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基于RNA-Seq高通量测序技术的大口黑鲈转录组分析

黄勇 龚望宝 陈海刚 熊建利 孙西红

黄勇, 龚望宝, 陈海刚, 熊建利, 孙西红. 基于RNA-Seq高通量测序技术的大口黑鲈转录组分析[J]. 南方水产科学, 2019, 15(1): 106-112. doi: 10.12131/20180066
引用本文: 黄勇, 龚望宝, 陈海刚, 熊建利, 孙西红. 基于RNA-Seq高通量测序技术的大口黑鲈转录组分析[J]. 南方水产科学, 2019, 15(1): 106-112. doi: 10.12131/20180066
Yong HUANG, Wangbao GONG, Haigang CHEN, Jianli XIONG, Xihong SUN. Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq[J]. South China Fisheries Science, 2019, 15(1): 106-112. doi: 10.12131/20180066
Citation: Yong HUANG, Wangbao GONG, Haigang CHEN, Jianli XIONG, Xihong SUN. Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq[J]. South China Fisheries Science, 2019, 15(1): 106-112. doi: 10.12131/20180066

基于RNA-Seq高通量测序技术的大口黑鲈转录组分析

doi: 10.12131/20180066
基金项目: 国家科技支撑计划项目 (2012BAD25B04);河南省自然科学基金项目 (162300410069);河南省高等学校重点科研项目 (16A240002);广东省渔业生态环境重点实验室开放基金 (LFE-2016-13)
详细信息
    作者简介:

    黄勇:黄 勇(1979—),男,博士,副教授,从事水产经济动物非编码RNA调控研究。E-mail: huangyong1979111@126.com

  • 中图分类号: S 917.4

Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq

  • 摘要: 文章以大口黑鲈(Micropterus salmoides)组织作为研究对象,利用RNA-seq技术进行转录本测序和数据分析,经拼接组装,最终获得35 659条unigenes,序列平均长度738 bp,序列长度中位数 (N50)为1 052 bp。另外从长度分布与GC含量等方面对unigenes进行评估,数据显示测序质量好、可信度高。使用6大数据库 (KOG、Nr、Pfam、Swiss-Prot、GO和KEGG) 注释大口黑鲈转录组unigenes,分别对应有15 832、21 279、14 524、16 973、15 024和11 185条unigenes获得注释。其中,5 617条unigenes在以上所有数据库中同时注释成功,17 253条unigenes至少被一个数据库注释。KEGG分析结果显示,获得注释的11 185条unigenes被划分到267个代谢通路中,参与信号转导通路的unigenes数量最多,共有1 349条(12.06%)。另外还检测到4 030个微卫星 (SSR)位点。通过对大口黑鲈转录组测序,获得了大量的转录组信息,为大口黑鲈的功能基因克隆、基因组学、遗传多样性分析、分子标记开发及遗传改良等研究奠定了基础。
  • 图  1  Unigenes GC含量分布

    Figure  1.  GC content distribution of unigenes

    图  2  转录组transcript和unigenes长度分布

    A. transcript的长度分布;B. unigenes的长度分布

    Figure  2.  Length distribution of assembled transcripts and unigenes of transcriptome

    A. size distribution of transcripts; B. size distribution of unigenes

    图  3  Unigenes GO功能注释

    1. 转录、DNA依赖性;2. 转录调控、DNA依赖性;3. 蛋白质转运;4. 凋亡;5. 细胞分化;6. 细胞黏附;7. 蛋白质水解;8. 多细胞器官发育;9. 细胞周期;10. 细胞分化;11. 胞内信号转导;12. mRNA加工;13. 信号转导;14. 小G蛋白介导信号转导;15. 转运;16. 转录正调控;17. 有丝分裂;18. 染色质修饰;19. 转录负调控;20. RNA剪切;21. 胞内蛋白质运输;22. 翻译;23. DNA修复;24. 转录;25. 内噬作用;26. 细胞核;27. 细胞浆;28. 必须膜;29. 胞液;30. 细胞质膜;31. 内质网膜;32. 核仁;33. 线粒体;34. 胞外区;35. 核质;36. 隔膜;37. 高尔基体膜;38. 细胞骨架;39. 高尔基体;40. 细胞核周区;41. ATP结合;42. 锌离子结合;43. 蛋白结合;44. DNA结合;45. 金属离子结合;46. RNA结合;47. 钙离子结合;48. 特异序列DNA结合;49. 结合;50. 蛋白质丝氨酸特异酶结合

    Figure  3.  GO functional annotation of unigenes

    1. transcription, DNA-dependent; 2. regulation of transcription, DNA-dependent; 3. protein transport; 4. apoptosis; 5. cell division; 6. cell adhesion; 7. proteolysis; 8. multicellular organismal development; 9. cell cycle; 10. cell differentiation; 11. intracellular signal transduction; 12. mRNA procession; 13. signal transduction; 14. small GTPase mediated signal transduction; 15. transport; 16. negative regulation of transcription; 17. mitosis; 18. chromatin modification; 19. positive regulation of transcription; 20. RNA splicing; 21. intracellular protein; 22. translation; 23. DNA repair; 24. transcription; 25. endocytosis; 26. nucleus; 27. cytoplasm; 28. integral to membrane; 29. cytosol; 30. plasma membrane; 31. endoplasmic reticulum membrane; 32. nuclelous; 33. mitochondrion; 34. extracellular region; 35. nucleoplasm; 36. membrane; 37. golgi membrane; 38. cytoskeleton; 39. golgi apparatus; 40. perinuclear region of cytoplasm; 41. ATP binding; 42. zinc ion binding; 43. protein binding; 44. DNA binding; 45. metal ion binding; 46. RNA binding; 47. calcium ion binding; 48. specific DNA sequence binding; 49. binding; 50. protein serine/threonine-specific kinase

    图  4  Unigenes的KOG注释

    A. RNA加工和修饰;B. 染色体结构和动力学;C. 能源生产和转换;D. 细胞周期调控-细胞分裂-染色体分离;E. 氨基酸转运和代谢;F. 氨基酸转运和代谢;G. 碳水化合物转运和代谢;H. 辅酶转运和代谢;I. 脂质转运和代谢;J. 翻译-核糖体结构-生物合成;K. 转录;L. 复制-重组-修复;M. 细胞壁-细胞膜合成;N. 细胞运动;O. 翻译后修饰-蛋白质周转-分子伴侣;P. 无机离子转运与代谢;Q. 次生代谢产物生物合成、转运和分解代谢;R. 一般功能预测;S. 功能未知;T. 信号转导机制;U. 细胞内分泌和囊泡运输;V. 防御机制;W. 胞外结构;Y. 核结构;Z. 细胞骨架

    Figure  4.  KOG annotation of unigenes

    A. RNA processing and modification; B. chromatin structure and dynamics; C. energy production and conversion; D. cell cycle control, cell division, chromosome partitioning; E. amino acid transport and metabolism; F. nucleotide transport and metabolism; G. carbohydrate transport and metabolism; H. coenzyme transport and metabolism; I. lipid transport and metabolism; J. translation, ribosomal structure and biogenesis; K. transcription; L. replication, recombination and repair; M. cell wall/membrane/envelope biogenesis; N. cell motility; O. posttranslational modification, protein turnover, chaperones; P. inorganic ion transport and metabolism; Q. secondary metabolites biosynthesis, transport and catabolism; R. general function prediction only; S. function unknown; T. signal transduction mechanisms; U. intracellular trafficking, secretion, and vesicular transport; V. defense mechanisms; W. extracellular structure; Y. nuclear structure; Z. cytoskeleton

    图  5  Unigenes的KEGG注释

    Figure  5.  KEGG annotation of unigenes

    表  1  转录组数据拼接结果统计

    Table  1.   Assembly result of transcriptome data

    序列种类
    category
    总数
    total number
    N50长度/bp
    N50 length
    总长度/bp
    total length
    最大长度/bp
    maximum length
    中等长度/bp
    median length
    最小长度/bp
    minimum length
    平均长度/bp
    average length
    transcript 42 264 1 331 36 549 208 35 516 522 201 864
    unigene 35 659 1 052 26 340 493 35 516 472 201 738
     注:N50表示将转录本从长到短排序,依次累加碱基数,当累计碱基数达到转录本总碱基数的50%时的转录本的长度  Note: N50 of transcript or unigenes was calculated by ordering all sequences, then adding the lengths from longest to shortest until the summed length exceeded 50% of the total length of all sequences.
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出版历程
  • 收稿日期:  2018-04-10
  • 修回日期:  2018-06-15
  • 网络出版日期:  2018-12-05
  • 刊出日期:  2019-02-05

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