斑点叉尾全基因组微卫星分布特征分析*

唐荣叶 苏孟园 杨汶珊 徐杰杰 王 涛 尹绍武

唐荣叶 苏孟园 杨汶珊 徐杰杰 王 涛①尹绍武①

(南京师范大学海洋科学与工程学院 江苏省特色水产育种与绿色高效养殖技术工程研究中心 江苏 南京 210023)

微卫星又称简单序列重复(simple sequence repeats, SSRs)，广泛分布于真核、原核生物以及病毒中，是由1～6 bp碱基为单元重复串联而成的DNA序列。根据核心序列的排列差异，又分为完整型和不完整型(Morgante, 2001)。其中，完整型指重复序列中不存在其他碱基或重复序列的情况，不完整型指重复序列中存在错配情况。目前，对微卫星的研究主要集中于完整型(郑燕等, 2012)，因其具有多态性高、共显性遗传等特点，目前被广泛应用于遗传图谱构建(Shen, 2007; Xia, 2010)、遗传多样性分析和种质资源保护(Narasimhamoorthy, 2008)等研究中。

1 材料与方法

1.1 全基因组来源

1.2 数据处理方法

2 结果与分析

2.1 斑点叉尾全基因组微卫星总体分布特征

2.2 斑点叉尾29条染色体不同重复类型微卫星分布特征

2.3 斑点叉尾全基因组微卫星各重复类别特征

图1 斑点叉尾各染色体微卫星数量分布

图2 斑点叉尾各染色体微卫星频率分布

Tab.1 Distribution of different types of SSRs in each chromosome of I. punctatus

图3 斑点叉尾全基因组微卫星各重复类型占比

2.4 斑点叉尾微卫星各重复类型拷贝数分布特征

3 讨论

3.1 斑点叉尾全基因组微卫星序列分布特征分析

在本研究中，染色体DNA序列的长度与染色体上所含有的微卫星数量具有高度相关性(SPSS,=0.98,<0.01)，这与黄杰等(2012)和戚文华等(2013)的研究结果一致。同时也支持了Hancock (1996)的假说：染色体序列越长，微卫星含量越高的趋势。统计各染色体上的各种类型微卫星数量，发现各类型的比例除27号和29号染色体二碱基大于单碱基外，均符合29条染色体整体微卫星分布特征，即单碱基最多，其次是二碱基、三碱基、四碱基、五碱基和六碱基。这个规律与张琳琳等(2008)对赤拟谷盗()的研究结果相似，而与黄杰等(2012)对红原鸡()各染色体微卫星分布情况的研究结果相差甚远。高焕等(2005)认为，同一物种的不同染色体上，各种类型的重复序列分布有很大差异。而本研究的结果表明，各种类型的微卫星在各染色体上的分布符合整体规律，这可能和不同物种的不同类型微卫星的特定功能有关系。

Tab.2 Top 10 repeated copy categories of microsatellites in genomes of I. punctatus

注：占比表示该类别在各自重复类型微卫星中的占比

Note: The percentage represents the proportion of different types of SSRs

图4 斑点叉尾全基因组微卫星重复类型重复数分布

3.2 斑点叉尾各碱基类型微卫星不同类别分布特征分析

四碱基、五碱基的数量较多的前2种类别分别是AAAT、AAAC和ATAAT、AAAAC，六碱基的数量相对于前5种重复类型比较少，数量最多的2种类别是TGACTA和ATAGTC。与前3种碱基类型一样，四碱基、五碱基和六碱基也表现出明显的A/T碱基优势。有研究表明，DNA序列中G/C含量越高，微卫星分布越少。对于这个现象，倪守胜等(2018)通过分析虾夷扇贝()基因组的微卫星分布特征，得出DNA复制滑动机制和重组机制使得A/T重复类型的产生几率更高的结论。Schorderet等(1992)认为，由于基因组中CpG甲基化，胞嘧啶C容易在脱氨基作用下突变为胸腺嘧啶T。这可能是二碱基中CG含量较少、TG (AC类型)含量较多的原因。然而Stallings (1992)的研究则表明，无论是否有CpG甲基化过程，基因组中的CG重复类别都是偏小的，他提出CpG结构是一种有害结构。

3.3 斑点叉尾各碱基类型拷贝数特征分析

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Analysis of Microsatellite Distribution Characteristics in the Channel Catfish () Genome

TANG Rongye, SU Mengyuan, YANG Wenshan, XU Jiejie, WANG Tao①, YIN Shaowu①

(College of Marine Science and Engineering, Nanjing Normal University Nanjing, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing, Jiangsu 210023, China)

To understand the distribution of perfect microsatellites in the genome of the channel catfish (), we used MISA, a bioinformatics software package, to search and analyze the microsatellites. A total of 510256 perfect microsatellites were isolated from 29 chromosomes of, with a total length of 11036941 bp. The chromosome containing the largest number of microsatellites was chromosome 2 (25284), followed by chromosomes 3, 1, and 5. Chromosome 29 had the lowest number of microsatellites (11591). The length of each chromosome was significantly correlated with the number of microsatellites it contained (SPSS,= 0.98,< 0.01). The highest relative abundance of microsatellites was found on chromosome 27 (785.03 ind./Mb), and the lowest was on chromosome 11 (615.89 ind./Mb). Among the six repeat types, mononucleotides were the most frequent, accounting for 45.31% of the total, followed by dinucleotides (38.53%), trinucleotides (8.73%), tetranucleotides (6.93%), pentanucleotides (0.46%), and hexanucleotides (0.04%). The predominantly repeated microsatellite sequences in thegenome were A, AC, AG, AT, AAT, AAAT, C, AAC, AAAC, and AAG, showing an obvious inclination towards A and T bases. The results of this study provide a reference for the further study ofgenome characteristics and contribute basic data for future investigations into molecular marker-assisted breeding and genetic information assessment of.

; Whole genome; Microsatellites; Distribution characteristics

WANG Tao, E-mail: seawater88@126.com; YIN Shaowu, E-mail: yinshaowu@163.com

S917.4

A

2095-9869(2022)02-0089-09

10.19663/j.issn2095-9869.20210126002

* 江苏省农业重大新品种创制项目(PZCZ201742)、江苏省重点研发计划(现代农业)重点项目(BE2017377)、江苏省农业科技自主创新资金[CX(19)2034]和南京师范大学大学生创新创业训练计划项目共同资助[This work was supported by Agricultural Major New Variety Creation Project of Jiangsu Province (PZCZ201742), Key Research and Development Program of Jiangsu Province (BE2017377), Jiangsu Agricultural Science and Technology Innovation Fund [CX(19)2034], and Innovation and Entrepreneurship Training Program for College Students in Nanjing Normal University].

唐荣叶，E-mail: 2508049280@qq.com

王 涛，副教授，E-mail: seawater88@126.com；尹绍武，教授，E-mail: yinshaowu@163.com

2021-01-26,

2021-02-23

TANG R Y, SU M Y, YANG W S, XU J J, WANG T, YIN S W. Analysis of microsatellite distribution characteristics in the channel catfish () genome. Progress in Fishery Sciences, 2022, 43(2): 89–97

(编辑 冯小花)