Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Abstract

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Angiosperm‐wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

“…Recently, low-copy nuclear genes have increasingly been used to resolve angiosperm evolutionary relationships at the family (Huang et al, 2016a(Huang et al, , 2016b(Huang et al, , 2022Xiang et al, 2017;Zhang et al, 2023) and order levels (Yang et al, 2015), or even among larger lineages (Zhang et al, 2012(Zhang et al, , 2020Wickett et al, 2014;Zeng et al, 2014Zeng et al, , 2017Zhao et al, 2016;Jin et al, 2017;Li et al, 2017;Leebens-Mack et al, 2019), as reviewed in Guo et al (2022) and Zhang and Ma (2024). Although the 1KP project (Leebens- Mack et al, 2019) sampled transcriptomes from 57 angiosperm orders and 251 families, some orders (e.g., Metteniusales, Picramniales, and Commelinales) were not included.…”