Genome‐scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Abstract

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

Dense Sampling of Taxa and Genomes Untangles the Phylogenetic Backbone of a Non-model Plant Lineage Rife with Deep Hybridization and Allopolyploidy

“…Researchers from specific regions may have an advantage in collecting taxon samples from their areas, but conducting comprehensive species sampling, especially for cosmopolitan lineages, becomes a challenge for a single laboratory. As a result, previous phylogenomic studies have mainly focused on resolving the phylogenetic backbone of major lineages at the family or even higher level, such as Xiang et al (2017), Zhao et al (2021), Huang et al (2022), Hu et al (2023), and Zhang et al (2023), due to the ease of conducting comprehensive taxon sampling covering most major clades. However, incomplete taxon sampling has substantially hindered shallow-level phylogenomic studies of non-model plants, except for some ecologically and economically important lineages, such as apples (Liu et al 2022) and Rhododendron (Xia et al 2022).…”

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

“…(G) An analysis using 296 and 756 nuclear genes with coalescent method of ASTRAL (Yang et al, 2020a). (H) OneKP analysis using 410 nuclear genes, a study using 257–2,329 nuclear genes, and a study using 482 genes, with coalescent method of ASTRAL (Leebens‐Mack et al, 2019; Guo et al, 2021; Hu et al, 2023). Support values are not available for trees (A) and (E) ; the RAxML bootstrap support values (BS) are indicated on branches for analyses (B–D , F) ; the ASTRAL multi‐locus bootstrap support values (BS) in the analysis using 756 genes are indicated for topology (G) ; maximal supports in B–D and F–H are indicated by red stars.…”

“…In another analysis using 756 nuclear genes, monocots and magnoliids again occupied the first and second divergent branches, respectively, but Chloranthales was placed as sister of Ceratophyllales plus eudicots (Yang et al, 2020a) (Figure 1G). Moreover, in the largest green plant phylogenomic analysis with ~1,300 transcriptomes (Leebens‐Mack et al, 2019) (hereafter referred to as OneKP) and another study using 482 nuclear genes (Hu et al, 2023), the monocots are the earliest diverged lineage among the five, while magnoliids are sister to Chloranthales and Ceratophyllales are sister to eudicots (Figure 1H). Recent analyses including sequenced genomes from Ceratophyllales, Chloranthales, and magnoliids have provided further support for the topology of the OneKP analysis (Chaw et al, 2019; Yang et al, 2020c; Guo et al, 2021) (Figure 1H).…”

“…The order names are indicated to the right of the family names; the families that have not been included in any nuclear phylogenomic analysis are given near the names of orders with asterisk markers (same for Figures 7–9). Relationships among orders of ANA grade and five mesangiospermae clades follow three analyses using 410–2,329 nuclear genes (Leebens‐Mack et al, 2019; Guo et al, 2021; Hu et al, 2023) (see Figure 1). Family relationships of Austrobaileyales and magnoliids, Nymphaeales, and monocots follow the results of OneKP analysis (Leebens‐Mack et al, 2019; Zhang et al, 2020b; Timilsena et al, 2022), respectively.…”

Single-Copy Orthologs (SCOs) improve species discrimination: A case study in subgusJensoa(Cymbidium)

“…SCOs have successfully improved and homogenized species delimitation and discrimination in Metazoa (Dietz et al, 2021;Joshi et al, 2022). SCOs have been used as molecular markers in plant phylogenetics for several year (Hu et al, 2023;Huang et al, 2022;Johnson et al, 2018;Liu et al, 2022;G. Zhang et al, 2023;Zhang et al, 2012), but no report on species identification yet.…”