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

doi:10.11843/j.issn.0366-6964.2013.11.005

畜牧兽医学报 ›› 2013, Vol. 44 ›› Issue (11): 1724-1733.doi: 10.11843/j.issn.0366-6964.2013.11.005

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

戚文华¹，蒋雪梅²，肖国生¹，黄小云¹，杜联明³

（1. 重庆三峡学院生命科学与工程学院，重庆 404100；2. 重庆三峡学院化学与环境工程学院，重庆 404100；3. 四川大学生命科学学院，四川省濒危野生动物保护生物学重点实验室，成都 610064）

收稿日期:2013-06-13 出版日期:2013-11-23 发布日期:2013-11-23
作者简介:戚文华（1982-），男，河南驻马店人，博士，主要从事动物遗传与分子生物学研究，Tel: 0235-8102522，E-mail: wenhuaqi357@163.com
基金资助:
国家973项目（2012CB722207）

Seeking and Bioinformatics Analysis of Microsatellite Sequence in the Genomes of Cow and Sheep

QI Wen-hua¹, JIANG Xue-mei², XIAO Guo-sheng¹, HUANG Xiao-yun¹, DU Lian-ming³

(1. School of Life Science and Engineering, Chongqing Three Gorges University, Chongqing 404100, China; 2. School of Chemistry and Environmental Engineering, Chongqing Three Gorges University, Chongqing 404100, China; 3. Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China)

Received:2013-06-13 Online:2013-11-23 Published:2013-11-23

摘要/Abstract

摘要：

本研究利用MSDB v2.4搜索牛和绵羊全基因组中完整型微卫星序列，并对其进行生物信息学分析。牛基因组共统计了806 272个微卫星位点，其微卫星数量最多的是第1条染色体，其次是第2、3、4、5、6条染色体，数量较少的是第25和28条染色体。绵羊基因组共统计了682 891个位点，其微卫星数量最多的也是第1条染色体，其次是第2、3条染色体和X性染色体，数量较少的是第24、25、26条染色体。通过检验表明，牛和绵羊染色体长度与其所含微卫星数量具有高度正相关性（r>0.80，P=0.000）。牛和绵羊基因组中单碱基重复类型微卫星数量最多（45.33% vs 44.42%），其次依次是二碱基>三碱基>五碱基>四碱基>六碱基重复类型。牛和绵羊基因组中微卫星重复拷贝类别数量较多的是A、AC、AT、AGC、ACG、AAC、AAT、AAAT、AAAC和AAAG，而其数量较少的是C、CG、AGT、CCG、ACT、AACG、AAGC、AACC、AACT、ACCG、AGCT、AGCG、CCGG 和 CCCG。

Abstract:

The complete microsatellite sequence were searched by using MSDB v2.4 (Microsatellite Search and Building Database) in cow (Bos taurus) and sheep (Ovis aries) genomes, and their number, frequency, density and distribution were comparatively analyzed by bioinformatics in the study. Microsatellite (Short tandem repeats, STRs) number in cow and sheep were 806 272 and 682 891 loci, respectively, which respectively account for 4.78‰ and 4.80‰ of whole genome length. The overall STRs number was comparable in each chromosome of cow and sheep. In cow genome, the largest STRs number was found in chromosome 1 followed by chromosome 2, 3, 4, 5 and 6, and the smaller STRs number was in chromosome 25 and 28. In sheep genome, the largest STRs number was also found in chromosome 1 followed by chromosome 2, 3 and chromosome X, and the smaller STRs number was in chromosome 24, 25 and 26. There were highly positive correlation between chromosome length and STRs numbers in cow and sheep genomes (r>0.80, P=0.000). The different STRs repeat types in cow and sheep genomes, mononucleotide repeat type motifs was the most abundance, followed by dinucleotide, trinucleotide, pentanucleotide, tetranucleotide and hexanucleotide repeat types. Repeat copy category of A, AC, AT, AGC, ACG, AAC, AAT, AAAT, AAAC, AAAG were predominate in cow and sheep genomes, whereas repeat motifs of C, CG, AGT, CCG, ACT, AACG, AAGC, AACC, AACT, ACCG, AGCT, AGCG, CCGG and CCCG were rare in cow and sheep genomes.

中图分类号:

S823
S826

戚文华，蒋雪梅，肖国生，黄小云，杜联明. 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.

QI Wen-hua, JIANG Xue-mei, XIAO Guo-sheng, HUANG Xiao-yun, DU Lian-ming. Seeking and Bioinformatics Analysis of Microsatellite Sequence in the Genomes of Cow and Sheep[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2013, 44(11): 1724-1733.

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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

Seeking and Bioinformatics Analysis of Microsatellite Sequence in the Genomes of Cow and Sheep

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