A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Abstract

Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

“…4) offers an alternative explanation for gene tree discordance, but discriminating between these alternatives is not straightforward. It is notable that other large plant clades, such as Pentapetalae (Zeng et al, 2017), Asteraceae (Barker et al, 2016;Huang et al, 2016), Brassicaceae (Couvreur et al, 2010;Huang et al, 2015) and Malvaceae (Conover et al, 2019), also show lack of resolution in clades subtended by WGDs similar to that revealed here for the legume family and subfamilies Papilionoideae and Detarioideae. This suggests that the association of polyploidy with rapid divergence, lack of phylogenetic signal and gene tree conflict, is a common feature in the evolution of angiosperms and origination of major plant clades.…”

“…Furthermore, the prevalence of WGDs across the plant tree of life (e.g. Wendel, 2015;Soltis et al, 2016;Yang et al, 2018;Cai et al, 2019;Conover et al, 2019;One Thousand Plant Transcriptomes Initiative, 2019), potentially in association with rapid environmental change more generally (Cai et al, 2019), as well as in relation to the diversification of several large clades (e.g. Jiao et al, 2012;Barker et al, 2016; this study), further emphasizes just how prevalent and important polyploidization has been for plant evolution.…”

Phylogeny and multiple independent whole‐genome duplication events in the Brassicales

“…Recently, an abundance of papers have highlighted the difficulties and complexities of determining WGD events across the tree of life (Conover et al, 2018; Tiley et al, 2018; Li and Barker, 2019 [Preprint]; Li et al, 2019; Nakatani and McLysaght, 2019; Zwaenepoel and van de Peer, 2019 [Preprint]; Zwaenepoel et al, 2019). We add another dimension to this conversation by demonstrating that the different taxonomic levels from which we sample, such as the order or family, make a difference in support of previously identified WGDs (i.e., the Brassiceae triplication).…”

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

“…Through detecting gene collinearity, five-times of duplicated regions in cotton to those in cacao and grape suggested a paleo-decaploidy, or penta-plication of the ancestral genome, implying a rather complex nature of the cotton genome, as compared to many other eudicot plants ( Wang et al., 2016 ). The obscurity whether cotton and the other Malvaceae plants share the event were discussed by comparing genomic information from durian and Bombax ( Teh et al., 2017 ; Conover et al., 2019 ). Exploration of the collinear genes, including inter-genomic ratio of retained homologs, homologous gene tree topology, and gene retention levels suggested that the above-mentioned decaploidy was not shared with durian, which was affected by an independent hexaploidization ( Wang J. et al., 2019 ).…”