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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.


Evolutionary analysis of the G. barbadense genome.(a) Ks distribution of orthologs in cotton genomes. Data are grouped into 0.001 Ks units. (b) Ks distribution of paralogs in the G. barbadense genome. Data are grouped into 0.01 Ks units, and the peak region corresponds to 50–70 million years. (c) The distribution curve of the insertion times in the LTR retrons in the G. barbadense genome. The LTR retrons bursts are separated by dashed lines. (d) Ks distribution of pseudogenes with their closest functional paralogous genes. Data are grouped into 0.001-Ks units. The genomes of allotetraploid cottons are labeled using At/Dt, and the genomes of G. arboreum (A2) and G. raimondii (D5) are labeled using Ga and Gr.
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f3: Evolutionary analysis of the G. barbadense genome.(a) Ks distribution of orthologs in cotton genomes. Data are grouped into 0.001 Ks units. (b) Ks distribution of paralogs in the G. barbadense genome. Data are grouped into 0.01 Ks units, and the peak region corresponds to 50–70 million years. (c) The distribution curve of the insertion times in the LTR retrons in the G. barbadense genome. The LTR retrons bursts are separated by dashed lines. (d) Ks distribution of pseudogenes with their closest functional paralogous genes. Data are grouped into 0.001-Ks units. The genomes of allotetraploid cottons are labeled using At/Dt, and the genomes of G. arboreum (A2) and G. raimondii (D5) are labeled using Ga and Gr.

Mentions: A total of 21,639 pairs of orthologs were identified between At and Dt. We compared the Ks values of orthologous gene pairs among G. barbadense (Gb), G. hirsutum (Gh) and G. raimondii (Gr) at the whole-genome level (Fig. 3a and Supplementary Table 5). A peak of 0.011 in both GbDt:GrD5 and GhDt:GrD5 indicates that the Dt subgenome in of both allotetraploids originated from a G. raimondii-like progenitor27. The peak values for GbAt:GaA2 and GhAt:GaA2 are lower but again similar, presumably due to a shorter time since divergence compared to that between D-genome species. In addition, unlike G. raimondii, which is a wild species, G. arboreum has long been cultivated in African and Asian countries. Another pair of similar Ks peaks (0.005) of GbAt:GhAt and GbDt:GhDt further supports the common origin of the two allotetraploid cottons and suggests their later divergence approximately 1 Mya (Fig. 3a). Based on the larger Ks value (0.04) for At:Dt, we estimated the divergence time between the Gossypium A- and D-genome species to be approximately 8 Mya, consistent with previous estimates that were based on a few single-copy genes1327. The Ks values of paralogs in the two subgenomes of G. barbadense both peak at 0.4–0.5, which indicate ancient WGD event(s) that occurred 50–70 Mya (Fig. 3b), which were responsible for the repeated genome expansion in Gossypium after divergence from the Theobroma cacao lineage more than 60 Mya10.


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)

Evolutionary analysis of the G. barbadense genome.(a) Ks distribution of orthologs in cotton genomes. Data are grouped into 0.001 Ks units. (b) Ks distribution of paralogs in the G. barbadense genome. Data are grouped into 0.01 Ks units, and the peak region corresponds to 50–70 million years. (c) The distribution curve of the insertion times in the LTR retrons in the G. barbadense genome. The LTR retrons bursts are separated by dashed lines. (d) Ks distribution of pseudogenes with their closest functional paralogous genes. Data are grouped into 0.001-Ks units. The genomes of allotetraploid cottons are labeled using At/Dt, and the genomes of G. arboreum (A2) and G. raimondii (D5) are labeled using Ga and Gr.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Evolutionary analysis of the G. barbadense genome.(a) Ks distribution of orthologs in cotton genomes. Data are grouped into 0.001 Ks units. (b) Ks distribution of paralogs in the G. barbadense genome. Data are grouped into 0.01 Ks units, and the peak region corresponds to 50–70 million years. (c) The distribution curve of the insertion times in the LTR retrons in the G. barbadense genome. The LTR retrons bursts are separated by dashed lines. (d) Ks distribution of pseudogenes with their closest functional paralogous genes. Data are grouped into 0.001-Ks units. The genomes of allotetraploid cottons are labeled using At/Dt, and the genomes of G. arboreum (A2) and G. raimondii (D5) are labeled using Ga and Gr.
Mentions: A total of 21,639 pairs of orthologs were identified between At and Dt. We compared the Ks values of orthologous gene pairs among G. barbadense (Gb), G. hirsutum (Gh) and G. raimondii (Gr) at the whole-genome level (Fig. 3a and Supplementary Table 5). A peak of 0.011 in both GbDt:GrD5 and GhDt:GrD5 indicates that the Dt subgenome in of both allotetraploids originated from a G. raimondii-like progenitor27. The peak values for GbAt:GaA2 and GhAt:GaA2 are lower but again similar, presumably due to a shorter time since divergence compared to that between D-genome species. In addition, unlike G. raimondii, which is a wild species, G. arboreum has long been cultivated in African and Asian countries. Another pair of similar Ks peaks (0.005) of GbAt:GhAt and GbDt:GhDt further supports the common origin of the two allotetraploid cottons and suggests their later divergence approximately 1 Mya (Fig. 3a). Based on the larger Ks value (0.04) for At:Dt, we estimated the divergence time between the Gossypium A- and D-genome species to be approximately 8 Mya, consistent with previous estimates that were based on a few single-copy genes1327. The Ks values of paralogs in the two subgenomes of G. barbadense both peak at 0.4–0.5, which indicate ancient WGD event(s) that occurred 50–70 Mya (Fig. 3b), which were responsible for the repeated genome expansion in Gossypium after divergence from the Theobroma cacao lineage more than 60 Mya10.

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.