Genome analysis ofHibiscus syriacusprovides insights of polyploidization and indeterminate flowering in woody plants

Abstract

Hibiscus syriacus (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the H. syriacus genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of H. syriacus, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including H. syriacus, Arabidopsis thaliana, Gossypium raimondii, Theobroma cacao and Amborella trichopoda. We inferred their evolutionary relationships based on divergence times among Malvaceae plant genes and found that gene families involved in flowering regulation and disease resistance were more highly divergent and expanded in H. syriacus than in its close relatives, G. raimondii (DD) and T. cacao. Clustered gene families and gene collinearity analysis revealed that two recent rounds of whole-genome duplication were followed by diploidization of the H. syriacus genome after speciation. Copy number variation and phylogenetic divergence indicates that WGDs and subsequent diploidization led to unequal duplication and deletion of flowering-related genes in H. syriacus and may affect its unique floral morphology.

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

“…The Ks approach identified a Ks peak in most species, corroborating prior analyses (Paterson et al ; Chen et al ; Kim et al ; Teh et al ; Gao et al ). While the modes of these distributions differ between species, the full distributions overlap markedly among species, and also overlap with speciation estimates.…”

“…We interpret the younger peak in Gossypium as part of the background gene duplication rate, most likely due to tandemly duplicated genes that retain high sequence similarity to one another, via gene conversion (Panchy et al ; Train et al ). The younger peak in Hibiscus, in contrast, is likely the result of a recent WGM unique to this lineage, as previous work suggests this was an independent event with respect to Gossypium (Kim et al ; Teh et al ). Furthermore, we established Hibiscus to have twice as many gene models as other taxa sampled (Table S1).…”

“…Allowing for differences in rates of molecular evolution across lineages, which can be considerable among Malvaceae subfamilies (Baum et al ), the pattern could be suggestive of a single shared WGM in all Malvadendrina subfamilies except Dombeyoideae (Kim et al ; Teh et al ). The peaks of these distributions closely coincide with Ks divergences associated with the divergence of Theobroma, Durio, Gossypium, and Bombax (see Methods), indicating that the WGM event(s) we detected occurred early in the group's radiation.…”

“…The release of a draft genome sequence of Hibiscus syriacus (Kim et al ) indicated two independent WGD events since its divergence from G. raimondii . We detected two broad peaks in the Ks plot for H. cannabinus , which has less than half as many chromosomes as H. syriacus (CCDB online: http://ccdb.tau.ac.il/), leading us to infer that at least the older Ks peak is a WGM shared with Gossypium .…”

Recent advances in understanding the roles of whole genome duplications in evolution

“…For example, the transcription of A and C genes became mutually exclusive 26 . Further evolutionary diversity in flower form occurred by mechanisms that include shifts in the spatial expression of ABC functions across flowers, and by further WGDs that elaborated and extended the ABC regulatory network 27 . For example, in stylised orchid flowers, subfunctionalisation of duplicated B genes underpins the development of three types of petals: three outer tepals, two inner tepals and a modified lip 28 .…”