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园艺学报 ›› 2022, Vol. 49 ›› Issue (3): 519-532.doi: 10.16420/j.issn.0513-353x.2020-1046

• 研究论文 • 上一篇    下一篇

番木瓜成熟过程中全基因组DNA甲基化和转录组变化分析

周陈平1, 杨敏1, 郭金菊2, 邝瑞彬1, 杨护1, 黄炳雄1, 魏岳荣1,*()   

  1. 1广东省农业科学院果树研究所,农业农村部南亚热带果树生物学与遗传资源利用重点实验室,广东省热带亚热带果树研究重点实验室,广州 510640
    2广东省农业科学院设施农业研究所,广州 510640
  • 收稿日期:2021-07-19 修回日期:2021-08-20 出版日期:2022-03-25 发布日期:2022-03-25
  • 通讯作者: 魏岳荣 E-mail:weid18@163.com
  • 基金资助:
    广东省基础与应用基础研究基金项目(2020A1515011166);广州市科技计划项目(202102020038);广东省现代农业产业技术体系创新团队建设项目(2021KJ116);广州市基础与应用基础研究一般项目(2060206-13)

Dynamic Changes in DNA Methylome and Transcriptome Patterns During Papaya Fruit Ripening

ZHOU Chenping1, YANG Min1, GUO Jinju2, KUANG Ruibin1, YANG Hu1, HUANG Bingxiong1, WEI Yuerong1,*()   

  1. 1Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization,Ministry of Agriculture and Rural Affairs,Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research,Institute of Fruit Tree Research,Guangdong Academy of Agricultural Sciences,Guangzhou 510640,China
    2Institute of Facility Agriculture,Guangdong Academy of Agricultural Sciences,Guangzhou 510640,China
  • Received:2021-07-19 Revised:2021-08-20 Online:2022-03-25 Published:2022-03-25
  • Contact: WEI Yuerong E-mail:weid18@163.com

摘要:

采用全基因组DNA甲基化(WGBS)和转录组测序(RNA-seq)技术对番木瓜4个成熟时期(绿熟期、破色期、熟化期、腐熟期)的果实样品进行高通量测序。C位点、CG、CHG和CHH序列平均甲基化水平分别为17.15%、49.33%、34.30%和8.28%。全基因组DNA甲基化水平在果实成熟过程中持续下降,同时差异表达基因(DEG)数量逐渐上升。全基因组DNA甲基化和转录组数据联合分析表明,基因表达水平与启动子及基因体甲基化水平呈显著正相关。筛选出CpACO4CpPDSCpXTH30CpXTH31等4个番木瓜果实成熟差异表达候选基因,利用荧光定量PCR和McrBC-PCR分别检测其表达水平和相应DMR序列甲基化水平,结果分别同转录组和全基因组DNA甲基化一致,推测这些基因在番木瓜果实成熟过程中起重要作用。

关键词: 番木瓜, 果实, 成熟, 全基因组, DNA甲基化, 基因, 差异表达

Abstract:

The whole genome bisulfite sequencing(WGBS)and transcriptome sequencing(RNA-seq)techniques were used to sequence papaya fruit samples at four stages,namely green stage,color break stage,half yellow stage and full yellow stage. The average methylation level of C locus,CG,CHG,and CHH sequence contexts were 17.15%,49.33%,34.30%,and 8.28%,respectively. The level of genome-wide DNA methylation decreased with the ripening of fruit,accompanied by the increased number of differentially expressed genes(DEGs). Combined analysis of genome-wide DNA methylation and transcriptome data showed that the gene expression presented an obvious positive correlation with promoter and genebody methylation. Four differentially expressed candidate genes possibly responsible for papaya fruit ripening,namely CpACO4,CpPDS,CpXTH30 and CpXTH31,were screened out. Their expression levels and DMRs methylation levels obtained by RT-qPCR and McrBC-PCR matched well with the results of the transcriptome and methylome,respectively. These genes might play an important role in papaya fruit ripening.

Key words: Carica papaya, fruit, ripening, whole genome, DNA methylation, gene, differentially expression

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