植物学报 ›› 2020, Vol. 55 ›› Issue (5): 551-563.DOI: 10.11983/CBB20026
王丽妍1, 卢梦瑶1, 童悦1, 徐祥斌1, 张正科1, 孟兰环1, 史学群1,*(), 宋海超2,*(
)
收稿日期:
2020-02-22
接受日期:
2020-05-08
出版日期:
2020-09-01
发布日期:
2020-09-03
通讯作者:
史学群,宋海超
作者简介:
songhaichao@sohu.com基金资助:
Liyan Wang1, Mengyao Lu1, Yue Tong1, Xiangbin Xu1, Zhengke Zhang1, Lanhuan Meng1, Xuequn Shi1,*(), Haichao Song2,*(
)
Received:
2020-02-22
Accepted:
2020-05-08
Online:
2020-09-01
Published:
2020-09-03
Contact:
Xuequn Shi,Haichao Song
摘要:
胶孢炭疽菌(Colletotrichum gloeosporioides)是引发芒果(Mangifera indica)炭疽病的主要病原体。室内平板培养胶孢炭疽菌不产生或产生很少分生孢子的情况时有发生, 但菌丝在机械损伤后24-48小时会产生大量分生孢子。胶孢炭疽菌应答机械损伤诱导产孢的核心基因及关键代谢通路尚未见报道。基于转录组测序(RNA-seq)技术检测了芒果胶孢炭疽菌菌丝在机械损伤处理后2小时内5个时间点的基因表达变化, 对差异表达基因进行GO富集和KEGG代谢通路富集分析, 并对菌丝响应胁迫的基因动态表达数据进行分析。基于常微分方程ODE模型结合变量选择技术, 构建了动态基因调控网络。结果表明, 有417个差异表达基因参与应答胶孢炭疽菌菌丝机械损伤, 分属12个聚类模块, 有4条通路存在显著富集, 分别是丙酮酸代谢、硫代谢、黄曲霉素合成途径和二萜合成途径。结合功能注释筛选出12个应答菌丝损伤胁迫的核心基因。研究结果为后续深入开展芒果胶孢炭疽菌产孢和致病机理研究奠定了重要基础。
王丽妍, 卢梦瑶, 童悦, 徐祥斌, 张正科, 孟兰环, 史学群, 宋海超. 芒果胶孢炭疽病菌应答菌丝机械损伤产生无性孢子的分子机制. 植物学报, 2020, 55(5): 551-563.
Liyan Wang, Mengyao Lu, Yue Tong, Xiangbin Xu, Zhengke Zhang, Lanhuan Meng, Xuequn Shi, Haichao Song. Molecular Mechanism of the Generation of Asexual Spores of the Mango Fungal Pathogen (Colletotrichum gloeosporioides) Induced by Mechanical Injuries. Chinese Bulletin of Botany, 2020, 55(5): 551-563.
Transcript | Upstream primer sequence (5°?3°) | Downstream primer sequence (5°?3°) |
---|---|---|
ELA27200 | CCTCAAACTTCGCAGATG | GGCTGTCGTGTAGAACTG |
ELA31518 | ACTGCGAATCACATCATCTCA | TAAGAGGTCGGCGTCAGA |
ELA26856 | CAGCAGATGGTCAAGAGG | GAGGAGACGAAGGAAGGA |
ELA23533 | TCAGCCTTGTTGGACCTTAG | CGTAGCATCGGACCTTGT |
ELA34567 | GAGCAGGTATCAGAAGACA | CCAGTTCGTAAGCCAGAT |
Actin | ACGCTTCTCATCTCCAAGATCCGT | AGAGAGCCTCGTTGTCAATGCAGA |
表1 实时荧光定量PCR所用引物
Table 1 Primers for real-time quantitative PCR
Transcript | Upstream primer sequence (5°?3°) | Downstream primer sequence (5°?3°) |
---|---|---|
ELA27200 | CCTCAAACTTCGCAGATG | GGCTGTCGTGTAGAACTG |
ELA31518 | ACTGCGAATCACATCATCTCA | TAAGAGGTCGGCGTCAGA |
ELA26856 | CAGCAGATGGTCAAGAGG | GAGGAGACGAAGGAAGGA |
ELA23533 | TCAGCCTTGTTGGACCTTAG | CGTAGCATCGGACCTTGT |
ELA34567 | GAGCAGGTATCAGAAGACA | CCAGTTCGTAAGCCAGAT |
Actin | ACGCTTCTCATCTCCAAGATCCGT | AGAGAGCCTCGTTGTCAATGCAGA |
图1 不同处理样品基因表达数据和差异表达基因GO富集结果 (A) 不同样本基因表达数据的分布; (B) 不同样本间的相关性; (C) 差异表达基因的GO富集分析。MF: 分子功能; BP: 生物过程; CC: 细胞组分
Figure 1 Gene expression data and GO enrichment for differentially expressed genes under different treatments (A) Gene expression in different samples; (B) Correlation between different samples; (C) GO enrichment for differentially expressed genes. MF: Molecular function; BP: Biological process; CC: Cell components
Description | Gene ratio | Bg ratio | P-value | Gene ID | Count |
---|---|---|---|---|---|
Aflatoxin biosynthesis | 6/113 | 46/2826 | 0.009071 | CGGC5_14023/CGGC5_13120/CGGC5_13638/ CGGC5_13456/CGGC5_10453/CGGC5_9572 | 6 |
Pyruvate metabolism | 7/113 | 72/2826 | 0.023327 | CGGC5_14045/CGGC5_7569/CGGC5_3411/ CGGC5_10319/CGGC5_11829/CGGC5_3455/ CGGC5_5764 | 7 |
Sulfur metabolism | 3/113 | 19/2826 | 0.037811 | CGGC5_5794/CGGC5_12200/CGGC5_15291 | 3 |
Diterpenoid biosynthesis | 3/113 | 21/2826 | 0.048998 | CGGC5_1921/CGGC5_15293/CGGC5_11451 | 3 |
表2 差异表达基因KEGG富集结果
Table 2 KEGG enrichment result for differentially expressed genes
Description | Gene ratio | Bg ratio | P-value | Gene ID | Count |
---|---|---|---|---|---|
Aflatoxin biosynthesis | 6/113 | 46/2826 | 0.009071 | CGGC5_14023/CGGC5_13120/CGGC5_13638/ CGGC5_13456/CGGC5_10453/CGGC5_9572 | 6 |
Pyruvate metabolism | 7/113 | 72/2826 | 0.023327 | CGGC5_14045/CGGC5_7569/CGGC5_3411/ CGGC5_10319/CGGC5_11829/CGGC5_3455/ CGGC5_5764 | 7 |
Sulfur metabolism | 3/113 | 19/2826 | 0.037811 | CGGC5_5794/CGGC5_12200/CGGC5_15291 | 3 |
Diterpenoid biosynthesis | 3/113 | 21/2826 | 0.048998 | CGGC5_1921/CGGC5_15293/CGGC5_11451 | 3 |
图3 差异表达基因聚类模块的富集分析 (A) GO富集分析; (B) KEGG富集分析。图中横坐标表示不同聚类, 纵坐标表示富集通路的名称。不同颜色的点代表不同P-value值, 点的大小表示该通路下差异表达基因的多少。P-value取值范围为0-0.15, 数值越接近0, 表示富集越显著。
Figure 3 Enrichment analysis for each gene cluster of differentially expressed genes (A) GO enrichment analysis for each cluster; (B) KEGG enrichment analysis for each cluster. The x-axis represents the different cluster and the y-axis is the name of enrichment pathway. Different P-value are represented by dots with different colors, while the number of differentially expressed genes in each pathway are displayed for the size of the dots. P-value ranges from 0-0.15. The closer the value to 0, the more significant the enrichment is.
Module | Gene numbers | Transcript | Gene description |
---|---|---|---|
1 | 1 | ELA23757 | Pep1 |
1 | 6 | ELA25282 | Cytochrome p450 |
1 | 16 | ELA23240 | Nad-dependent epimerase dehydratase |
2 | 20 | EFCGT00000013177 | 5.8S_rRNA |
2 | 25 | ELA35632 | Polyketide synthase |
2 | 44 | ELA25574 | Integral membrane protein |
2 | 49 | ELA24193 | Short chain dehydrogenase reductase family |
2 | 57 | ELA35820 | Ankyrin repeat-containing protein |
2 | 189 | ELA25228 | Ankyrin repeat protein |
2 | 26 | ELA33919 | Laccase |
6 | 76 | ELA24504 | Major facilitator superfamily transporter |
11 | 232 | ELA37190 | Catalase |
表3 差异表达基因12个聚类模块中的12个核心基因
Table 3 Twelve core genes identified in 12 cluster modules of differentially expressed genes
Module | Gene numbers | Transcript | Gene description |
---|---|---|---|
1 | 1 | ELA23757 | Pep1 |
1 | 6 | ELA25282 | Cytochrome p450 |
1 | 16 | ELA23240 | Nad-dependent epimerase dehydratase |
2 | 20 | EFCGT00000013177 | 5.8S_rRNA |
2 | 25 | ELA35632 | Polyketide synthase |
2 | 44 | ELA25574 | Integral membrane protein |
2 | 49 | ELA24193 | Short chain dehydrogenase reductase family |
2 | 57 | ELA35820 | Ankyrin repeat-containing protein |
2 | 189 | ELA25228 | Ankyrin repeat protein |
2 | 26 | ELA33919 | Laccase |
6 | 76 | ELA24504 | Major facilitator superfamily transporter |
11 | 232 | ELA37190 | Catalase |
图4 差异表达基因聚类模块内基因间调控网络重构建 不同颜色对应不同的聚类模块。方框中的数字代表核心模块中相互作用的基因编号, 12个核心基因包含其中。
Figure 4 Inter-module regulatory network reconstruction of differentially expressed genes Different colors correspond to different clustered modules. The numbers in the boxes represent the interacting gene numbers in core modules. The 12 core genes are included.
图5 5个核心基因的动态表达模式及数据相关性 不同小写字母表示各处理间差异显著(P<0.05)。
Figure 5 The dynamic expression patterns and data correlation of five core genes Different lowercase letters indicate significant differences among treatments (P<0.05).
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