The draft genome of tropical fruit durian (Durio zibethinus)

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).…”

“…This hypothesis provides an explanation for why all Malvadendrina except Dombeya (Dombeyoideae) have a peak in Ks plots. Additionally, collinearity analysis shows that at least some duplicate chromosomal arms are shared between Durio and Gossypium (Teh et al ), which supports such a shared WGM. This hybridization model is also consistent with the BUCKy results, since it explains why (i) a plurality of genes support a Durio + Malvatheca clade, which is the expected pattern for Durio genes from the tetraploid Malvatheca parent, (ii) a significant subset of genes support a Durio + Dombeya clade, which is the expected pattern for Durio genes from the diploid dombeyoid parent, and (iii) there are many fewer genes showing a Dombeya + Malvatheca clade, which can only arise by ILS.…”

“…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.…”

“…Subsequent analyses (using various lines of evidence) have attempted to infer whether this event consisted of two successive whole genome duplication/triplication events, or a single deca‐ or dodecaploidization event (Wang et al ). In addition, studies have investigated if any other Malvaceae taxa show evidence of the same event(s), namely Durio zibethinus (Teh et al ) and Firmiana danxiaensis (Chen et al ). The draft genome of D. zibethinus (Teh et al ) suggested a shared WGM history with G. raimondii ; however, while the 28 chromosomes of D. zibethinus show remarkable (hexaploid, 3×) synteny with respect to the 10 chromosomes of T. cacao , this inference is insufficient to explain the decaploid (5×) or dodecaploid (6×) multiplication history of G. raimondii relative to Theobroma .…”