 林麝全基因组微卫星分布规律研究[J]. 四川动物,2017,36(4):420-424.
[28]张雪莲,王红梅,王磊,等. 草地贪夜蛾基因组微卫星的分布规律[J]. 应用昆虫学报,2020,57(6):1287-1298.
[29]SCHUG M D,WETTERSTRAND K A,GAUDETTE M S,et al. The distribution and frequency of microsatellite loci in Drosophila melanogaster[J]. Molecular Ecology,1998,7(1):57-70.
[30]余泉友,李斌,李关荣,等. 蚊子全基因组中微卫星的丰度及其分布(英文)[J]. 生物化学与生物物理进展,2005,32(5):435-441.
[31]WEBSTER M T,SMITH N G C,ELLEGREN H. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments[J]. Proceedings of the National Academy of Sciences of the United States of America,2002,99(13):8748-8753.
[32]KATTI M V,RANJEKAR P K,GUPTA V S. Differential distribution of simple sequence repeats in eukaryotic genome sequences[J]. Molecular Biology and Evolution,2001,18(7):1161-1167.
[33]汪自立,黄杰,杜联明,等. 二斑叶螨和肩突硬蜱基因组微卫星分布规律研究[J]. 四川动物,2013,32(4):481-486.
[34]王小婷,张玉娟,何秀,等. 中华按蚊全基因组微卫星的鉴定、特征及分布规律[J]. 昆虫学报,2016,59(10):1058-1068.
[35]郭文久. 微卫星在基因组上的分布与功能及其计算方法初步研究[D]. 成都:四川农业大学,2004.
[36]SCHL?TTERER C,TAUTZ D. Slippage synthesis of simple sequence DNA[J]. Nucleic Acids Research,1992,20(2):211-215.
[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]CUMMINGS C J,ZOGHBI H Y. Fourteen and counting:unraveling trinucleotide repeat diseases[J]. Human Molecular Genetics,2000,9(6):909-916.
[39]ARCHIE E A,MOSS C J,ALBERTS S C. Characterization of tetranucleotide microsatellite loci in the African Savannah Elephant(Loxodonta africana africana)[J]. Molecular Ecology Notes,2003,3(2):244-246.
[40]吴旭东,连总强,侯玉霞,等. 大口鲇微卫星标记在三个鲇形目鱼类种群间适用性研究[J]. 水生生物学报,2011,35(4):638-645.
[41]魏朝明,孔光耀,廉振民,等. 蜜蜂全基因组中微卫星的丰度及其分布[J]. 昆虫知识,2007,44(4):501-504.
[42]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.
[43]SCHORDERET D F,GARTLER S M. Analysis of CpG suppression in methylated and nonmethylated species[J]. Proceedings of the National Academy of Sciences of the United States of America,1992,89(3):957-961.
[44]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,2004,35(5):424-431.
[45]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.
[46]HARR B,SCHL?TTERGER C. Long microsatellite alleles in drosophila melanogaster have a downward mutation bias and short persistence times,which cause their genome-wide under representation[J]. Genetics,2000,155(3):1213-1220.
[47]ELLEGREN H. Heterogeneous mutation processes in human microsatellite DNA sequences[J]. Nature Genetics,2000,24(4):400-402.

Memo

Memo:
-
Last Update: 2021-09-30