Mitochondrial phylogenomics of liverworts

<b>Abstract</b><br/><p><strong>Premise: </strong>Liverworts, with approximately 7,300 species worldwide, exhibit remarkable morphological diversity, in terms of growth form, ontogeny and architecture. Based on phylogenetic inferences drawn from DNA data, including recent genomic-scale data, the relationships among families and orders have been constantly revised and refined, although new topological incongruences have emerged. The liverwort mitochondrial genome exhibits lower average substitution rates compared to their nuclear and plastid genomes, and shows less structural variation, suggesting its suitability for inferring relationships at higher taxonomic levels.</p> <p><strong>Methods:</strong> The mitochondrial genomes of 112 liverworts were sequenced, covering 105 species, 52 families and 18 orders. We analysed the structures of the liverwort mitogenomes using Mauve alignment. Maximum likelihood and Bayesian inference methods were used to infer a family-level phylogeny of liverworts.</p> <p><strong>Results: </strong>We assembled the complete mitochondrial genome for 23 species and identified four new structural variants. Phylogenetic inferences from mitochondrial genome sequences confirmed the monophyly of most suprafamilial taxa, with the expectations of Porellales, Ptilidiales, and Pelliidae. <em>Herzogianthus</em> (Ptilidiales) was well-supported as a sister group to Jungermanniales sensu lato, rather than forming a monophyletic lineage with <em>Ptilidium </em>(Ptilidiales). Given its distinct morphological traits, this genus should be singled out and elevated to a new order.</p> <p><strong>Conclusions: </strong>The overall architecture of liverwort mitogenomes remains highly conserved, with taxa that diverged over 470 Mya still having co-linear mitogenomes. This study provides a genetic resource for future evolutionary research across the liverworts and highlights the utility of mitogenome across lineages diversifying for 470 Mya, including for family‐level classification.</p>

**摘要**

**研究背景：** 全球范围内约有7300种地钱类（liverworts），其在生长型、个体发育及结构架构上展现出显著的形态多样性。基于包括最新基因组规模数据在内的DNA系统发育推断（phylogenetic inferences），地钱类各科、目级分类群间的系统发育关系虽持续得到修订与完善，但新的拓扑结构不一致性也不断涌现。地钱类的线粒体基因组（mitochondrial genome）相较于核基因组（nuclear genome）与质体基因组（plastid genome），平均替换率更低，且结构变异更少，这表明其适用于更高分类阶元的系统发育关系推断。

**研究方法：** 本研究对覆盖105种、52科、18目的112份地钱类样本的线粒体基因组进行了测序。采用Mauve比对工具分析地钱类线粒体基因组的结构特征，并通过最大似然法（maximum likelihood）与贝叶斯推断法（Bayesian inference）构建地钱类的科级系统发育树。

**研究结果：** 本研究组装得到23种地钱类的完整线粒体基因组，同时鉴定出4种全新的结构变异类型。基于线粒体基因组序列的系统发育分析证实，多数超科级分类群为单系群（monophyly），但光萼苔目（Porellales）、羽苔目（Ptilidiales）以及被蒴苔亚纲（Pelliidae）除外。赫氏苔属（*Herzogianthus*，隶属于羽苔目）被强烈支持为广义叶苔目（Jungermanniales sensu lato）的姊妹群，而非与羽苔属（*Ptilidium*，同为羽苔目）构成单系类群。鉴于其独特的形态特征，该属应被单独划出并提升为新目。

**研究结论：** 地钱类线粒体基因组的整体结构高度保守，即便分化时长超过4.7亿年的类群，其线粒体基因组仍保持共线性（co-linear）。本研究为未来地钱类群的进化研究提供了遗传资源，并凸显了线粒体基因组在经历4.7亿年分化的各演化支中，包括在科级分类系统构建中的应用价值。

搜集汇总

背景与挑战

背景概述

该数据集包含112种苔藓植物的线粒体基因组测序数据，覆盖105个物种、52个科和18个目，揭示了苔藓植物线粒体基因组结构的高度保守性，并为苔藓植物的系统发育和分类提供了重要依据。