[植物資料庫] 一千種植物的轉錄基因組。 20191104 Nature

One thousand plant transcriptomes and the phylogenomics of green plants

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Abstract

Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

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綠色植物中，一千種植物的轉錄基因組與基因體演化樹

摘要

綠色植物大約包含有45 - 50萬種物種之多，其中有非常多的多樣性，在陸地以及水中生態都佔有重要的角色。在此，作為一千種植物轉錄基因組的起始點，我們定序了1124種植物影養生長狀態下的轉錄基因組。這些廣泛的泛植物物種中包含有綠色植物、灰藻門與紅藻門。我們的分析為研究綠色植物演化，提供了一個強而有力的基因體演化框架。多數物種推定的演化關係在許多物種的演化樹與多重模型分析中，都有很好的證據支持。然而在一些重要的演化節點上，細胞核中的基因與質體中的基因演化樹有不同調的現象，顯示出植物基因體演化的複雜性，包含了多倍體、快速的物種分化以及滅亡。在早期變異、多倍體以及基因家族的大量擴張上無法完整的分類，也更加強調了綠色植物演化的歷史。值得一提的是，我們發現在綠色植物、陸生植物與維管束植物的起始，基因家族就已經大量擴張。然而，全基因體的複製據推測，是重複的發生在開花植物與蕨類植物演化的過程中。隨著越來越多高品質的植物基因體序列的發布以及功能性基因體研究的推進，使得在整個綠色植物的演化上研究基因體的演進更為方便可行了。