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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.


Phylogenetic analysis of (+)-δ-cadinene synthase (CDN) family genes and their genome distribution.(a) The amino acid sequences of CDNs of G. arboreum (Cotton_A), G. raimondii (Gorai), G. hirsutum (Gh) and G. barbadense (GOBAR) and T. cacao (Thecc) were used to build the phylogenetic tree using a neighbor-joining algorithm via the MEGA software. The Arabidopsis thaliana sesquiterpene synthase gene At5g23960 was used as a phylogenetic outgroup. (b) Chromosomal locations of the CDN genes in four Gossypium species as indicated.
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f6: Phylogenetic analysis of (+)-δ-cadinene synthase (CDN) family genes and their genome distribution.(a) The amino acid sequences of CDNs of G. arboreum (Cotton_A), G. raimondii (Gorai), G. hirsutum (Gh) and G. barbadense (GOBAR) and T. cacao (Thecc) were used to build the phylogenetic tree using a neighbor-joining algorithm via the MEGA software. The Arabidopsis thaliana sesquiterpene synthase gene At5g23960 was used as a phylogenetic outgroup. (b) Chromosomal locations of the CDN genes in four Gossypium species as indicated.

Mentions: The cotton sesquiterpene synthase (+)-δ-cadinene synthase (CDN) catalyzes the first step of gossypol biosynthesis50. The G. barbadense genome harbors 19 CDN family genes (sharing >80% nucleotide identity), whereas G. raimondii, G. arboreum and G. hirsutum harbor 11, 14 and 13 of these genes, respectively (Fig. 6 and Supplementary Table 18). These genes evolved faster than cotton speciation; thus, the CDN family evolved approximately 60 Mya based on the phylogenetics of cotton plants (Fig. 1). The CDN subfamilies A and E were found closer to the ancient type and duplicated after the divergence of the cotton and cacao lineages (Fig. 6 and Supplementary Fig. 14). The variable CDN gene numbers in cotton species possibly refer to recent small-scale duplication events, e.g., CDN-A member duplication in the D genome ~1 Mya (Supplementary Table 18 and Supplementary Fig. 14). Thus, the CDN subfamilies in Gossypium represent an example of the rapid lineage-specific evolution of critical genes for specialized metabolites.


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)

Phylogenetic analysis of (+)-δ-cadinene synthase (CDN) family genes and their genome distribution.(a) The amino acid sequences of CDNs of G. arboreum (Cotton_A), G. raimondii (Gorai), G. hirsutum (Gh) and G. barbadense (GOBAR) and T. cacao (Thecc) were used to build the phylogenetic tree using a neighbor-joining algorithm via the MEGA software. The Arabidopsis thaliana sesquiterpene synthase gene At5g23960 was used as a phylogenetic outgroup. (b) Chromosomal locations of the CDN genes in four Gossypium species as indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Phylogenetic analysis of (+)-δ-cadinene synthase (CDN) family genes and their genome distribution.(a) The amino acid sequences of CDNs of G. arboreum (Cotton_A), G. raimondii (Gorai), G. hirsutum (Gh) and G. barbadense (GOBAR) and T. cacao (Thecc) were used to build the phylogenetic tree using a neighbor-joining algorithm via the MEGA software. The Arabidopsis thaliana sesquiterpene synthase gene At5g23960 was used as a phylogenetic outgroup. (b) Chromosomal locations of the CDN genes in four Gossypium species as indicated.
Mentions: The cotton sesquiterpene synthase (+)-δ-cadinene synthase (CDN) catalyzes the first step of gossypol biosynthesis50. The G. barbadense genome harbors 19 CDN family genes (sharing >80% nucleotide identity), whereas G. raimondii, G. arboreum and G. hirsutum harbor 11, 14 and 13 of these genes, respectively (Fig. 6 and Supplementary Table 18). These genes evolved faster than cotton speciation; thus, the CDN family evolved approximately 60 Mya based on the phylogenetics of cotton plants (Fig. 1). The CDN subfamilies A and E were found closer to the ancient type and duplicated after the divergence of the cotton and cacao lineages (Fig. 6 and Supplementary Fig. 14). The variable CDN gene numbers in cotton species possibly refer to recent small-scale duplication events, e.g., CDN-A member duplication in the D genome ~1 Mya (Supplementary Table 18 and Supplementary Fig. 14). Thus, the CDN subfamilies in Gossypium represent an example of the rapid lineage-specific evolution of critical genes for specialized metabolites.

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.