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双孢蘑菇As2796菌株气生与贴生菌丝遗传差异的转录组分析

戴建清 陈文智 曾志恒 蔡志欣 陈美元

戴建清,陈文智,曾志恒,等. 双孢蘑菇As2796菌株气生与贴生菌丝遗传差异的转录组分析 [J]. 福建农业学报,2024,39(9):1−12
引用本文: 戴建清,陈文智,曾志恒,等. 双孢蘑菇As2796菌株气生与贴生菌丝遗传差异的转录组分析 [J]. 福建农业学报,2024,39(9):1−12
DAI J Q, CHEN W Z, ZENG Z H, et al. Transcriptome analysis of genetic differences between aerial and strandy hyphae of Agaricus bisporus strain As2796 [J]. Fujian Journal of Agricultural Sciences,2024,39(9):1−12
Citation: DAI J Q, CHEN W Z, ZENG Z H, et al. Transcriptome analysis of genetic differences between aerial and strandy hyphae of Agaricus bisporus strain As2796 [J]. Fujian Journal of Agricultural Sciences,2024,39(9):1−12

双孢蘑菇As2796菌株气生与贴生菌丝遗传差异的转录组分析

基金项目: 福建省科技计划公益类专项(2023R1033002);国家现代农业产业技术体系专项(CARS-20);福建省种业创新与产业化工程项目(zycxny2021011);福建省农业高质量发展超越“5511”协同创新工程项目(XTCXGC2021007);福建省农业科学院科技创新团队建设项目(CXTD2021007-1)
详细信息
    作者简介:

    戴建清(1972 —),男,高级农艺师,主要从事食用菌良种繁育研究,E-mail:317152396@qq.com

    通讯作者:

    陈美元(1972 — ),男,教授级高级工程师,主要从事双孢蘑菇遗传育种研究,E-mail: 401061326@qq.com

  • 中图分类号: S646

Transcriptome analysis of genetic differences between aerial and strandy hyphae of Agaricus bisporus strain As2796

  • 摘要:   目的  挖掘双孢蘑菌落形态变化可能涉及的重要基因,为双孢蘑菇种质资源评价、新品种选育提供科学依据。  方法  以双孢蘑菇主栽品种As2796为试验菌株,收集同一平板上生长的贴生与气生菌丝,提取样品的RNA进行转录组测序分析。  结果  通过转录组分析,A601(As2796气生组)与A602(As2796贴生组)共鉴定出965个差异表达基因(DEGs)。GO富集分析结果表明,在真菌细胞壁组成方面有疏水蛋白相关的DEGs富集,其中AGABI2DRAFT_13655AGABI2DRAFT_136569AGABI2DRAFT_193057属于ABH3蛋白基因家族,在气生菌丝的表达水平显著高于贴生菌丝,可能与气生菌丝的产生有关。研究还发现了疏水表面结合蛋白A(HsbA)相关基因AGABI2DRAFT_194662在气生菌丝中FPKM表达水平为0,在贴生菌丝中为10.24。通过对DEGs进一步分析,富集到8个可能与脂酶同工酶相关的DEGs,气生菌丝中这些基因的表达水平显著高于贴生菌丝。SNP/InDel分析结果表明,As2796气生组SNP数为110601,贴生组SNP数为111188,单核苷酸发生变化的主要以C:G>T: A为主,共筛选出2 374个共同InDel。  结论  成功获得双孢蘑菇不同形态菌丝的转录组数据,并从中挖掘出潜在的相关基因和SNP位点,为双孢蘑菇相关分子标记开发及辅助育种提供参考。
  • 图  1  双孢蘑菇As2796菌株(A)、贴生菌丝(B)和气生菌丝(C)

    红色箭头为气生菌落,黑色箭头为贴生菌落。

    Figure  1.  Plate of Agaricus bisporus As2796 strain (A)、strandy mycelium (B) and aerial hypha (C)

    Red arrows are aerial hypha and black arrows are strandy mycelium.

    图  2  差异表达基因火山图和数目统计图

    Figure  2.  Volcano plot and number statistics chart of DEGs

    图  3  双孢蘑菇贴生菌丝与气生菌丝共同差异表达基因的COG分类

    Figure  3.  COG annotation of common DEGs between strandy mycelium and aerial hypha of Agaricus bisporus

    图  4  差异表达基因GO二级节点注释统计图

    Figure  4.  GO secondary node annotation chart of DEGs

    图  5  双孢蘑菇贴生菌丝与气生菌丝共同差异表达基因的GO富集分析

    Figure  5.  GO enrichment analysis of common DEGs between strandy mycelium and aerial hypha of Agaricus bisporus

    图  6  差异表达基因KEGG通路富集分析

    Figure  6.  KEGG pathway analysis of differentially expressed genes

    图  7  吲哚二萜生物碱生物合成通路(A)和星形孢菌素生物合成通路(B)相关基因表达量分析

    Figure  7.  Gene expression related to indole diterpene alkaloid biosynthesis (A) and Staurosporine biosynthesis (B)

    图  8  SNP位点统计(A)和突变分布图(B)

    Figure  8.  SNP site statistics (A) and mutation distribution map (B)

    图  9  InDel Veen图(A)和位点统计图(B)

    Figure  9.  InDel Veen diagram (A) and site statistical diagram (B)

    表  1  样品测序数据及与参考基因组的序列比对结果

    Table  1.   Statistics of experimental data and alignnment with reference on genome sequence

    编号
    ID
    样品
    Sample
    总Read数
    Total clean reads
    比对到参考基因组的Reads数目
    Mapped reads
    比对到参考基因组的Reads百分比
    Mapped reads/%
    GC含量
    GC content/%
    ≥Q30的百分比
    ≥Q30/%
    A601 As2796气生 42 155 674 25 410 008 60.28 49.12 92.00
    A602 As2796贴生 45 225 288 28 324 702 62.63 49.28 92.37
    下载: 导出CSV

    表  2  新基因功能注释结果统计

    Table  2.   Number of new genes with functional annotation

    用于功能注释的数据库
    Annotated Database
    获得注释的新基因数目
    Annotated Gene Number
    长度在≥300~1000的新基因数目
    Gene Number (300≤gene length<1000)
    长度≥1000的新基因数目
    Gene Number (Gene length≥1000)
    COG 15 12 3
    GO 21 13 7
    KEGG 38 21 14
    KOG 20 12 8
    Pfam 34 20 12
    Swissprot 24 15 8
    nr 132 70 57
    All 139 76 57
    下载: 导出CSV

    表  3  部分差异表达基因

    Table  3.   Some significantly differentially expressed genes

    编号
    NO
    基因ID
    Gene ID
    相对表达量FPKM
    Relative expression FPKM
    Log2FC Pfam蛋白注释
    Pfam protein annotation
    基因注释
    Gene annotation
    A601 A602
    1 AGABI2DRAFT_194497 15.6653 0.0000 −6.78
    2 AGABI2DRAFT_177536 20.5777 0.0000 −4.47 假设蛋白OH76DRAFT_1359727
    3 AGABI2DRAFT_120985 1.0452 0.0000 −3.64 假设蛋白AN958_00580
    4 AGABI2DRAFT_203489 2.3380 0.0001 −3.85 假设蛋白 AN958_02967
    5 AGABI2DRAFT_44066 6.2585 0 −3.75 HhH-GPD超家族碱基
    切除DNA修复蛋白
    假设蛋白 AN958_02739
    6 AGABI2DRAFT_113583 0.0000 4.2489 4.73 假设蛋白 AN958_04089
    7 AGABI2DRAFT_117617 0.0008 6.9437 3.30 假设蛋白 AN958_03520
    8 AGABI2DRAFT_179131 0.0010 2.5569 4.28 假设蛋白 AN958_00324
    9 AGABI2DRAFT_194662 0 10.2374 4.66 疏水表面结合蛋白A 假设蛋白AN958_09554
    10 AGABI2DRAFT_136569 196.301 32.0293 −2.58 真菌疏水蛋白 假定的疏水蛋白 [双孢蘑菇]
    11 AGABI2DRAFT_193057 999.26 189.163 −2.38 真菌疏水蛋白 假定的疏水蛋白 [双孢蘑菇]
    12 AGABI2DRAFT_136557 19733 3086.17 −2.67 真菌疏水蛋白 假定的疏水蛋白 [双孢蘑菇]
    13 AGABI2DRAFT_143464 100.031 896.356 3.21 真菌疏水蛋白 假定的疏水蛋白 [双孢蘑菇]
    14 AGABI2DRAFT_178707 31.7555 666.848 4.35 真菌疏水蛋白 假定的疏水蛋白 [双孢蘑菇]
    下载: 导出CSV

    表  5  SNP突变统计表

    Table  5.   SNP mutation statistics table

    编号 ID T:A>G:C C:G>G:C T:A>A:T C:G>T:A C:G>A:T T:A>C:G 转化 Ts 颠换 Tv 转换/颠换比 ts/tv
    A601 6312 5221 7641 42864 6405 42158 85022 25579 3.32
    A602 6276 5239 7586 43273 6338 42476 85749 25439 3.37
    下载: 导出CSV

    表  6  全基因组和编码区InDel长度分布表

    Table  6.   Genome-wide and coding region InDel sites length distribution

    编号
    ID
    区域
    Region
    −10 −9 −8 −7 −6 −5 −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10
    A601 基因组
    Genome
    11 2 0 0 1 2 0 6 106 1235 1559 121 1 0 0 2 0 0 0 0
    A601 外显子
    Exonic
    7 1 0 0 1 0 0 3 2 99 221 14 1 0 0 2 0 0 0 0
    A602 基因组
    Genome
    14 3 0 0 1 2 0 11 100 1080 1434 121 3 0 0 3 0 0 0 0
    A602 外显子
    Exonic
    9 1 0 0 1 0 0 7 2 100 229 15 3 0 0 3 0 0 0 0
    下载: 导出CSV
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出版历程
  • 收稿日期:  2024-08-09
  • 修回日期:  2024-09-01
  • 网络出版日期:  2024-10-31

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