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Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)
Journal of Systematics and Evolution ( IF 3.4 ) Pub Date : 2020-06-23 , DOI: 10.1111/jse.12651 Chun‐Lin Chen 1 , Lei Zhang 1 , Jia‐Liang Li 1 , Xing‐Xing Mao 1 , Lu‐Shui Zhang 1 , Quan‐Jun Hu 1 , Jian‐Quan Liu 1, 2 , Zhen‐Xiang Xi 1
Journal of Systematics and Evolution ( IF 3.4 ) Pub Date : 2020-06-23 , DOI: 10.1111/jse.12651 Chun‐Lin Chen 1 , Lei Zhang 1 , Jia‐Liang Li 1 , Xing‐Xing Mao 1 , Lu‐Shui Zhang 1 , Quan‐Jun Hu 1 , Jian‐Quan Liu 1, 2 , Zhen‐Xiang Xi 1
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Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome-scale phylogeny and identify large-scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.
中文翻译：
植物转录组学揭示龙胆亚科（Gentianaceae）中广泛的基因重复
基因复制在植物多样化和适应新栖息地方面发挥着重要作用。在这项研究中，我们旨在重建基因组规模的系统发育并鉴定龙胆亚科（龙胆科）的大规模基因重复事件，龙胆科是青藏高原高山植物的重要标志。我们对来自 67 个物种的 70 个转录组进行了测序和组装，代表了龙胆亚科以及密切相关的外群中所有六个公认的属。使用系统发育方法，龙胆亚科的骨干关系在高引导支持下几乎完全解决。尽管在核和质体系统发育之间观察到冲突的实例，但在两个系统发育中始终恢复了龙胆亚科的六个主要进化枝。此外，我们揭示了转录组组装中重复基因的高发生率。使用几种基因树协调方法，我们共同确定了物种树中具有大量重复基因的 10 个节点。进一步的分析表明，许多这些重复基因可能来自杂种多倍体，这也可能解释了龙胆亚科核和质体系统发育之间的一些拓扑不一致。
更新日期：2020-06-23
中文翻译：
植物转录组学揭示龙胆亚科（Gentianaceae）中广泛的基因重复
基因复制在植物多样化和适应新栖息地方面发挥着重要作用。在这项研究中，我们旨在重建基因组规模的系统发育并鉴定龙胆亚科（龙胆科）的大规模基因重复事件，龙胆科是青藏高原高山植物的重要标志。我们对来自 67 个物种的 70 个转录组进行了测序和组装，代表了龙胆亚科以及密切相关的外群中所有六个公认的属。使用系统发育方法，龙胆亚科的骨干关系在高引导支持下几乎完全解决。尽管在核和质体系统发育之间观察到冲突的实例，但在两个系统发育中始终恢复了龙胆亚科的六个主要进化枝。此外，我们揭示了转录组组装中重复基因的高发生率。使用几种基因树协调方法，我们共同确定了物种树中具有大量重复基因的 10 个节点。进一步的分析表明，许多这些重复基因可能来自杂种多倍体，这也可能解释了龙胆亚科核和质体系统发育之间的一些拓扑不一致。
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