Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.
Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.
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DOI：
10.1093/plphys/kiad209
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发表时间：
2023-07-03
期刊：
影响因子：
7.4
通讯作者：
Juenger, Thomas E.
中科院分区：
文献类型：
--
作者：
Weng, Xiaoyu;Song, Haili;Sreedasyam, Avinash;Haque, Taslima;Zhang, Li;Chen, Cindy;Yoshinaga, Yuko;Williams, Melissa;O'Malley, Ronan C.;Grimwood, Jane;Schmutz, Jeremy;Juenger, Thomas E.
花序的形态多样性决定了花和种子的产生，这对植物的适应性至关重要。霍尔草（Panicum hallii， P. hallii）是一种野生多年生草本植物，已被发展成为研究多年生草生物学和适应进化的模型。哈里花的两种主要生态型在花序形态上已经进化出高度分化，即花序紧凑、种子大的山地生态型（哈里花，HAL2基因型）和花序开放、种子小的低地生态型（哈里花，FIL2基因型）。在这里，我们使用基因组参考对每个生态型的不同花序发育阶段的转录组和DNA甲基组（影响基因表达调控的表观遗传标记）进行了比较分析。对差异表达基因（DEGs）和共同表达模块的全球转录组分析揭示了细胞分裂素信号在异慢性变化中的潜在作用。比较DNA甲基化谱揭示了与哈里花花序进化相关的显著水平的差异DNA甲基化。我们发现很大比例的差异甲基化区域（DMRs）位于基因的侧翼调控区域。有趣的是，我们在FIL2基因的启动子中观察到CHH超甲基化的显著偏倚。deg、DMRs和Ka/Ks比值的综合结果表征了dmr相关deg对哈里花花序分化的进化特征。本研究为深入了解哈里哈里花序分化的转录组和表观遗传格局提供了新的思路，并为多年生草本植物生物学提供了基因组资源。通过对高原生态型和低地生态型鸢尾花序不同阶段的转录组和DNA甲基化分析，揭示了鸢尾基因表达和DNA甲基化的差异。
The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology. A comparative transcriptome and DNA methylome analysis of different stages of inflorescence between upland and lowland ecotypes reveals gene expression and DNA methylation divergence in Panicum hallii.
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影响因子：
5.8
作者：
Gu, Zuguang;Eils, Roland;Schlesner, Matthias
通讯作者：
Schlesner, Matthias
影响因子：
64.5
作者：
Kawakatsu T;Huang SC;Jupe F;Sasaki E;Schmitz RJ;Urich MA;Castanon R;Nery JR;Barragan C;He Y;Chen H;Dubin M;Lee CR;Wang C;Bemm F;Becker C;O'Neil R;O'Malley RC;Quarless DX;1001 Genomes Consortium;Schork NJ;Weigel D;Nordborg M;Ecker JR
通讯作者：
Ecker JR
影响因子：
7.4
作者：
Feng, Nan;Song, Gaoyuan;Mao, Long
通讯作者：
Mao, Long
影响因子：
7.2
作者：
Harrop, Thomas W. R.;Din, Israr Ud;Kater, Martin M.
通讯作者：
Kater, Martin M.
影响因子：
4.2
作者：
Fernandez-Nohales, P.;Domenech, M. J.;Madueno, F.
通讯作者：
Madueno, F.