Ogoma Catherine A, Liu Jie, Stull Gregory W, Wambulwa Moses C, Oyebanji Oyetola, Milne Richard I, Monro Alexandre K, Zhao Ying, Li De-Zhu, Wu Zeng-Yuan
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
University of Chinese Academy of Sciences, Beijing, China.
Front Plant Sci. 2022 May 20;13:870949. doi: 10.3389/fpls.2022.870949. eCollection 2022.
Urticeae , a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the gene, losses of the gene, and the intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for , , and , which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) as a sister to the ------ clade and (2) as sister to the recently transcribed . Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.
荨麻族是荨麻科中以其刺毛而闻名的一个族，由10多个属和约220个物种组成。由于先前研究中分子和分类取样有限，该族内的关系仍知之甚少，叶绿体基因组（CP基因组/质体基因组）的进化在很大程度上仍未得到解决。为了解决这些问题，我们首次使用基因组浅层测序数据——CP基因组和核糖体DNA（18S - ITS1 - 5.8S - ITS2 - 26S）；106个样本——来尝试解决顽固的关系问题，并探索整个类群的叶绿体结构进化。此外，我们组装了一个包含291个样本的、丰富的两基因座数据集，该数据集包含间隔区和ITS序列，以补充我们的基因组浅层测序数据集。我们发现荨麻族质体基因组呈现出被子植物典型的四分体结构，大小从145到161 kb不等，编码一组110 - 112个独特基因。所研究的质体基因组也经历了几种结构变异，包括反向重复序列（IR）的扩增和收缩、基因的倒位、基因的缺失以及内含子，还有多种重复类型的增殖；还鉴定出了11个高变区。我们的系统发育基因组分析在很大程度上解决了荨麻族内的主要关系，支持了该族及其大多数属的单系性，但除外，这几个属被强烈支持为多系的。我们的分析还以强有力的支持解决了几个先前有争议的分支：（1）作为与——分支的姐妹分支以及（2）作为与最近转录的分支的姐妹分支。对丰富的两基因座数据集的分析显示支持度较低，但在很大程度上与CP基因组和核糖体DNA数据集的结果一致。总体而言，我们的研究突出了基因组浅层测序数据在改善系统发育分辨率方面的作用，并为荨麻族的系统发育关系和叶绿体结构进化提供了新的见解。
