Volume 18 Issue 1
Feb.  2022
Turn off MathJax
Article Contents
Abstract
References
PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168
Citation: PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168
shu

Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli

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

More Information
  • Received Date: June 03, 2021
  • Revised Date: June 29, 2021
  • Accepted Date: July 22, 2021
  • Available Online: August 03, 2021
    Graphical Abstract
    • Abstract
  • In this study, MISA (MIcroSAtellite identification tool) was used to screen and analyze the distribution characteristics of microsatellites in the whole genome of Pelteobagrus vachelli, aiming to provide a basis for the selection of functional microsatellite markers. The genes containing microsatellites in the exon regions were subjected to GO annotation and KEGG enrichment. In the whole genome of P. vachelli (Approximately 663.53 Mb), 417 724 perfect microsatellites were identified, accounting for 1.48% of the total length. The relative abundance of microsatellites in P. vachelli was 630 pcs·Mb−1. Among the six repeat types, dinucleotides were the most frequent, accounting for 43.36% of the total microsatellites, followed by mononucleotides (39.02%), tetranucleotides (9.05%), trinucleotides (7.34%), pentanucleotides (1.12%) and hexanucleotides (0.12%). By investigating the locations of microsatellites in the genome, we found that 10 924 microsatellites which belonged to 5 788 genes were located in the exons. The GO annotation shows that the number of genes annotated to biological process was the largest, mainly associated with binding activity and cellular macromolecular metabolism. KEGG enrichment analysis shows that these genes were enriched in 273 pathways, among which, flavonoids and flavonol biosynthesis (P=0) were the most significantly enriched pathways. Integrated analysis indicates that the microsatellites located in the exons of genes in P. vachelli were closely related to the biological metabolism processes.
    • FullText(HTML)
    • References (41)
  • [1]
    TAUTZ D, RENZ M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes[J]. Nucleic Acids Res, 1984, 12(10): 4127-4138. doi: 10.1093/nar/12.10.4127
    [2]
    何平. 真核生物中的微卫星及其应用[J]. 遗传, 1998, 20(4): 44-49.
    [3]
    罗文永, 胡骏, 李晓方. 微卫星序列及其应用[J]. 遗传, 2003, 25(5): 615-619. doi: 10.3321/j.issn:0253-9772.2003.05.027
    [4]
    ZHAO X Y, TAN Z Y, FENG H P, et al. Microsatellites in different Potyvirus genomes: survey and analysis[J]. Gene, 2011, 488(1/2): 52-56.
    [5]
    张增翠, 侯喜林. SSR分子标记开发策略及评价[J]. 遗传, 2004(5): 763-768. doi: 10.3321/j.issn:0253-9772.2004.05.037
    [6]
    WU X P, FENG Y W, JIANG H L, et al. A preliminary genetic linkage map of Sinonovacula constricta (Lamarck, 1818) based on microsatellites derived from RAD sequencing[J]. J Ocean U China, 2018, 17(4): 947-956. doi: 10.1007/s11802-018-3543-5
    [7]
    赵娜, 常剑波, 陶江平, 等. 基于微卫星标记的中华鲟亲子关系判别及案例分析[J/OL]. 水生态学杂志. [2021-01-15]. http://kns.cnki.net/kcms/detail/42.1785.X.20200915.1323.002.html.
    [8]
    苏胜彦, 张林兵, 李海洋, 等. 基于微卫星标记的大口黑鲈 (Micropterus salmoides) 原种和养殖群体遗传多样性和结构分析[J]. 浙江大学学报 (农业与生命科学版), 2020, 46(6): 687-698.
    [9]
    蔡焰值, 蔡烨强, 何长仁. 瓦氏黄颡鱼生物学的初步研究[J]. 北京水产, 2003(6): 24-29.
    [10]
    李明锋. 瓦氏黄颡鱼研究进展及前景展望[J]. 现代渔业信息, 2011, 26(1): 5-12.
    [11]
    巩高瑞, 张晋, 丹成, 等. 应用DNA分子标记鉴定黄颡鱼、瓦氏黄颡鱼及其杂交种的研究[J]. 水生生物学报, 2017, 41(2): 321-325. doi: 10.7541/2017.39
    [12]
    葛学亮, 尹洪滨, 毕冰, 等. 黄颡鱼遗传图谱构建及生长相关性状的QTL定位[J]. 水产学报, 2010, 34(2): 185-193.
    [13]
    李大宇, 殷倩茜, 侯宁, 等. 黄颡鱼 (Pelteobagrus fulvidraco) 不同生态地理分布群体遗传多样性的微卫星分析[J]. 海洋与湖沼, 2009, 40(4): 460-469. doi: 10.3321/j.issn:0029-814X.2009.04.011
    [14]
    李林, 梁宏伟, 李忠, 等. 瓦氏黄颡鱼线粒体全基因组序列分析及系统进化[J]. 遗传, 2011, 33(6): 627-635.
    [15]
    郑翔, 徐杰杰, 张佳佳, 等. 4个瓦氏黄颡鱼群体遗传多样性的微卫星分析[J]. 水产科学, 2020, 39(5): 657-668.
    [16]
    何晶晶, 黄建华, 牛红艳, 等. 猪蛔虫全基因组微卫星分子标记开发与特征分析[J]. 中国兽医杂志, 2020, 56(9): 11-14, 19.
    [17]
    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.
    [18]
    徐杰杰, 毕宜慧, 程景颢, 等. 中华绒螯蟹 (Eriocheir sinensis) 全基因组微卫星分布特征研究[J/OL]. 基因组学与应用生物学. [2021-03-21]. http://61.175.198.136:8083/rwt/CNKI/http/NNYHGLUDN3WXTLUPMW4A/kcms/detail/45.1369.Q.20210118.1225.006.html.
    [19]
    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. doi: 10.11924/j.issn.1000-6850.casb18030101
    [20]
    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. doi: 10.3969/j.issn.1673-9159.2020.04.002
    [21]
    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]. 南京师范大学学报(自然科学版), 2021, 44(3): 103-111.
    [22]
    CONESA A, GÖTZ S, GARCÍA-GÓMEZ J M, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 2005, 21(18): 3674-3676. doi: 10.1093/bioinformatics/bti610
    [23]
    XIE C, MAO X, HUANG J, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases[J]. Nucleic Acids Res, 2011, 39(Suppl2): W316-W322. doi: 10.1093/nar/gkr483
    [24]
    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 Biol, 2003, 4(2): 1-10. doi: 10.1186/gb-2003-4-2-p1
    [25]
    TONG X L, DAI F Y, LI B, et al. Microsatellite repeats in mouse: abundance, distribution and density[J]. 动物学报, 2006, 52(1): 138-152.
    [26]
    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.
    [27]
    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. [2021-01-25]. http://kns.cnki.net/kcms/detail/45.1369.q.20191126.1019.002.html.
    [28]
    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.
    [29]
    王月月, 刘雪雪, 董坤哲, 等. 7种家养动物全基因组微卫星分布的差异研究[J]. 中国畜牧兽医, 2015, 42(9): 2418-2426.
    [30]
    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: 53-54.
    [31]
    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.
    [32]
    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. doi: 10.11984/j.issn.1000-7083.20180096
    [33]
    黄杰, 刘磊, 杨波, 等. 普通鸬鹚基因组微卫星分布规律研究[J]. 野生动物学报, 2020, 41(1): 108-114. doi: 10.3969/j.issn.1000-0127.2020.01.015
    [34]
    TÓTH G, GÁSPÁRI Z, JURKA J. Microsatellites in different eukaryotic genomes: survey and analysis[J]. Genome Res, 2000, 10(7): 967-981. doi: 10.1101/gr.10.7.967
    [35]
    上官清, 陈昆慈, 刘海洋, 等. 斑鳢基因组中微卫星分布特征及野生种群遗传结构分析[J]. 南方水产科学, 2020, 16(3): 47-60.
    [36]
    SCHORDERET D F, GARTLER S M. Analysis of CpG suppression in methylated and nonmethylated species[J]. P Natl Acad Sci USA, 1992, 89(3): 957-961. doi: 10.1073/pnas.89.3.957
    [37]
    PEARSON C E, SINDEN R R. Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci[J]. Biochemistry-US, 1996, 35(15): 5041-5053. doi: 10.1021/bi9601013
    [38]
    XU Y, LI W, HU Z, et al. Genome-wide mining of perfect microsatellites and tetranucleotide orthologous microsatellites estimates in six primate species[J]. Gene, 2018, 643: 124-132. doi: 10.1016/j.gene.2017.12.008
    [39]
    XIAO T W, YU J Z, LIAO Q, et al. Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: identification, characterization and distribution (Diptera: Culicidae)[J]. Insect Sci, 2019, 26: 607-619. doi: 10.1111/1744-7917.12577
    [40]
    ELLEGREN H. Heterogeneous mutation processes in human microsatellite DNA sequences[J]. Nature Genet, 2000, 24(4): 400-402. doi: 10.1038/74249
    [41]
    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. doi: 10.1093/genetics/146.3.769
    • Related Articles

  • Cited by

    Periodical cited type(9)

    1. 曾志锋，邵伟伟，马力，陶宇慧，韦力. 棘皮动物海星（Patiria miniata）全基因组微卫星分布特征. 丽水学院学报. 2024(02): 31-39 .
    2. 周全，王家琪，于贵杰，吴建开，王德忠，熊阳，郭稳杰，张茂森，唐琴，梅洁. 精液添加精氨酸和亮氨酸对杂交黄颡鱼受精和孵化的影响. 水生生物学报. 2023(10): 1585-1594 .
    3. 范嗣刚，黄皓，王鹏飞，赵超，闫路路，邱丽华. 基于微卫星标记的花鲈亲子鉴定技术. 广东海洋大学学报. 2023(05): 26-33 .
    4. 杨尉，司圆圆，许瑞雯，陈兴汉. 基于基因组survey数据的疣吻沙蚕微卫星特征分析及多态标记开发. 南方水产科学. 2023(05): 123-133 . 本站查看
    5. 刘士力，刘一诺，李飞，郑建波，程顺，蒋文枰，迟美丽，赵金良. 3种鲌亚科鱼类全基因组微卫星分布特征分析. 上海海洋大学学报. 2023(06): 1176-1183 .
    6. 葛健辉，关文志，任晋东，牛宝龙，胡金春，王伟，翁旭东，楼宝，于瑾，许晓军. 马口鱼全基因组简单重复序列特征分析与多态性标记开发. 浙江农业学报. 2023(11): 2584-2593 .
    7. 吴晓雲，陈叶雨，龚全，刘亚，宋明江，李飞扬，李鹏程，邹巧林，欧军，赖见生. 基于三代全长转录组测序的极边扁咽齿鱼SSR分子标记开发. 南方农业学报. 2023(09): 2525-2532 .
    8. 全德润，王李宝，黎慧，史文军，朱健强，顾舒文，顾晨，任乾，万夕和. 虾肝肠胞虫全基因组SSR位点分布及比较分析. 中国水产科学. 2023(11): 1398-1408 .
    9. 卢凯妹，王天骄，董世武，邢秀梅，苏伟林. 梅花鹿基因组微卫星分布特征研究. 特产研究. 2022(06): 8-15+23 .

    Other cited types(1)

Catalog

    Get Citation
    PDF
    XML
    Article views (843) PDF downloads (52) Cited by(10)
    Related

    Supported by: Beijing Renhe Information Technology Co., Ltd.  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return