Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae

doi:10.1093/aob/mcac062

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	Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae
	Zhao, Lei; Yang, Ying-Ying; Qu, Xiao-Jian; Ma, Hong; Hu, Yi; Li, Hong-Tao; Yi, Ting-Shuang; Li, De-Zhu
	2022
发表期刊	ANNALS OF BOTANY
摘要	Background and Aims The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. Methods New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. Key Results Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event psi (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the psi-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. Conclusions Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
关键词	Araceae diversification phylogenomics WGDs adaptation TRAIT-DEPENDENT SPECIATION GENE DUPLICATION ANGIOSPERM DIVERSIFICATION PHYLOGENOMIC ANALYSES NUCLEAR GENES POLYPLOIDY EVOLUTIONARY FAMILY RATES TOOL
DOI	10.1093/aob/mcac062
收录类别	SCI
WOS记录号	WOS:000827117200001
引用统计	被引频次：10[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74683
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Zhao, Lei,Yang, Ying-Ying,Qu, Xiao-Jian,et al. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae[J]. ANNALS OF BOTANY,2022.
APA	Zhao, Lei.,Yang, Ying-Ying.,Qu, Xiao-Jian.,Ma, Hong.,Hu, Yi.,...&Li, De-Zhu.(2022).Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae.ANNALS OF BOTANY.
MLA	Zhao, Lei,et al."Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae".ANNALS OF BOTANY (2022).

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