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玉足海参变态附着阶段转录组分析

吴晓鹏 黄敏伟 陈晓瑛 彭凯 赵吉臣 钟平 刘凤坤 张业辉 黄文

吴晓鹏, 黄敏伟, 陈晓瑛, 彭凯, 赵吉臣, 钟平, 刘凤坤, 张业辉, 黄文. 玉足海参变态附着阶段转录组分析[J]. 南方水产科学. doi: 10.12131/20230105
引用本文: 吴晓鹏, 黄敏伟, 陈晓瑛, 彭凯, 赵吉臣, 钟平, 刘凤坤, 张业辉, 黄文. 玉足海参变态附着阶段转录组分析[J]. 南方水产科学. doi: 10.12131/20230105
WU Xiaopeng, HUANG Minwei, CHEN Xiaoying, PENG Kai, ZHAO Jichen, ZHONG Ping, LIU Fengkun, ZHANG Yehui, HUANG Wen. Transcriptome analysis of metamorphosis stage of Holothuria leucospilota[J]. South China Fisheries Science. doi: 10.12131/20230105
Citation: WU Xiaopeng, HUANG Minwei, CHEN Xiaoying, PENG Kai, ZHAO Jichen, ZHONG Ping, LIU Fengkun, ZHANG Yehui, HUANG Wen. Transcriptome analysis of metamorphosis stage of Holothuria leucospilota[J]. South China Fisheries Science. doi: 10.12131/20230105

玉足海参变态附着阶段转录组分析

doi: 10.12131/20230105
基金项目: 广东省农业科学院协同创新中心课题 (水产研究中心,XT202302);广东省基础与应用基础研究基金自然科学基金(2020A1515011115);广东省农业科学院“青年科技骨干”人才引进项目 (R2020YJ-QG001, R2022YJ-QG001)
详细信息
    作者简介:

    吴晓鹏 (1996—),男,硕士研究生,研究方向为水产动物遗传与育种。E-mail: 2012152036@qq.com

    通讯作者:

    黄敏伟(1991—),男,副研究员,博士,研究方向为水产动物遗传育种与基因组学。E-mail: huangminwei@gdaas.cn

    黄 文(1987—),男,研究员,博士,研究方向为水产动物遗传与育种。E-mail: huangwen549@126.com

  • 中图分类号: Q 953;S 917.4

Transcriptome analysis of metamorphosis stage of Holothuria leucospilota

  • 摘要: 海参幼苗发育需要经历耳状幼体、樽形幼体、五触手幼体及幼苗阶段,而从浮游幼体变态发育至附着幼苗阶段的高死亡率是热带海参繁育中的共性问题,目前有关热带海参变态发育的调控机制仍不清楚。以玉足海参 (Holothuria leucospilota) 为研究对象,采集小耳幼体 (A)、中耳幼体 (B)、大耳幼体 (C) 和樽形幼体 (D) 4个时期样品进行高通量转录组测序分析,以探究其变态发育的分子机制。结果显示,共产生83.6 GB Raw reads,拼接获得93 528个Unigenes。对4个组测序文库的相邻组间 (A_vs_B, B_vs_C, C_vs_D) 进行两两比较,A_vs_B、B_vs_C和C_vs_D的差异表达基因数目分别为17 732、11 757和11 319 个。GO功能富集显示,差异基因主要富集于分子功能、催化活性等与细胞成长相关的GO功能。此外对KEGG通路进行了分析,结果显示差异基因显著富集于PI3K-Akt、细胞周期、癌症途径等与细胞分化增殖、凋亡相关的信号通路中,其中在幼体由浮游的大耳状幼体变态至附着的樽形幼体过程中,癌症途径的富集频率显著上升,表明其在幼体生长发育模式转换上发挥了关键作用。筛选的差异表达基因及预测的功能信息可为热带海参生长发育调控机制研究、人工繁育及分子改良应用提供参考。
  • 图  1  玉足海参幼体 4 个发育时期的形态

    注: a. 小耳幼体 (A期); b. 中耳幼体 (B期);c. 大耳幼体 (C期);d. 樽形幼体 (D期)。

    Figure  1.  Morphology of H. leucospilota larva at four developmental stages

    Note: a. Early auricularia (Stage A); b. Mid auricularia (Stage B); c. Late auricularia (Stage C); d. Doliolaria (Stage D).

    图  2  NR 数据库比对统计图

    Figure  2.  Comparison chart of NR database

    图  3  Unigene GO 功能注释结果

    Figure  3.  GO annotation results of unigene

    图  4  Unigene KEGG 功能注释结果

    Figure  4.  KEGG annotation results of unigene

    图  5  相邻组间差异表达基因火山图

    注:A_vs_B. B期以A期为参照基准比较;B_vs_C. C期以B期为参照基准比较;C_vs_D. D期以C期为参照基准比较。后图同此。

    Figure  5.  Volcano map of differentially expressed genes between adjacent groups

    Note: A_vs_B. Stage B was compared with Stage A; B_vs_C. Stage C was compared with Stage B; C_vs_D. Stage D was compared with Stage C. The same case in following figures.

    图  6  相邻组间差异表达基因 KEGG 通路分析

    Figure  6.  KEGG pathway analysis of differentially expressed genes between adjacent groups

    图  7  qRT-PCR 验证 RNA-seq 结果

    Figure  7.  RNA-Seq results verified by qRT-PCR

    表  1  引物信息

    Table  1.   Primer information

    基因 ID    
    Gene ID    
    正向引物
    Forward primer
    反向引物
    Reverse primer
    U_57660 CACTCACGCAGAAGATGT CCAGCAATTCCAAGTTCAAT
    U_166100 CCTCATCCTTGCTGCTATT GTCACTCCAACACCAACA
    U_10254 AGTCACAGAACAGAGGTAAT CGAACGGTCCACATATCA
    U_21303 ACACCGAACACAGGAATC CCGTTAAGGAGTAAGAGTCA
    U_27749 TCATTGTTCGGATTGATTGC AACTGCTGACATTGACCAT
    U_179808 GGATGGCAAGATGAATACTG CGTCGCTATTAAGATTAGGAG
    β-Actin GTCAGGTCATCACTATCGGCAAT AGAGGTCTTTACGGATGTCAACGT
    下载: 导出CSV

    表  2  转录本组装结果统计分析

    Table  2.   Statistics analysis of transcript assembly results

    项目类型
    Item type
    数量
    Number
    总序列数 Total sequence number 93 528
    碱基总数 Total base 287 791 031
    最长转录本长度 Maximum transcript length 9 920
    最短转录本长度 Minimum transcript length 133
    转录本平均长度 Average transcript length 3 077.06
    N50 长度 N50 length 3 608
    E90N50 长度 E90N50 length 3 575
    GC 百分比 GC percent 38.67%
    Mapped 率 Mapped percent 73.71%
    下载: 导出CSV

    表  3  相邻组间差异表达基因 GO 富集分析 (前 5)

    Table  3.   GO enrichment analysis of differentially expressed genes between adjacent groups (Top five)

    相邻组间
    Intergroup
    GO IDGO 分类
    GO Term
    频率
    Frequency
    P
    P value
    类型
    Type
    A _vs _B GO: 0071840 细胞成分组织或生物发生
    Cellular component organization or biogenesis
    0.072 0.091 233
    GO: 0016043 细胞成分组织
    Cellular component organization
    0.068 0.303 803
    GO: 0044281 小分子代谢过程
    Small molecule metabolic process
    0.066 0.000 836 生物过程
    Biological process
    GO: 0007017 基于微管的过程
    Microtubule-based process
    0.039 0.000 702
    GO: 0019752 羧酸代谢过程
    Carboxylic acid metabolic process
    0.037 0.000 818
    GO: 0005575 细胞组分
    Cellular_component
    0.661 0.081 363
    GO: 0110165 细胞解构实体
    Cellular anatomical entity
    0.594 0.061 953
    GO: 0005576 细胞外区
    Extracellular region
    0.053 0.000 702 细胞组分
    Cellular component
    GO: 0042995 细胞投影
    Cell projection
    0.031 0.000 858
    GO: 0099080 超分子复合物
    Supramolecular complex
    0.030 0.001 038
    GO: 0043167 离子结合
    Ion binding
    0.325 0.014 108
    GO: 0016787 水解酶活性
    Hydrolase activity
    0.170 0.000 939
    GO: 0036094 小分子结合
    Small molecule binding
    0.163 0.000 962 分子功能
    Molecular function
    GO: 1901265 核苷磷酸结合
    Nucleoside phosphate binding
    0.151 0.001 825
    GO: 0000166 核苷酸结合
    Nucleotide binding
    0.151 0.001 825
    B_vs_C
    GO: 0044281 小分子代谢过程
    Small molecule metabolic process
    0.063 0.097 450
    GO: 0005975 碳水化合物代谢过程
    Carbohydrate metabolic process
    0.030 0.000 614
    GO: 0019637 有机磷代谢过程
    Organophosphate metabolic process
    0.026 0.289 465 生物过程
    Biological process
    GO: 0044283 小分子生物合成过程
    Small molecule biosynthetic process
    0.021 0.076 630
    GO: 0006091 前体代谢物和能量的产生
    Generation of precursor metabolites and energy
    0.018 0.011 235
    GO: 0005575 细胞组分
    Cellular_component
    0.676 0.001 002
    GO: 0110165 细胞解构实体
    Cellular anatomical entity
    0.597 0.085 132
    GO: 0031224 膜的内在成分
    Intrinsic component of membrane
    0.307 0.071 058 细胞组分
    Cellular component
    GO: 0016021 膜的组成部分
    Integral component of membrane
    0.306 0.087 041
    GO: 000557 6 细胞外区
    Extracellular region
    0.067 0.000 566
    GO: 0043169 阳离子结合
    Cation binding
    0.204 0.134 971
    GO: 0046872 金属离子结合
    Metal ion binding
    0.204 0.121 753
    GO: 0016491 氧化还原酶活性
    Oxidoreductase activity
    0.090 0.002 897 分子功能
    Molecular function
    GO: 0005215 转运蛋白活性
    Transporter activity
    0.075 0.029 888
    GO: 0005509 钙离子结合
    Calcium ion binding
    0.073 0.000 626
    C_ vs _D GO: 0005975 碳水化合物代谢过程
    Carbohydrate metabolic process
    0.025 0.162 444
    GO: 0044283 小分子生物合成过程
    Small molecule biosynthetic process
    0.023 0.022 217
    GO: 0007166 细胞表面受体信号通路
    Cell surface receptor signaling pathway
    0.022 0.113 132 生物过程
    Biological process
    GO: 0006790 硫化合物代谢过程
    Sulfur compound metabolic process
    0.021 0.000 184
    GO: 0032259 甲基化
    Methylation
    0.020 0.014 144
    GO: 0031224 膜的内在成分
    Intrinsic component of membrane
    0.325 0.000 333
    GO: 0016021 膜的组成部分
    Integral component of membrane
    0.325 0.000 332
    GO: 0005576 细胞外区
    Extracellular region
    0.063 0.000 185 细胞组分
    Cellular component
    GO: 0005581 胶原蛋白三聚体
    Collagen trimer
    0.031 0.000 184
    GO: 0005615 细胞外空间
    Extracellular space
    0.019 0.000 207
    GO: 0003674 分子功能
    Molecular_function
    0.820 0.000 312
    GO: 0043169 阳离子结合
    Cation binding
    0.214 0.000 417
    GO: 0046872 金属离子结合
    Metal ion binding
    0.214 0.000 382 分子功能
    Molecular function
    GO: 0140096 催化活性,作用于蛋白质
    Catalytic activity, acting on a protein
    0.113 0.020 871
    GO: 0016491 氧化还原酶活性
    Oxidoreductase activity
    0.095 0.000 247
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-05-19
  • 修回日期:  2023-07-18
  • 录用日期:  2023-07-21
  • 网络出版日期:  2023-08-08

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