Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids
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DOI：
10.1111/1755-0998.13833
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发表时间：
2023-07
影响因子：
7.7
通讯作者：
Luxian Liu;Mengzhen Chen;R. Folk;M. Wang;Tao Zhao;F. Shang;D. Soltis;Pan Li
中科院分区：
文献类型：
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作者：
Luxian Liu;Mengzhen Chen;R. Folk;M. Wang;Tao Zhao;F. Shang;D. Soltis;Pan Li
被子植物中一些最棘手的深层次关系问题涉及蔷薇超目。蔷薇超目分支包含了所有被子植物物种的四分之一，其三个亚分支（葡萄目、虎耳草目和核心蔷薇类）中的18个目展现出显著的形态和生态多样性。为助力解析深层次关系，我们构建了多叶黄水枝（虎耳草科）高质量的染色体水平基因组组装，从而为虎耳草目提供更广泛的基因组代表性。对蔷薇超目的全基因组微共线性分析表明，相较于葡萄目，虎耳草目与核心蔷薇类共享更多的共线性簇，进一步支持虎耳草目与核心蔷薇类的亲缘关系更近。为解析蔷薇超目的目级系统发育，我们从代表蔷薇超目全部18个目的36个物种的基因组中筛选出122个单拷贝核基因。分析结果显示，葡萄目是其他所有蔷薇超目（虎耳草目 + 核心蔷薇类）的姊妹类群。我们的数据表明，与早期对核心蔷薇类的研究相比，其内部关系存在显著差异。豆类分支应仅限于固氮分支，而苦木目、卫矛目 - 金虎尾目（CM）分支、美洲苦木目、酢浆草目、无患子目、锦葵目和十字花目形成了一个 “扩展的” 锦葵类分支。卫矛目 - 酢浆草目 - 金虎尾目（COM）分支（按照APG IV系统）并非单系类群。燧体木目、牻牛儿苗目、桃金娘目和蒺藜目既不属于得到有力支持的锦葵类，也不属于豆类。关于蔷薇超目关系，核基因和质体基因的系统发育假设之间存在强烈的不一致；我们表明，这种情况最好用不完全谱系分选和古老的网状进化相结合来解释。
Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep‐level relationships, we constructed a high‐quality chromosome‐level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen‐fixing clade, while Picramniales, the Celastrales‐Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an “expanded” malvid clade. The Celastrales‐Oxalidales‐Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well‐supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.