Table_3_Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).docx

Urticeae s.l., 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 trnL-F 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 trnN-GUU gene, losses of the rps19 gene, and the rpl2 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 Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. 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（广义，Urticeae s.l.）是荨麻科（Urticaceae）中以螫毛（stinging trichomes）为标志性特征的类群，包含超过10个属和约220个物种。受限于既往研究中分子与分类采样的不足，该族内部的系统发育关系至今仍未得到充分解析，叶绿体基因组（chloroplast genome，CP基因组/质体基因组）的演化机制也尚未得到充分研究。为解决上述问题，本研究首次采用基因组浅层测序（genome skimming）数据——涵盖叶绿体基因组与核糖体DNA（nuclear ribosomal DNA，18S-ITS1-5.8S-ITS2-26S）的106份采集样品数据——尝试解析该类群中难以解析的系统发育关系，并探究其叶绿体结构演化特征。此外，本研究还组装了涵盖291份采集样品的两基因座分类丰富度数据集，包含trnL-F间隔区与内转录间隔区（ITS）序列，以补充基因组浅层测序数据集。研究结果显示，荨麻族质体基因组具有被子植物（angiosperms）典型的四分体结构，基因组大小介于145~161 kb之间，共编码110~112个独特基因。所分析的质体基因组还经历了多种结构变异，包括反向重复序列（inverted repeat，IR）的扩张与收缩、trnN-GUU基因的倒位、rps19基因与rpl2内含子的缺失，以及多种重复序列的增殖；同时本研究还鉴定出11个高变区。系统基因组学分析基本解析了荨麻族内部的主要系统发育关系，支持该族及其多数属的单系性，仅艾麻属（Laportea）、火麻树属（Urera）和荨麻属（Urtica）被鉴定为具有强支持度的多系群。本研究还以强支持度解析了此前存在争议的两个分支：（1）蝎子草属（Girardinia）为树火麻属（Dendrocnide）-盘托麻属（Discocnide）-艾麻属（Laportea）-微荨麻属（Nanocnide）-征镒麻属（Zhengyia）-荨麻属（Urtica）-异荨麻属（Hesperocnide）演化支的姐妹群；（2）球序麻属（Poikilospermum）为狭义火麻树属（Urera sensu stricto）的姐妹群。基于分类群覆盖度更高的两基因座数据集的分析支持度较低，但整体结果与叶绿体基因组及核糖体DNA数据集基本一致。综上，本研究证实了基因组浅层测序数据在提升系统发育解析度方面的应用价值，并为荨麻族的系统发育关系与叶绿体结构演化提供了全新的认知。