Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications

Abstract

<jats:title>Abstract</jats:title> <jats:p>Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other datasets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the K-Pg boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. WGD analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four supra-familial and seven familial/sub-familial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.</jats:p>

Phylogenomics of the hyperdiverse daisy tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae

“…Five experienced additional WGDs during the Miocene along the branches of at least three of the five tribes including the smaller Calenduleae (~20 MYA) and the large and diverse Senecioneae (~18 MYA) and Gnaphalieae (~10 MYA; Huang et al, 2016;Zhang et al, 2020).…”

“…However, the topological incongruence between these plastid and nuclear trees calls into question the intertribal relationships among the five tribes, which may be explained, in part, by ancient hybridization, whole‐genome duplication (WGD), incomplete lineage sorting (ILS), rapid radiation, or some combination of these processes. Asteraceae is notorious for WGD (Barker et al, 2008, 2016; Huang et al, 2016; Zhang et al, 2020) and extensive polyploidy (Semple & Watanabe, 2009). In addition, reticulation due to hybridization has been inferred for each of the Fab Five tribes (e.g., Barker et al, 2009; Pelser et al, 2010; Galbany‐Casals et al, 2012; Wang et al, 2013; Vargas et al, 2017; Liew et al, 2018; Allen et al, 2019), increasing the likelihood that conflict in the data is to be expected.…”

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

“…Recent developments in genomics and museomics present new opportunities to tackle such obstacles, though. Several Oleaceae nuclear and cytoplasmic genomes, as well as transcriptomes have been released [31,[38][39][40][41][42][43]. Also herbarium samples, previously deemed unusable, are now accessible allowing for a more comprehensive sampling, and the inclusion of rare, or recently extinct species [31,[44][45][46].…”

Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

“…To estimate the origin and divergence of CLC genes, an maximum likelihood (ML) tree of these genes was reconstructed using iQ-TREE and used to map on a species tree of land-plants, which is a part of the tree of life as inferred in the OneKP project [40], by using the methods in Zhang et al [59]. All of the puative CLC proteins were aligned using MUSCLE v3.8.31 [60] with the 'auto' setting.…”

“…The conserved blocks were retained by Gblocks v0.91b [62], and then, phylogenetic analysis was preformed using iQ-TREE v2 [63] with the LG+R6 model, 1000 bootstraps, and the Shimodaira-Hasegawa-like aLRT (SH-aLRT) test. Putative functional homologs were identi ed from a gene clade that contained the query gene from Arabidopsis and was likely derived from an ancestral gene from land plants [59].…”