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Of the two cultivated species of allopolyploid cotton,  Gossypium barbadense  produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD) 2  and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11–20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator,  PRE1 , is strikingly A t  biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose.  G. barbadense  and  G. hirsutum  contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in  G. barbadense  compared with  G. hirsutum , conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The  G. barbadense  genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites