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| 十足目甲壳动物的EST-SSR分析 |
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高海钰1,2,3, 李健1,2,3, 王佳佳2,3, 李吉涛2,3
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1.上海海洋大学 上海 201306;2.青岛海洋科学与技术试点国家实验室海洋渔业科学与食品产出过程功能实验室 青岛 266071;3.农业农村部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071
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| 摘要: |
| 本研究应用生物信息学方法，对21种十足目甲壳动物EST-SSR的特点进行了归纳总结和分析。结果显示，不同物种间的EST-SSR丰度存在明显差异，腹胚亚目中脊尾白虾(Exopalaemon carinicauda)的EST-SSR位点最为丰富(868.02个/Mb)，拟穴青蟹(Scylla paramamosain)位点丰度最低(286.48个/Mb)；枝鳃亚目中斑节对虾(Penaeus monodon) EST-SSR位点最为丰富(641.19个/Mb)，白滨对虾(Litopenaeus setiferus)位点丰度最低(166.96个/Mb)；腹胚亚目和枝鳃亚目中均是二、三、四核苷酸基元的SSR较为常见，在腹胚亚目中占总数的41.11%，在枝鳃亚目中占总数的28.00%；复合(Ⅰ)类型的SSR在腹胚亚目(51.38%)和枝鳃亚目(65.13%)中占很大比例；腹胚亚目二核苷酸基元的SSR中AC/GT分布频率最高，三核苷酸基元的SSR中ACC/GGT和AAT/ATT占优势；枝鳃亚目二核苷酸基元的SSR中AG/CT占优势，三核苷酸基元的SSR中AAT/ATT的分布频率高于其他三核苷酸基元。此外，对脊尾白虾含有SSR的EST进行GO分析后发现，细胞代谢过程、链接产物、细胞组分和细胞的比例分别在3个类型的注释中占优势。本研究加深了对十足目甲壳动物SSR分布规律的认识，可为甲壳动物EST-SSR标记的开发及实际应用提供参考。 |
| 关键词: 十足目 甲壳动物 EST-SSR |
| DOI：10.19663/j.issn2095-9869.20171226002 |
| 分类号: |
| 基金项目:农业产业技术体系(CARS-48)、山东省泰山产业领军人才工程项目(LNJY2015002)、国家自然科学基金(31472275)和青岛市产业培育计划科技惠民专项(17-3-3-62-nsh)共同资助 |
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| Analysis of SSR information in EST resource of decapod crustaceans |
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GAO Haiyu1,2,3, LI Jian1,2,3, WANG Jiajia2,3, LI Jitao2,3
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1.Shanghai Ocean University, Shanghai 201306;2.Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071;3.Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071
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| Abstract: |
| The distribution frequency and characteristic of base repeats of EST-SSR (expressed sequence tag - simple sequence repeats) were induced and analyzed in 21 kinds of decapod crustaceans by applying bioinformatics methods. The results showed that EST-SSR abundances were different between various crustacean species. Exopalaemon carinicauda had the most abundant EST-SSR (868.02/Mb), whereas Scylla paramamosain had the least (286.48/Mb) in pleocyemata. Penaeus monodon had the most abundant EST-SSR (641.19/Mb), whereas Litopenaeus setiferus had the least (166.96/Mb) in dendrobranchiata. The abundance of EST-SSR with di-, tri-, and tetra-nucleotide motifs was more than that of those with penta- and hex- nucleotide motifs, which accounts for 41.11% in pleocyemata and 28.00% in dendrobranchiata. EST-SSR of compound (Ⅰ) type occupied a large proportion in the pleocyemata (51.38%) and dendrobranchiata (65.13%). The frequency of the AC/GT repeat motif distribution was highest in dinucleotides, and ACC/GGT and AAT/ATT repeat motifs were the most abundant in the trinucleotide repeats in the pleocyemata. The frequency of AG/CT repeat motif distribution was highest in dinucleotides, and the distribution frequency of AAT/ATT motifs was significantly higher than other motifs of dinucleotide repeats in the dendrobranchiata. A total of 12,155 sequences containing SSRs were predicted; moreover, Gene Ontology (GO) Classification with the blast2go application was performed based on sequences containing SSRs of Exopalaemon carinicauda. The results demonstrated that ‘cellular process’ comprised the largest proportion in the biological process category, whereas ‘binding’ comprised the largest proportion in the molecular function category. Additionally, the cellular component category showed that many sequences likely possessed ‘cell parts’ and ‘cell’ by GO annotation. This study compared the characteristics of EST-SSR in different species of crustaceans and the diverse regions of the species genome. The consequences deepened our understanding of the distribution of SSRs and provided a reference for the development and practical applications of EST-SSR markers. The results also provided powerful information for future conservation and breeding research. |
| Key words: Decapoda Crustacean EST-SSR |