| 摘要: |
| 为探究牦牛全基因组中重复序列的组成特征，本研究以染色体水平的牦牛全基因组（BosGru3.1）为研究对象，利用生物信息学方法对牦牛基因组中的单纯型SSRs序列进行了检测，并对其分布特征进行综合分析。结果表明：1）在牦牛全基因组（2.83 Gb）中，共筛选出778 413个单纯型SSRs，总长度为14.42 Mb，占全基因组序列总长的0.51%，相对频率和相对密度分别为274.92 loci/Mb和5 094.43 bp/Mb。2）牦牛31条染色体中，1号染色体所含的SSRs数量最多（48 592个，6.24%），29号染色体所含的SSRs数量最少（11 758个，1.51%），染色体DNA序列长度与其所含SSRs数量呈显著正相关（P＜0.001）。3）6种重复类型的单纯型SSRs在牦牛基因组中分布不均匀，其中单碱基重复类型的SSRs数量最多（320 592个，41.19%），其次是两碱基（197 824个，25.41%）、三碱基（130 441个，16.76%）、五碱基（75 056个，9.64%）、四碱基（52 523个，6.75%）和六碱基（1 977个，0.25%）。4）各重复类型分别以A、AC、AT、AGC、AAC、AAAT、AAAC、AACTG、AGATC和AACCCT类别的SSRs分布较多，表现出明显的A（T）碱基组成优势。5）各重复类型的SSRs其重复拷贝数分别集中在12~25次（单碱基）、7~26次（两碱基）、5~13次（三碱基）、4~8次（四碱基）、4~7次（五碱基）和4~6次（六碱基）。综上，本研究揭示了牦牛全基因组中单纯型SSRs的分布特征，表明各重复类型的SSRs其频率、密度、优势碱基类别及重复拷贝数均存在差异，呈现出一定的规律性。本研究为深入了解牦牛基因组中重复序列特别是单纯型SSRs的组成和分布特征提供参考，也为后续发掘牦牛特异性SSRs标记、构建遗传图谱及开展标记与性状间的关联分析等研究奠定基础。 |
| 关键词: 牦牛 基因组 单纯型微卫星 丰度 |
| DOI：10.11841/j.issn.1007-4333.2024.03.12 |
| 投稿时间：2023-07-28 |
| 基金项目:国家自然科学基金项目（31960656）；青海省“昆仑英才·高端创新创业人才”计划项目（领军人才） |
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| Analysis on the distribution features of perfect microsatellite in the whole genome of yak |
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XU Yuhui1, MA Zhijie1*, GUO Weixing1, MO Yanxin2, CHEN Shengmei1
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| (1.Plateau Livestock Genetic Resources Protection and Innovative Utilization key Laboratory of Qinghai Province/Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau of Ministry of Agriculture and Rural Affairs/Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;2.Qinghai Provincial Livestock Genetic Resources Conservation and Utilization Center, Xining 810016, China) |
| Abstract: |
| To explore the distribution and feature of repetitive sequences in yak genome （BosGru3.1）， the perfect SSRs were detected by bioinformatics methods in the yak genome， and its distribution characteristics were comprehensively analyzed .The results showed that： 1） A total of 778 413 perfect SSRs were screened out in yak genome （2.83 Gb）， with a total length of 14.42 Mb， accounting for 0.51% of the total length of the genome sequence. The relative frequency and relative density were 274.92 loci/Mb and 5 094.43 bp/Mb， respectively. 2） Among the 31 chromosomes of yak， chromosome 1 contained the largest number of SSRs （48 592， 6.24%）， and chromosome 29 contained the lowest number of SSRs （11 758， 1.51%）. The length of the chromosomal DNA sequence was significantly positively correlated with the number of SSRs contained. 3） In yak genome， the distribution of six repeat types of perfect SSRs was uneven. Among them， the number of SSRs with mononucleotide repeat type was the highest （320 592， 41.19%）， followed by dinucleotide （197 824， 25.41%）， trinucleotide （130 441， 16.76%）， pentanucleotide （75 056， 9.64%）， tetranucleotide （52 523， 6.75%）， and hexanucleotide （1 977， 0.25%）. 4） Repeat copy category of A， AC， AT， AGC， AAC， AAAT， AAAC， AACTG， AGATC， and AACCCT was predominate in six repeat types， showing a distinct A（T） base composition advantage. 5） The repeat copy numbers of different type of perfect SSRs were concentrated at 12-25 （mononucleotide）， 7-26 （dinucleotide）， 5-13 （trinucleotide）， 4-8 （tetranucleotide）， 4-7 （pentanucleotide）， and 4-6 （hexanucleotide）. In conclusion， there are differences in the frequency， density， dominant base categories， and copy numbers among different types of SSRs， showing certain regularity. The results of this study can provide a reference for a deeper understanding of the composition and distribution features of repetitive sequences， especially perfect SSRs， and lay a foundation for subsequent studies on mining yak-specific SSR markers， constructing genetic maps， and carrying out marker-trait association analyses. |
| Key words: yak genome perfect microsatellite abundance |
