您好，欢迎访问江苏省农业科学院 机构知识库！
江苏省农业科学院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

De novo assembly of the transcriptome of Neottopteris nidus using Illumina paired-end sequencing and development of EST-SSR markers

文献类型： 外文期刊

作者： Jia, Xinping 1 ; Deng, Yanming 1 ; Sun, Xiaobo 1 ; Liang, Lijian 1 ; Su, Jiale 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Hort, Jiangsu Key Lab Hort Crop Genet Improvement, Nanjing 210014, Jiangsu, Peoples R China

关键词： Neottopteris nidus;De novo assembly;Transcriptome sequencing;EST-SSR

期刊名称：MOLECULAR BREEDING （ 影响因子：2.589； 五年影响因子：2.75 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： Neottopteris nidus is an economically important foliage plant. However, the EST sequence resources available for N. nidus are still very limited. In this study, we present the first transcriptome analysis of N. nidus using the Illumina sequencing technology. More than 53 million reads were generated in transcriptome analysis, and de novo assembly generated 41,173 unigenes with an average length of 969 bp. The similarity search indicated that 24,801 unigenes (60.23 %) had significant similarity with proteins in the NR and Swiss-Prot protein databases. Among these annotated unigenes, 15,683 and 7942 unigenes were assigned to gene ontology categories and Clusters of Orthologous Groups, respectively. A total of 5548 unigenes were mapped into 116 pathways by the Kyoto Encyclopedia of Genes and Genomes Pathway database. Some abundant transcripts related to photomorphogenesis and development, including chlorophyll a-b-binding protein, phototropin, amino acid transporter, ATP-binding protein, expansin, and ribosomal protein, were identified in the N. nidus transcriptome. In total, 5792 potential EST-SSRs were identified among the unigenes. The most abundant type of repeat was dinucleotide (3836, 66.24 %), followed by trinucleotide (1575, 27.19 %) and tetranucleotide (207, 3.57 %) repeats. The dominant repeat motif was CT/GA (1229, 21.22 %), followed by AG/TC (905, 15.63 %), CA/GT (504, 11.32 %), and AC/TG (339, 8.70 %). In addition, a total of 100 potential marker sites were selected to validate the assembly quality and develop EST-SSR markers. This study generated a substantial fraction of N. nidus transcriptome sequences, which were very useful resources for gene discovery and molecular marker development.

  • 相关文献

[1]High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica. Qi, Weicong,Lin, Feng,Zhao, Han,Liu, Yuhe,Huang, Bangquan,Cheng, Jihua,Zhang, Wei. 2016

[2]Identification and characterization of expressed TIR- and non-TIR-NBS-LRR resistance gene analogous sequences from radish (Raphanus sativus L.) de novo transcriptome. Wang, Yan,Song, Zhaohui,Zhang, Wei,Xu, Liang,Muleke, Everlyne M'mbone,Liu, Liwang,Su, Xiaojun.

[3]Screening and transcriptome analysis of water deficiency tolerant germplasms in peanut (Arachis hypogaea). Shen, Yi,Liu, Yonghui,Chen, Zhide,Shen, Yi,Zhiguo, E.,Zhang, Xiaojun.

[4]Investigating right ovary degeneration in chick embryos by transcriptome sequencing. Yu, Jianning,Yan, Leyan,Chen, Zhe,Li, Hui,Ying, Shijia,Zhu, Huanxi,Shi, Zhendan.

[5]Characterization of the global transcriptome using Illumina sequencing and novel microsatellite marker information in seashore paspalum. Jia, Xinping,Deng, Yanming,Sun, Xiaobo,Liang, Lijian,Ye, Xiaoqing.

[6]藜麦EST-SSR的开发及通用性分析. 张体付,戚维聪,顾闽峰,张晓林,李坦,赵涵. 2016

[7]基于苹果EST-SSR的梨种质资源遗传多样性分析. 路娟,吴俊,张绍铃,吴华清,张妤艳. 2010

[8]基于RNA-seq的两种柳树转录组微卫星特征比较分析. 郑纪伟,周洁,王保松,何旭东. 2019

[9]藜科6种耐盐植物遗传多样性的EST-SSR分析. 徐照龙,易金鑫,余桂红,张大勇,何晓兰,王秀娥,马鸿翔. 2011

[10]海滨雀稗EST资源的SSR信息分析及EST-SSR标记开发. 李华勇,王显生,王艳平,吴燕,沈奇,贾新平. 2016

[11]草莓EST-SSR标记的开发与应用. 王静,赵密珍,于红梅,王壮伟. 2011

[12]鸟巢蕨EST-SSR标记的开发与应用. 贾新平,邓衍明,孙晓波,梁丽建. 2015

[13]基于海甘蓝RNA-Seq序列开发EST-SSR分子标记. 戚维聪,程计华,黄邦全,李坦,林峰. 2014

[14]辣椒EST-SSRs分布特征及其应用. 支莉,王述彬,刁卫平,刘金兵,潘宝贵,戈伟,于彩云. 2010

[15]辣椒EST-SSR标记的开发. 李晶晶,王述彬,刘金兵,潘宝贵,陈劲枫. 2008

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：江苏省农业科学院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台