斑點(diǎn)叉尾全基因組微衛(wèi)星分布特征分析*

唐榮葉 蘇孟園 楊汶珊 徐杰杰 王 濤 尹紹武

唐榮葉 蘇孟園 楊汶珊 徐杰杰 王 濤①尹紹武①

(南京師范大學(xué)海洋科學(xué)與工程學(xué)院 江蘇省特色水產(chǎn)育種與綠色高效養(yǎng)殖技術(shù)工程研究中心 江蘇 南京 210023)

微衛(wèi)星又稱簡單序列重復(fù)(simple sequence repeats, SSRs)，廣泛分布于真核、原核生物以及病毒中，是由1～6 bp堿基為單元重復(fù)串聯(lián)而成的DNA序列。根據(jù)核心序列的排列差異，又分為完整型和不完整型(Morgante, 2001)。其中，完整型指重復(fù)序列中不存在其他堿基或重復(fù)序列的情況，不完整型指重復(fù)序列中存在錯配情況。目前，對微衛(wèi)星的研究主要集中于完整型(鄭燕等, 2012)，因其具有多態(tài)性高、共顯性遺傳等特點(diǎn)，目前被廣泛應(yīng)用于遺傳圖譜構(gòu)建(Shen, 2007; Xia, 2010)、遺傳多樣性分析和種質(zhì)資源保護(hù)(Narasimhamoorthy, 2008)等研究中。

1 材料與方法

1.1 全基因組來源

1.2 數(shù)據(jù)處理方法

2 結(jié)果與分析

2.1 斑點(diǎn)叉尾全基因組微衛(wèi)星總體分布特征

2.2 斑點(diǎn)叉尾29條染色體不同重復(fù)類型微衛(wèi)星分布特征

2.3 斑點(diǎn)叉尾全基因組微衛(wèi)星各重復(fù)類別特征

圖1 斑點(diǎn)叉尾各染色體微衛(wèi)星數(shù)量分布

圖2 斑點(diǎn)叉尾各染色體微衛(wèi)星頻率分布

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

圖3 斑點(diǎn)叉尾全基因組微衛(wèi)星各重復(fù)類型占比

2.4 斑點(diǎn)叉尾微衛(wèi)星各重復(fù)類型拷貝數(shù)分布特征

3 討論

3.1 斑點(diǎn)叉尾全基因組微衛(wèi)星序列分布特征分析

在本研究中，染色體DNA序列的長度與染色體上所含有的微衛(wèi)星數(shù)量具有高度相關(guān)性(SPSS,=0.98,<0.01)，這與黃杰等(2012)和戚文華等(2013)的研究結(jié)果一致。同時也支持了Hancock (1996)的假說：染色體序列越長，微衛(wèi)星含量越高的趨勢。統(tǒng)計(jì)各染色體上的各種類型微衛(wèi)星數(shù)量，發(fā)現(xiàn)各類型的比例除27號和29號染色體二堿基大于單堿基外，均符合29條染色體整體微衛(wèi)星分布特征，即單堿基最多，其次是二堿基、三堿基、四堿基、五堿基和六堿基。這個規(guī)律與張琳琳等(2008)對赤擬谷盜()的研究結(jié)果相似，而與黃杰等(2012)對紅原雞()各染色體微衛(wèi)星分布情況的研究結(jié)果相差甚遠(yuǎn)。高煥等(2005)認(rèn)為，同一物種的不同染色體上，各種類型的重復(fù)序列分布有很大差異。而本研究的結(jié)果表明，各種類型的微衛(wèi)星在各染色體上的分布符合整體規(guī)律，這可能和不同物種的不同類型微衛(wèi)星的特定功能有關(guān)系。

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

注：占比表示該類別在各自重復(fù)類型微衛(wèi)星中的占比

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

圖4 斑點(diǎn)叉尾全基因組微衛(wèi)星重復(fù)類型重復(fù)數(shù)分布

3.2 斑點(diǎn)叉尾各堿基類型微衛(wèi)星不同類別分布特征分析

四堿基、五堿基的數(shù)量較多的前2種類別分別是AAAT、AAAC和ATAAT、AAAAC，六堿基的數(shù)量相對于前5種重復(fù)類型比較少，數(shù)量最多的2種類別是TGACTA和ATAGTC。與前3種堿基類型一樣，四堿基、五堿基和六堿基也表現(xiàn)出明顯的A/T堿基優(yōu)勢。有研究表明，DNA序列中G/C含量越高，微衛(wèi)星分布越少。對于這個現(xiàn)象，倪守勝等(2018)通過分析蝦夷扇貝()基因組的微衛(wèi)星分布特征，得出DNA復(fù)制滑動機(jī)制和重組機(jī)制使得A/T重復(fù)類型的產(chǎn)生幾率更高的結(jié)論。Schorderet等(1992)認(rèn)為，由于基因組中CpG甲基化，胞嘧啶C容易在脫氨基作用下突變?yōu)樾叵汆奏。這可能是二堿基中CG含量較少、TG (AC類型)含量較多的原因。然而Stallings (1992)的研究則表明，無論是否有CpG甲基化過程，基因組中的CG重復(fù)類別都是偏小的，他提出CpG結(jié)構(gòu)是一種有害結(jié)構(gòu)。

3.3 斑點(diǎn)叉尾各堿基類型拷貝數(shù)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

* 江蘇省農(nóng)業(yè)重大新品種創(chuàng)制項(xiàng)目(PZCZ201742)、江蘇省重點(diǎn)研發(fā)計(jì)劃(現(xiàn)代農(nóng)業(yè))重點(diǎn)項(xiàng)目(BE2017377)、江蘇省農(nóng)業(yè)科技自主創(chuàng)新資金[CX(19)2034]和南京師范大學(xué)大學(xué)生創(chuàng)新創(chuàng)業(yè)訓(xùn)練計(jì)劃項(xiàng)目共同資助[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].

唐榮葉，E-mail: 2508049280@qq.com

王 濤，副教授，E-mail: seawater88@126.com；尹紹武，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

(編輯 馮小花)