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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.


Expansion and diversification of PRE genes in Gossypium.(a) Phylogenetic analysis of PRE family genes in Amborella trichopoda, Arabidopsis thaliana, G. raimondii and G. barbadense. Subfamilies are overlaid with different colors, and the curved dotted lines indicate homoeologous gene pairs expressed in fiber. (b) GbPRE1 (GOBAR_AA33780, GOBAR_DD03693) is a fiber-specific gene with strong At bias expression. The expression levels (RPKM) in ovules (0 DPA) and fiber cells (5, 10, 20, and 30 DPA) are shown. Detailed expression data are provided in Supplementary Table 10. (c) Hierarchical clustering analysis of expression of PRE genes in G. barbadense. LB, leaf bud; YL, young leaf; ML, mature leaf; O, ovule; F, fiber; DPA, days post-anthesis.
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f4: Expansion and diversification of PRE genes in Gossypium.(a) Phylogenetic analysis of PRE family genes in Amborella trichopoda, Arabidopsis thaliana, G. raimondii and G. barbadense. Subfamilies are overlaid with different colors, and the curved dotted lines indicate homoeologous gene pairs expressed in fiber. (b) GbPRE1 (GOBAR_AA33780, GOBAR_DD03693) is a fiber-specific gene with strong At bias expression. The expression levels (RPKM) in ovules (0 DPA) and fiber cells (5, 10, 20, and 30 DPA) are shown. Detailed expression data are provided in Supplementary Table 10. (c) Hierarchical clustering analysis of expression of PRE genes in G. barbadense. LB, leaf bud; YL, young leaf; ML, mature leaf; O, ovule; F, fiber; DPA, days post-anthesis.

Mentions: Consistent with a previous report34, equal numbers of genes in the At and Dt subgenomes demonstrated biased expression patterns (Supplementary Tables 15 and 16). Transcription factors play an important role in controlling agronomic novelty, and the MYB and homeodomain-containing factors have been shown to be key regulators of cotton fiber traits development10353637. We then analyzed transcription factor genes expressed in G. barbadense fiber in detail (Supplementary Table 17 and Supplementary Fig. 11). Paclobutrazol Resistance (PRE) genes encode a group of transcription regulators known in other plants to promote cell elongation383940. We identified 13 PRE family genes in G. raimondii; their 26 orthologous genes were recovered in G. barbadense. Analyzing the PRE-containing synteny blocks in plants revealed that cacao41 has five PRE genes, each of which has at least two orthologs in the Gossypium diploid genomes or the allotetraploid subgenomes (Fig. 4a and Supplementary Fig. 12). This expansion of PRE genes in cotton may have occurred during a complex 5–6-fold polyploidy process1011, which was followed by differential gene loss but the retention of the ancient orthologs. Interestingly, two PRE genes are located in the two At translocation regions (chrA2/chrA3 and chrA4/chrA5) (Fig. 2c and Supplementary Fig. 12). In cotton, PRE genes are preferentially expressed in young tissues (Fig. 4b,c), which is consistent with their role in controlling cell size. Moreover, the expression of At and DtPRE homoeologous genes was biased in G. barbadense (Supplementary Tables 11–12). In particular, the expression level of At-subgenome PRE1 was high and fiber specific, whereas the expression the Dt homoeolog was nearly undetectable (Fig. 4b). The At-specific expression of a cell growth regulator provides a clue to support the origin or early evolution of spinnable fiber in the A-genome species1011. The expansion and subsequent selection1134 of PRE genes in Gossypium may have increased their regulatory activity and recruited specific member(s) for the rapid and extensive elongation of cotton fiber (Figs 1 and 4c).


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)

Expansion and diversification of PRE genes in Gossypium.(a) Phylogenetic analysis of PRE family genes in Amborella trichopoda, Arabidopsis thaliana, G. raimondii and G. barbadense. Subfamilies are overlaid with different colors, and the curved dotted lines indicate homoeologous gene pairs expressed in fiber. (b) GbPRE1 (GOBAR_AA33780, GOBAR_DD03693) is a fiber-specific gene with strong At bias expression. The expression levels (RPKM) in ovules (0 DPA) and fiber cells (5, 10, 20, and 30 DPA) are shown. Detailed expression data are provided in Supplementary Table 10. (c) Hierarchical clustering analysis of expression of PRE genes in G. barbadense. LB, leaf bud; YL, young leaf; ML, mature leaf; O, ovule; F, fiber; DPA, days post-anthesis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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f4: Expansion and diversification of PRE genes in Gossypium.(a) Phylogenetic analysis of PRE family genes in Amborella trichopoda, Arabidopsis thaliana, G. raimondii and G. barbadense. Subfamilies are overlaid with different colors, and the curved dotted lines indicate homoeologous gene pairs expressed in fiber. (b) GbPRE1 (GOBAR_AA33780, GOBAR_DD03693) is a fiber-specific gene with strong At bias expression. The expression levels (RPKM) in ovules (0 DPA) and fiber cells (5, 10, 20, and 30 DPA) are shown. Detailed expression data are provided in Supplementary Table 10. (c) Hierarchical clustering analysis of expression of PRE genes in G. barbadense. LB, leaf bud; YL, young leaf; ML, mature leaf; O, ovule; F, fiber; DPA, days post-anthesis.
Mentions: Consistent with a previous report34, equal numbers of genes in the At and Dt subgenomes demonstrated biased expression patterns (Supplementary Tables 15 and 16). Transcription factors play an important role in controlling agronomic novelty, and the MYB and homeodomain-containing factors have been shown to be key regulators of cotton fiber traits development10353637. We then analyzed transcription factor genes expressed in G. barbadense fiber in detail (Supplementary Table 17 and Supplementary Fig. 11). Paclobutrazol Resistance (PRE) genes encode a group of transcription regulators known in other plants to promote cell elongation383940. We identified 13 PRE family genes in G. raimondii; their 26 orthologous genes were recovered in G. barbadense. Analyzing the PRE-containing synteny blocks in plants revealed that cacao41 has five PRE genes, each of which has at least two orthologs in the Gossypium diploid genomes or the allotetraploid subgenomes (Fig. 4a and Supplementary Fig. 12). This expansion of PRE genes in cotton may have occurred during a complex 5–6-fold polyploidy process1011, which was followed by differential gene loss but the retention of the ancient orthologs. Interestingly, two PRE genes are located in the two At translocation regions (chrA2/chrA3 and chrA4/chrA5) (Fig. 2c and Supplementary Fig. 12). In cotton, PRE genes are preferentially expressed in young tissues (Fig. 4b,c), which is consistent with their role in controlling cell size. Moreover, the expression of At and DtPRE homoeologous genes was biased in G. barbadense (Supplementary Tables 11–12). In particular, the expression level of At-subgenome PRE1 was high and fiber specific, whereas the expression the Dt homoeolog was nearly undetectable (Fig. 4b). The At-specific expression of a cell growth regulator provides a clue to support the origin or early evolution of spinnable fiber in the A-genome species1011. The expansion and subsequent selection1134 of PRE genes in Gossypium may have increased their regulatory activity and recruited specific member(s) for the rapid and extensive elongation of cotton fiber (Figs 1 and 4c).

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.