Genome sequence of the cultivated cotton Gossypium arboreum

The draft genome of tropical fruit durian (Durio zibethinus)

“…These included the APS (ATP sulfurylase) family, involved in hydrogen sulfide biosynthesis; OASA1 (cysteine synthase), involved in maintaining sulfur levels; the THIK (3-ketoacyl-COA thiolase) family, involved in the production of lipid volatiles; XBAT32 (an E3 ubiquitin-protein ligase), a regulator of ethylene biosynthesis; and ETR2 (ethylene receptor) and AHK5 (histidine kinase), involved in ethylene signaling. Interestingly, some genes in these pathways were expanded in both durian and cotton, supporting findings of the importance of ethylene processing in cotton 21 . Taken together, these results suggest that a WGD event in durian's lineage led to the expansion and diversification of pathways related to durian volatiles, such as those involved in sulfur processing (including MGL), lipid volatiles, and ethylene.…”

“…2b). For the other plant species, phylogenetic placement and estimated speciation dates were mostly in broad consensus with other studies 20,21 .…”

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…6a and 7). However, this colinearity was not obvious with either the A-progenitor genome (G. arboreum) 2 or another version of the D-progenitor genome (G. raimondii) 3 because of numerous mis-assemblies. For example, many scaffolds from several different pseudochromosomes were present in one pseudomolecule ( Supplementary Figs.…”

“…Asymmetric evolution of the A and D subgenomes By comparing the synonymous substitution values (Ks) of 21,618 orthologous gene sets between the sequenced progenitor genomes 2,4 and the two subgenomes, the divergence time between the A-and D-progenitor genomes was estimated to be 6.0-6.3 MYA (Ks peaks at 0.031 and 0.033, respectively), and the allotetraploid was formed approximately 1-1.5 MYA (Ks peaks at 0.005 and 0.008, respectively) (Fig. 2b).…”

“…We generated a genome sequence containing two-to about fourfold longer sequence scaffolds (N50 = 1,600 kb) than that produced for other allopolyploid species Brassica napus (N50 = 764 kb) 9 , Nicotiana tabacum sequencing of allotetraploid cotton (Gossypium hirsutum l. acc. tM-1) provides a resource for fiber improvement A r t i c l e s (N50 = 345~386 kb) 11 and wheat (contig N50 = 515~4,297 bp) 6 , as well as the extant diploid A-genome progenitor of G. arboreum (N50 = 666 kb) 2 (N50, the size above which 50% of the total length of the sequence assembly can be found). Compared with canola and wheat, which emerged 4,000-8,000 years ago, allotetraploid cotton is much older (1-2 MYA), and its subgenomes have undergone asymmetric evolution, including biased subgenomic arrangements and transposable element amplification, selective gene loss, unequal distribution of disrupted genes, and expression bias of homoeologous genes related to fiber development and wider adaptation, respectively.…”