Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (3): 519-532.doi: 10.16420/j.issn.0513-353x.2020-1046
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ZHOU Chenping1, YANG Min1, GUO Jinju2, KUANG Ruibin1, YANG Hu1, HUANG Bingxiong1, WEI Yuerong1,*()
Received:
2021-07-19
Revised:
2021-08-20
Online:
2022-03-25
Published:
2022-03-25
Contact:
WEI Yuerong
E-mail:weid18@163.com
CLC Number:
ZHOU Chenping, YANG Min, GUO Jinju, KUANG Ruibin, YANG Hu, HUANG Bingxiong, WEI Yuerong. Dynamic Changes in DNA Methylome and Transcriptome Patterns During Papaya Fruit Ripening[J]. Acta Horticulturae Sinica, 2022, 49(3): 519-532.
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URL: https://www.ahs.ac.cn/EN/10.16420/j.issn.0513-353x.2020-1046
用途 Application | 基因名称 Gene name | 上游引物(5′-3′) Forward primer | 下游引物(5′-3′) Reverse primer |
---|---|---|---|
McrBC-PCR | CpXTH30 | GGTTGGCTAATGATTGT | AGAAGGAAGGAGGGTGC |
CpPDS | CTAGTTTCTAACTGCGTAT | AACCATTATCATGTGGG | |
CpACO4 | GAAGACCATTAGCCACA | TTCGCTTAACTTAAACAC | |
CpXTH31 | ATGAAGTAGGGTGAGAA | ATGGTGGAATAAGTGTT | |
qRT-PCR | CpXTH30 | GTTCCATCGGTATAGCAT | CTTTGTATCTTCCACCTGA |
CpPDS | AGTTGGCGTCCCTGTTA | GGATTGATTTGGGTTGTA | |
CpACO4 | CACGAGCAGCCAAACGA | TCACCCACCCATCCCAC | |
CpXTH31 | GGGAACCCTACACTTTG | CTTGGATACCTCCGAAT |
Table 1 Primers used for McrBC-PCR and qRT-PCR
用途 Application | 基因名称 Gene name | 上游引物(5′-3′) Forward primer | 下游引物(5′-3′) Reverse primer |
---|---|---|---|
McrBC-PCR | CpXTH30 | GGTTGGCTAATGATTGT | AGAAGGAAGGAGGGTGC |
CpPDS | CTAGTTTCTAACTGCGTAT | AACCATTATCATGTGGG | |
CpACO4 | GAAGACCATTAGCCACA | TTCGCTTAACTTAAACAC | |
CpXTH31 | ATGAAGTAGGGTGAGAA | ATGGTGGAATAAGTGTT | |
qRT-PCR | CpXTH30 | GTTCCATCGGTATAGCAT | CTTTGTATCTTCCACCTGA |
CpPDS | AGTTGGCGTCCCTGTTA | GGATTGATTTGGGTTGTA | |
CpACO4 | CACGAGCAGCCAAACGA | TCACCCACCCATCCCAC | |
CpXTH31 | GGGAACCCTACACTTTG | CTTGGATACCTCCGAAT |
成熟期 Stage | 序列总数量 Total reads | 对比参考基 因组获得的 序列数量 Mapped reads | 匹配率/% Mapping rate | 重复序列 占比/% Duplication rate | ≥ Q30/% | 测序深度 Sequencing depth | 甲基化C位点 数量Number of Methylated C site | 平均甲基化水平/% Mean methylation level | |||
---|---|---|---|---|---|---|---|---|---|---|---|
C | CG | CHG | CHH | ||||||||
绿熟期 Green | 49 375 154 | 35 135 889 | 70.97 | 14.37 | 92.78 | 21.87 | 251 784 698 | 17.79 | 51.22 | 35.59 | 8.62 |
破色期 Color break | 49 361 724 | 34 881 444 | 70.67 | 12.75 | 91.56 | 22.08 | 258 718 931 | 17.51 | 50.64 | 35.09 | 8.44 |
熟化期 Half yellow | 49 461 069 | 34 774 513 | 70.36 | 12.62 | 92.57 | 21.95 | 232 054 629 | 17.04 | 48.60 | 33.76 | 8.26 |
腐熟期 Full yellow | 48 863 321 | 34 071 375 | 70.61 | 10.79 | 92.19 | 22.54 | 233 578 504 | 16.26 | 46.88 | 32.77 | 7.81 |
Table 2 Summary of WGBS data of papaya fruits at different ripening stages
成熟期 Stage | 序列总数量 Total reads | 对比参考基 因组获得的 序列数量 Mapped reads | 匹配率/% Mapping rate | 重复序列 占比/% Duplication rate | ≥ Q30/% | 测序深度 Sequencing depth | 甲基化C位点 数量Number of Methylated C site | 平均甲基化水平/% Mean methylation level | |||
---|---|---|---|---|---|---|---|---|---|---|---|
C | CG | CHG | CHH | ||||||||
绿熟期 Green | 49 375 154 | 35 135 889 | 70.97 | 14.37 | 92.78 | 21.87 | 251 784 698 | 17.79 | 51.22 | 35.59 | 8.62 |
破色期 Color break | 49 361 724 | 34 881 444 | 70.67 | 12.75 | 91.56 | 22.08 | 258 718 931 | 17.51 | 50.64 | 35.09 | 8.44 |
熟化期 Half yellow | 49 461 069 | 34 774 513 | 70.36 | 12.62 | 92.57 | 21.95 | 232 054 629 | 17.04 | 48.60 | 33.76 | 8.26 |
腐熟期 Full yellow | 48 863 321 | 34 071 375 | 70.61 | 10.79 | 92.19 | 22.54 | 233 578 504 | 16.26 | 46.88 | 32.77 | 7.81 |
Fig. 2 DNA methylation levels of genes and TEs(A)and C,CG,CHG,and CHH contexts(B)at different ripening stages of papaya fruits GS:Green stage;CB:Color break stage;HY:Half yellow stage;FY:Full yellow stage;-2K and 2K:2 kb upstream and downstream regions of genes;5′ and 3′:5′ and 3′ flanking regions of genes;rep1 and rep2:Two biological replicates. The same below.
Fig. 4 Circos plot of twenty genome scaffold methylation density Number on outer rim:Number of the twenty genome scaffolds;Scales of 5mC/RNA,TE and Gene:The methylation levels of CG,CHG,CHH sequence context,RNA abundance,the ratio of transposon repeats and gene number were from low to high,respectively.
Fig. 5 Relationship between distribution of methylation levels in three contexts within the genebody,upstream,and downstream 2 kb rigions(A)and methylation levels of genebody and promoterwith the gene expression levels(B) -2K and 2K:2 kb upstream and downstream regions of genes;Expression:genes with FPKM value < 1 were considered as none(non-expressed),expressed genes(FPKM value ≥ 1)were ranked from small to large and divided into three groups based on the upper and lower quartile;Methylation group:Methylation levels of genebodies or promoters were ranked from small to large and divided into quinitiles.
Fig. 7 Homologous alignment of DNA methylation genes(A)and their expression changes at different ripening stages in papaya fruits(B) Scale:From blue to red represent the gene expression levels was from low to high. 1-3:Three biological replicates.*:P < 0.05;-:No significant difference.
Fig. 8 Expression changes of carotenoid biosynthetic-related genes at different ripening stages of papaya fruits Scale:From blue to red represent the gene expression levels was from low to high;1-3:Three biological replicates.
Fig. 9 The DMRs methylation and expression levels of four candidate genes at different maturation stages of papaya fruits A:DMRs methylation levels of CpACO4,CpXTH30 and CpXTH31 promoters and CpPDS genebody;B:The McrBC-PCR validation(M:PCR products been digested by McrBC,Un:PCR products not been digested);C:Fold change(FC);D:qRT-PCR validation.
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