Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).
Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).
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DOI：
10.3389/fpls.2022.870949
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发表时间：
2022
影响因子：
5.6
通讯作者：
中科院分区：
文献类型：
--
作者：
荨麻疹属（Urticeae s.l）是荨麻疹科的一个分支，以其带刺的毛状体而闻名，由10多个属和大约220种组成。由于以前的研究中分子和分类采样有限，这个部落内部的关系仍然知之甚少，叶绿体基因组（CP基因组/质体）的进化仍然很大程度上没有解决。为了解决这些问题，我们使用基因组略读数据- cp基因组和核糖体DNA (18S-ITS1-5.8S-ITS2-26S)；106个加入，这是第一次尝试解决这种不协调的关系，并探索整个群体的叶绿体结构进化。此外，我们还在291份文献中构建了trnL-F间隔序列和ITS序列丰富的双位点数据集，以补充我们的基因组略读数据集。研究发现，荨麻质体具有被子植物的四分体结构，大小在145 ~ 161 kb之间，编码110 ~ 112个独特基因。所研究的质体也经历了一些结构变化，包括倒置重复序列（IR）扩张和收缩、trnN-GUU基因的倒置、rps19基因和rpl2内含子的缺失以及多种重复类型的增殖；还鉴定出11个高变区。我们的系统基因组分析在很大程度上解决了跨部落荨科的主要关系，支持部落及其大部分属的单系性，除了Laportea， Urera和Urtica，这些属被恢复为多系性，具有强有力的支持。我们的分析还强有力地支持了几个先前有争议的分支：(1)Girardinia是dendrocnide - discnide - laportea - nanocnide - zhengjia - urtica - hesperocnide的姐妹分支；(2)Poikilospermum是最近转录的Urera sensu stricto的姐妹分支。对分类群丰富的双位点数据集的分析显示支持度较低，但与CP基因组和核糖体DNA数据集的结果基本一致。总的来说，我们的研究突出了基因组略读数据在改善系统发育分辨率方面的力量，并为荨麻疹的系统发育关系和叶绿体结构进化提供了新的见解。
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.
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影响因子：
3.7
作者：
Gu C;Tembrock LR;Johnson NG;Simmons MP;Wu Z
通讯作者：
Wu Z
影响因子：
3
作者：
Bodros, Edwin;Baley, Christophe
通讯作者：
Baley, Christophe
影响因子：
4.1
作者：
Grosse-Veldmann, Bernadette;Nuerk, Nicolai M.;Weigend, Maximilian
通讯作者：
Weigend, Maximilian
影响因子：
4.6
作者：
Dong W;Xu C;Li C;Sun J;Zuo Y;Shi S;Cheng T;Guo J;Zhou S
通讯作者：
Zhou S
影响因子：
4.6
作者：
Dugas DV;Hernandez D;Koenen EJ;Schwarz E;Straub S;Hughes CE;Jansen RK;Nageswara-Rao M;Staats M;Trujillo JT;Hajrah NH;Alharbi NS;Al-Malki AL;Sabir JS;Bailey CD
通讯作者：
Bailey CD