Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation

Abstract

Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole‐genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous–Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower‐like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.

Plastome Diversity and Phylogenomic Relationships in Asteraceae

“…While ML and BI yielded Calenduleae as an early diverging group of the remaining tribes, the pseudocoalescence analysis (ASTRAL) resulted in a high support for a different topology, with Senecioneae as the sister tribe to a clade of the four remaining Asterodae tribes. The same position of Senecioneae -despite not showing full statistical support -was obtained in the reconstruction of [67], also indicating that supertribe Senecionodae would not be monophyletic. Despite the limited sampling, our work provided full resolution and congruence among phylogenetic analyses for those basal nodes in subfamily Asteroideae, supporting the reconstructions obtained by Mandel et al (2019) using the ASTRAL approach and by [67] using transcriptomic data; i.e.…”

“…The same position of Senecioneae -despite not showing full statistical support -was obtained in the reconstruction of [67], also indicating that supertribe Senecionodae would not be monophyletic. Despite the limited sampling, our work provided full resolution and congruence among phylogenetic analyses for those basal nodes in subfamily Asteroideae, supporting the reconstructions obtained by Mandel et al (2019) using the ASTRAL approach and by [67] using transcriptomic data; i.e. Senecioneae as sister tribe to the clade constituted by Anthemideae, Astereae, Gnaphalieae and Calenduleae (i.e., supertribe Asterodae).…”

“…in an early-diverging position within the Heliantheae alliance (Figure 1). In contrast, in the phylogenomic reconstructions based on nuclear data by [17] or [67], Coreopsidae is placed in a much derived position as sister tribe of Heliantheae s.s. There are other incongruences between plastid and nuclear genomes regarding the position of some tribes in the Heliantheae alliance.…”

“…Including data of 36 species from 19 tribes and 5 subfamilies of Asteraceae, this study represents the most comprehensive phylogenomic reconstruction using whole plastome data obtained to date in this family (114 loci, 70,000 nt). Previous phylogenetic works had also approached the evolution of this huge and complex family, among the most relevant: (1) a meta-tree analysis combining results at lower taxonomic levels from several research works, based in 10 plastid DNA and one nuclear DNA marker (ITS) [1] and representing all tribes and subfamilies; (2) a phylogenetic inference based on 12 plastid markers representing 13 subfamilies and 40 tribes (length 17,319 nt) [16], (3) an exhaustive phylogenomic study based on target sequence capture of 763 nuclear loci representing 13 subfamilies and 45 tribes (269,585 nt) [17] and (4) a phylotranscriptomic analysis with data from 243 species (13 subfamilies and 41 tribes) within the family [67].…”

Chromosome Numbers in Verbesina (Asteraceae, Heliantheae, Verbesininae)

“…This result was used by Panero (2007) to remove Podachaenium, Squamopappus, and Verbesina from subtribe Ecliptinae (sensu Robinson, 1981a) and amend the concept of subtribe Verbesininae to include only these three genera and Tetrachyron, the latter of which was previously classified in subtribe Neurolaeninae. Molecular studies using transcriptomic data of the nuclear DNA indicate that Verbesina is sister to the Engelmanniinae but this relationship is not strongly supported (Zhang et al, 2021). All chromosome numbers for Verbesina to date show that the genus has a base number of x ¼ 17 or 18 with some tetraploid species (Robinson et al, 1981b;Jansen et al, 1984;Carr et al, 1999) and two records for taxa with higher ploidy levels (Jansen et al, 1984;Strother, 1976).…”