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| 海带转录组SSR序列特征及其相关基因功能分析 |
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李秋莹1,2,3, 张 杰1,2,3, 姚建亭1,2, 王秀良1,2, 段德麟1,2
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1.中国科学院海洋研究所;2.青岛海洋科学与技术国家实验室实验海洋生物学与生物技术实验室;3.中国科学院大学
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| 摘要: |
| 对海带(Saccharina japonica)转录组测序数据进行分析, 从70 497条Unigenes中共检测到9 237个简单序列重复(SSR)位点, 并对包含SSR序列的Unigenes进行功能注释。海带转录组中SSR的类型十分丰富, 其中单核苷酸和三核苷酸重复SSR的数量最多, 分别占SSR总数的40.9%和39.4%, 其次为四核苷酸、二核苷酸、五核苷酸和六核苷酸重复, 分别占SSR总数的9.8%, 6.1%, 3.1%和0.7%。SSR重复单元类型共有147种, 其重复次数的范围为5～70次。功能注释发现约50%含有SSR的Unigenes获得了注释信息, 并且大多数与已知蛋白有同源性。COG、GO功能分类结果均表明, 大量含有SSR序列的基因与多种生物功能有关, 其中与碳水化合物代谢及参与细胞组成相关的基因数量最多。本研究结果为深入开发功能性SSR标记奠定基础, 也为开展海带分子标记辅助选育提供支持。 |
| 关键词: 微卫星 转录组 简单序列重复(SSR) 海带(Saccharina japonica) |
| DOI：10.11759/hykx20150206001 |
| 分类号: |
| 基金项目:国家自然科学基金项目(31272660); 国家科技支撑计划项目(2013BAB01B01); 国家海洋公益性行业科研专项(201405040) |
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| Characterization of SSR in Saccharina japonica transcriptome and functional analysis of SSR-containing unigenes |
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LI Qiu-ying,ZHANG Jie,YAO Jian-ting,WANG Xiu-liang,DUAN De-lin
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| Abstract: |
| In this study, we identified a total of 9 237 SSR (simple sequence repeat) loci in 70 497 unigenes from the transcriptome data of Saccharina japonica and conducted a function analysis of unigenes containing SSR. SSRs were abundant in the transcriptome of S. japonica, and the most commonly repeating motifs were mononucleotides and trinucleotides (40.9% and 39.4% of the total SSRs, respectively), followed by tetranucleotides, dinucleotides, pentanucleotides, and hexanucleotides (9.8%, 6.1%, 3.1%, and 0.7% of the total SSRs, respectively). There were 147 repeated motif types ranging from 5 to 70 repetitions. Our analysis of the functional annotation revealed that nearly 50% of the unigenes containing SSRs contain annotation information and that most of them are homologous to known proteins. Our clusters of orthologous group (COG) classification and gene ontology (GO) assignment results indicate that genes containing SSR are involved in various biological functions, of which carbohydrate metabolism and cell components are the top two. These SSRs provide new resources for further developing functional SSR markers, which can play important roles in molecular marker-assisted selection while breeding S. japonica. |
| Key words: microsatellite transcriptome simple sequence repeat (SSR) Saccharina japonica |