Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

Abstract

Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

“…Cotton contained more SWEET genes than species mentioned above, indicating that SWEET family genes undergo extensive expansion during cotton evolution. Although polyploidization was the main contributor in duplication, segment repeats also play an irreplaceable role in the expansion (Paterson et al 2012;Li et al 2015). Fifty-one segment repeat pairs in 4 cotton species were found in our study, suggesting that segment duplication further promote the expansion of the SWEET family.…”

“…With the release of genomes sequences of two diploid cotton (A2, D5) and two allotetraploid cotton (AD1, AD2) (Phillips et al 2017;Li et al 2014;Paterson et al 2012;Wang et al 2012;Li et al 2015;Zhang et al 2015;Yuan et al 2015;Liu et al 2015) facilitates the survey of SWEETs in cotton. In this study, we identified the SWEETs in four cotton species by genome-wide analysis.…”

The genome of Chenopodium quinoa

“…The annotation contains 44,776 gene models (Supplementary Table 2, Extended Data Fig. 2b), which is in line with sequenced tetraploid species 15 , and includes 33,365 genes with annotation edit distance (AED) 16,17 values ≤ 0.3 (Extended Data Fig. 2c).…”

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

“…It might, however, miss some uncommon elements, most of which were defined as unclassified elements in our data set. The Repbase and ab initio databases were used for retrotransposon identification in a second G. hirsutum paper 28 , which might include additional TEs or other elements that were not present either in MIPS or in our analysis. Our analysis shows that there were more TEs in the A subgenome (at least 843.5 Mb) than in the D subgenome (at least 433 Mb).…”