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| 基于RNA-Seq的杜仲转录组微卫星特征分析 |
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冯延芝1,2, 李芳东1,2, 魏琦琦3, 莫文娟4, 王璐1,2, 黄地歌5, 傅建敏1,2
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| (1.中国林业科学研究院 经济林研究开发中心, 郑州 450003;2.国家林业局 泡桐研究开发中心, 郑州 450003;3.中南林业科技大学 经济林培育与保护教育部重点实验室, 长沙 410004;4.中国林业科学研究院 华北林业实验中心, 北京 102300;5.中南林业科技大学 林学院, 长沙 410004) |
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| 摘要: |
| 对杜仲（Eucommia ulmoides）国审良种‘华仲6号’和‘华仲10号’花后70和160 d的种仁共4个样本进行转录组测序，对测序数据进行组装和功能注释分类，并对转录组获得的单基因簇（unigene）进行微卫星特征分析。利用新一代高通量测序技术Illumina HiSeqTM 2000对杜仲样品进行转录组测序，采用软件Trinity进行组装；利用BLAST软件将unigene序列分别与Nr、GO、COG和KEGG等数据库比对分析；利用MISA软件对转录组的96 469条unigenes进行SSR搜索。结果表明：转录组测序分析，共得到72 791 399个高质量的序列读取片段（Clean reads），包含了14 702 548 161个的碱基序列（bp）信息。对reads进行序列组装，共获得96 469个平均长度为690 bp的unigene，序列信息量达到了66.56 Mb。同源性分析结果显示，有49 856个与其它物种同源的unigenes得到注释，占All-unigene的51.68%。将杜仲转录组中的unigene与GO数据库进行比对分析，根据其功能可将注释到的38 983条unigene分成3大类（细胞组分、分子功能和生物学过程）56个分支；根据COG功能可将注释的14 796条unigene基因划分成25个类别；KEGG数据库作为参照，可将注释到的11 260条unigene定位到117个代谢途径分支；SSR位点搜索结果显示，96 469条unigenes中共包含9 621个完整型SSR位点，占总SSR位点的84.14%。完整型SSR位点共包含55种重复基元，其中出现频率最高的重复基序类型为单核苷酸重复中的A/T（4 597个），其次是AG/CT（2 597个）、AT/AT（439个）。 |
| 关键词: 杜仲 转录组 转录组测序 单基因簇 SSR |
| DOI：10.11841/j.issn.1007-4333.2016.09.08 |
| 投稿时间：2015-11-12 |
| 基金项目:国家自然科学基金面上项目（31370682） |
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| Microsatellites characteristics of transcriptomic sequences from Eucommia ulmoides Oliv.based on RNA-Seq |
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FENG Yan-zhi1,2, LI Fang-dong1,2, WEI Qi-qi3, MO Wen-Juan4, WANG Lu1,2, HUANG Di-ge5, FU Jian-min1,2
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| (1.Non-timber Forestry Research and Development Centre, Chinese Academy of Forestry, Zhengzhou 450003, China;2.Paulownia Research and Development Center of State Forestry Administration, Zhengzhou 450003, China;3.Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China;4.Forestry Experiment Center of North China, Chinese Academy of Forestry, Beijing 102300, China;5.College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China) |
| Abstract: |
| The transcriptomes of Eucommia ulmoides Oliv. kernels of 70 and 160 d after flowering in varieties ‘Huazhong 6 and 10’ were sequenced.The transcriptome data was assembled and classified by function,and microsatellites characteristics from obtained unigenes and analyzed.The Illumina HiSeqTM 2000,a new generation of high-throughput sequencing technology was used to sequence the transcriptomes of kernels of assembled by software Trinity.The unigenes were annotated according to Nr,GO,COG and KEGG category by BLAST searches.A total of 72 791 399 clean reads fragment including 14 702 548 161 bp in sequence information were generated,and then de novo assembly generated a total of 96 469 unigenes with an average length of 690 bp,which contains 66.56 Mb in sequence information.Among them,49 856 unigenes accounted for 51.68% were annotated by BLAST searches.All 38 983 annotated unigenes according to GO were divided into three categories (cellular components,molecular function and biological processes) of 56 branches by gene ontology;14 796 annotated unigenes based on COG were grouped into 25 functional categories;KEGG pathway analysis presented that 11 260 annotated unigenes were divided into 117 classes according to its function.There were 9 621 complete SSR located in 96 469 unigenes,which accounted for 84.14% of the total SSR.The complete SSR included 55 frequent motifs,and the highest repeat of complete SSR type was A/T (4 597),following by AG/CT (2 597)、AT/AT (439).The characteristics of SSRs can provide useful information for the analysis of genetic polymorphism and map structure in E.ulmoides. |
| Key words: Eucommia ulmoides oliv. transcriptome RNA-Seq unigene SSR |
