Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China.
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
Ann Bot. 2022 Dec 31;130(7):951-964. doi: 10.1093/aob/mcac113.
With some 7300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole-genome duplications, are still contentious.
Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55 taxon liverwort species tree.
Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole-genome duplication events along the backbone phylogeny of liverworts.
With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole-genome duplication during the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole-genome duplications.
现存的约 7300 种苔类植物代表了主要的陆生植物谱系之一。骨干关系，如叶苔目的系统发育位置，以及全基因组加倍的发生和时间，仍然存在争议。
基于对 38 种苔类植物新生成的转录组数据的分析，并辅以公共可用的数据，我们重建了苔类植物的进化历史，并推断了沿 55 个分类群苔类植物种系发生树的基因复制事件。
我们的系统发育基因组学研究提供了一个科级水平的苔类植物核系统发育，并确定了广泛的基因树冲突和核质不和谐。基于整合的系统发育基因组学和 Ks 分布的基因复制分析表明，在苔类植物的骨干系统发育中没有全基因组加倍事件的证据。
通过广泛的苔类植物转录组采样，我们重新评估了苔类植物的骨干系统发育，并提供了古老杂交后不完全谱系分选的证据，这些证据塑造了苔类植物的深层进化历史。在苔类植物的深层进化过程中没有全基因组加倍表明，苔类植物可能代表了少数几个主要的胚胎植物谱系之一，其进化不是由全基因组加倍驱动的。
