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

Liu X, Zhao B, Zheng HJ, Hu Y, Lu G, Yang CQ, Chen JD, Chen JJ, Chen DY, Zhang L, Zhou Y, Wang LJ, Guo WZ, Bai YL, Ruan JX, Shangguan XX, Mao YB, Shan CM, Jiang JP, Zhu YQ, Jin L, Kang H, Chen ST, He XL, Wang R, Wang YZ, Chen J, Wang LJ, Yu ST, Wang BY, Wei J, Song SC, Lu XY, Gao ZC, Gu WY, Deng X, Ma D, Wang S, Liang WH, Fang L, Cai CP, Zhu XF, Zhou BL, Jeffrey Chen Z, Xu SH, Zhang YG, Wang SY, Zhang TZ, Zhao GP, Chen XY - Sci Rep (2015)

Bottom Line: Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles.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 G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

View Article: PubMed Central - PubMed

Affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.

ABSTRACT
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 At 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.

No MeSH data available.


G. barbadense genome atlas and chromosome-level translocations.(a) Genome atlas. The outermost circle represents the numbered chromosomes of At and Dt, and chromosome sizes are marked by a scale plate. The three tracks moving inside successively represent gene, peudogene and repeat densities (calculated with 1 Mb windows) across the chromosomes. The core ribbon-link shows collinearity between At and Dt. (b,c) chromosomal translocations. The translocations among chromosome 2 and chromosome 3 of either At or Dt are indicated with blue lines (b) and those among chromosome 4 and chromosome 5 with blue and purple lines (c). The vertical colored lines from left to right represent chromosomes. The loci of PRE1 implicated in fiber cell elongation are specifically marked with red in the chromosomes A05 and D04. Digits (01 to 13) after A, D or Gr indicate the chromosome of the At/Dt subgenome of G. barbadense or of G. raimondii, respectively.
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f2: G. barbadense genome atlas and chromosome-level translocations.(a) Genome atlas. The outermost circle represents the numbered chromosomes of At and Dt, and chromosome sizes are marked by a scale plate. The three tracks moving inside successively represent gene, peudogene and repeat densities (calculated with 1 Mb windows) across the chromosomes. The core ribbon-link shows collinearity between At and Dt. (b,c) chromosomal translocations. The translocations among chromosome 2 and chromosome 3 of either At or Dt are indicated with blue lines (b) and those among chromosome 4 and chromosome 5 with blue and purple lines (c). The vertical colored lines from left to right represent chromosomes. The loci of PRE1 implicated in fiber cell elongation are specifically marked with red in the chromosomes A05 and D04. Digits (01 to 13) after A, D or Gr indicate the chromosome of the At/Dt subgenome of G. barbadense or of G. raimondii, respectively.

Mentions: The combination of these methods resulted in a draft genome for G. barbadense with an overall contig N50 of 72 kilobases (kb) and scaffold N50 of 503 kb covering 1.395 Gigabases (Gb) of the A subgenome (At) and 0.776 Gb of the D subgenome (Dt) (Table 1 and Fig. 2). In total, ~88% of the 2.470 Gb genome was based on k-mer estimation (Supplementary Fig. 3). The genome contains at least 63.2% repeated sequences (Supplementary Table 3), half of which are transposable elements (TEs) that primarily consist of long-terminal-repeat retrotransposons (LTR retrons) (Supplementary Fig. 4).


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

Liu X, Zhao B, Zheng HJ, Hu Y, Lu G, Yang CQ, Chen JD, Chen JJ, Chen DY, Zhang L, Zhou Y, Wang LJ, Guo WZ, Bai YL, Ruan JX, Shangguan XX, Mao YB, Shan CM, Jiang JP, Zhu YQ, Jin L, Kang H, Chen ST, He XL, Wang R, Wang YZ, Chen J, Wang LJ, Yu ST, Wang BY, Wei J, Song SC, Lu XY, Gao ZC, Gu WY, Deng X, Ma D, Wang S, Liang WH, Fang L, Cai CP, Zhu XF, Zhou BL, Jeffrey Chen Z, Xu SH, Zhang YG, Wang SY, Zhang TZ, Zhao GP, Chen XY - Sci Rep (2015)

G. barbadense genome atlas and chromosome-level translocations.(a) Genome atlas. The outermost circle represents the numbered chromosomes of At and Dt, and chromosome sizes are marked by a scale plate. The three tracks moving inside successively represent gene, peudogene and repeat densities (calculated with 1 Mb windows) across the chromosomes. The core ribbon-link shows collinearity between At and Dt. (b,c) chromosomal translocations. The translocations among chromosome 2 and chromosome 3 of either At or Dt are indicated with blue lines (b) and those among chromosome 4 and chromosome 5 with blue and purple lines (c). The vertical colored lines from left to right represent chromosomes. The loci of PRE1 implicated in fiber cell elongation are specifically marked with red in the chromosomes A05 and D04. Digits (01 to 13) after A, D or Gr indicate the chromosome of the At/Dt subgenome of G. barbadense or of G. raimondii, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588572&req=5

f2: G. barbadense genome atlas and chromosome-level translocations.(a) Genome atlas. The outermost circle represents the numbered chromosomes of At and Dt, and chromosome sizes are marked by a scale plate. The three tracks moving inside successively represent gene, peudogene and repeat densities (calculated with 1 Mb windows) across the chromosomes. The core ribbon-link shows collinearity between At and Dt. (b,c) chromosomal translocations. The translocations among chromosome 2 and chromosome 3 of either At or Dt are indicated with blue lines (b) and those among chromosome 4 and chromosome 5 with blue and purple lines (c). The vertical colored lines from left to right represent chromosomes. The loci of PRE1 implicated in fiber cell elongation are specifically marked with red in the chromosomes A05 and D04. Digits (01 to 13) after A, D or Gr indicate the chromosome of the At/Dt subgenome of G. barbadense or of G. raimondii, respectively.
Mentions: The combination of these methods resulted in a draft genome for G. barbadense with an overall contig N50 of 72 kilobases (kb) and scaffold N50 of 503 kb covering 1.395 Gigabases (Gb) of the A subgenome (At) and 0.776 Gb of the D subgenome (Dt) (Table 1 and Fig. 2). In total, ~88% of the 2.470 Gb genome was based on k-mer estimation (Supplementary Fig. 3). The genome contains at least 63.2% repeated sequences (Supplementary Table 3), half of which are transposable elements (TEs) that primarily consist of long-terminal-repeat retrotransposons (LTR retrons) (Supplementary Fig. 4).

Bottom Line: Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles.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 G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

View Article: PubMed Central - PubMed

Affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.

ABSTRACT
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 At 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.

No MeSH data available.