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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.


Related in: MedlinePlus

Cotton CesA genes and their expression in developing fiber cells of G. barbadense and G. hirsutum.(a) CesA genes from four cotton species were clustered (left) via MAGE5 using the maximum likelihood method. G. arboreum (Cotton_A) and G. raimondii (Gorai) contain 14 and 15 CesA genes, respectively, which are shown in the left column. The heat map (middle) shows the transcript level (FPKM, Reads Per Kilobase of exon model per Million mapped reads) of each homeologous gene in G. barbadense and G. hirsutum (Table 2) fibers at different DPA. The relative expression level in the two allotetraploid cottons was compared (right). CesA1, CesA3 and CesA6 are implicated in primary cell wall biosynthesis, and CesA4, CesA7 and CesA8 are implicated in secondary cell wall biosynthesis. (b) Temporal expression patterns of secondary cell wall CesA genes (CesA7, CesA4 and CesA8 clades) in G. barbadense and G. hirsutum fiber. Note that the expression was generally delayed in G. barbadense fiber. X-axis: day post-anthesis. Y-axis: FPKM.
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f5: Cotton CesA genes and their expression in developing fiber cells of G. barbadense and G. hirsutum.(a) CesA genes from four cotton species were clustered (left) via MAGE5 using the maximum likelihood method. G. arboreum (Cotton_A) and G. raimondii (Gorai) contain 14 and 15 CesA genes, respectively, which are shown in the left column. The heat map (middle) shows the transcript level (FPKM, Reads Per Kilobase of exon model per Million mapped reads) of each homeologous gene in G. barbadense and G. hirsutum (Table 2) fibers at different DPA. The relative expression level in the two allotetraploid cottons was compared (right). CesA1, CesA3 and CesA6 are implicated in primary cell wall biosynthesis, and CesA4, CesA7 and CesA8 are implicated in secondary cell wall biosynthesis. (b) Temporal expression patterns of secondary cell wall CesA genes (CesA7, CesA4 and CesA8 clades) in G. barbadense and G. hirsutum fiber. Note that the expression was generally delayed in G. barbadense fiber. X-axis: day post-anthesis. Y-axis: FPKM.

Mentions: Cellulose, which consists of linear chains of β (1–4)-linked D-glucose, is the major component of higher plant cell walls and the most abundant biopolymer on land. Plants express multiple cellulose synthases (CesAs) that, together with CesA-associated proteins, form the cellulose synthase complex4243. Cotton fiber is distinct not only in its extensive elongation (ELS cotton fiber is longer than 35 mm) but also in its exceptionally high amount of cellulose, which constitutes more than 95% of the dry weight of mature fiber1644. Notably, the first higher plant cellulose synthase gene was cloned from cotton45. Ten, 14 and 15 CesA genes are expressed in Arabidopsis thaliana4243, G. arboreum12 and G. raimondii10, respectively (Fig. 5 and Table 2). We identified 29 CesA genes, including 14 At and 15 Dt, in the G. barbadense genome, whereas 30 (14 At and 16 Dt) CesA genes were identified in G. hirsutum; most CesA genes had been retained after the merger of the A and D genomes (Table 2 and Supplementary Fig. 13). Compared to Arabidopsis, each cotton genome or subgenome contains more genes in the CesA3, CesA4, CesA7 and CesA8 clades. Notably, chromosome 5 of both the At and Dt subgenomes of G. barbadense (GOBAR_AA25282, GOBAR_AA25287/GOBAR_DD32643, GOBAR_DD32648 and GOBAR_DD32650) and G. hirsutum (Gh_A05G3959, Gh_A05G3965, Gh_A05G3967/Gh_D05G0077, Gh_D05G0079 and Gh_D05G0084) as well as G. arboreum and G. raimondii contain a CesA cluster composed of 3 or, rarely, 2 genes, in addition to the CesA-like (CSL) genes (Table 2); thus, the duplication(s) occurred in the ancient cotton genome.


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)

Cotton CesA genes and their expression in developing fiber cells of G. barbadense and G. hirsutum.(a) CesA genes from four cotton species were clustered (left) via MAGE5 using the maximum likelihood method. G. arboreum (Cotton_A) and G. raimondii (Gorai) contain 14 and 15 CesA genes, respectively, which are shown in the left column. The heat map (middle) shows the transcript level (FPKM, Reads Per Kilobase of exon model per Million mapped reads) of each homeologous gene in G. barbadense and G. hirsutum (Table 2) fibers at different DPA. The relative expression level in the two allotetraploid cottons was compared (right). CesA1, CesA3 and CesA6 are implicated in primary cell wall biosynthesis, and CesA4, CesA7 and CesA8 are implicated in secondary cell wall biosynthesis. (b) Temporal expression patterns of secondary cell wall CesA genes (CesA7, CesA4 and CesA8 clades) in G. barbadense and G. hirsutum fiber. Note that the expression was generally delayed in G. barbadense fiber. X-axis: day post-anthesis. Y-axis: FPKM.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Cotton CesA genes and their expression in developing fiber cells of G. barbadense and G. hirsutum.(a) CesA genes from four cotton species were clustered (left) via MAGE5 using the maximum likelihood method. G. arboreum (Cotton_A) and G. raimondii (Gorai) contain 14 and 15 CesA genes, respectively, which are shown in the left column. The heat map (middle) shows the transcript level (FPKM, Reads Per Kilobase of exon model per Million mapped reads) of each homeologous gene in G. barbadense and G. hirsutum (Table 2) fibers at different DPA. The relative expression level in the two allotetraploid cottons was compared (right). CesA1, CesA3 and CesA6 are implicated in primary cell wall biosynthesis, and CesA4, CesA7 and CesA8 are implicated in secondary cell wall biosynthesis. (b) Temporal expression patterns of secondary cell wall CesA genes (CesA7, CesA4 and CesA8 clades) in G. barbadense and G. hirsutum fiber. Note that the expression was generally delayed in G. barbadense fiber. X-axis: day post-anthesis. Y-axis: FPKM.
Mentions: Cellulose, which consists of linear chains of β (1–4)-linked D-glucose, is the major component of higher plant cell walls and the most abundant biopolymer on land. Plants express multiple cellulose synthases (CesAs) that, together with CesA-associated proteins, form the cellulose synthase complex4243. Cotton fiber is distinct not only in its extensive elongation (ELS cotton fiber is longer than 35 mm) but also in its exceptionally high amount of cellulose, which constitutes more than 95% of the dry weight of mature fiber1644. Notably, the first higher plant cellulose synthase gene was cloned from cotton45. Ten, 14 and 15 CesA genes are expressed in Arabidopsis thaliana4243, G. arboreum12 and G. raimondii10, respectively (Fig. 5 and Table 2). We identified 29 CesA genes, including 14 At and 15 Dt, in the G. barbadense genome, whereas 30 (14 At and 16 Dt) CesA genes were identified in G. hirsutum; most CesA genes had been retained after the merger of the A and D genomes (Table 2 and Supplementary Fig. 13). Compared to Arabidopsis, each cotton genome or subgenome contains more genes in the CesA3, CesA4, CesA7 and CesA8 clades. Notably, chromosome 5 of both the At and Dt subgenomes of G. barbadense (GOBAR_AA25282, GOBAR_AA25287/GOBAR_DD32643, GOBAR_DD32648 and GOBAR_DD32650) and G. hirsutum (Gh_A05G3959, Gh_A05G3965, Gh_A05G3967/Gh_D05G0077, Gh_D05G0079 and Gh_D05G0084) as well as G. arboreum and G. raimondii contain a CesA cluster composed of 3 or, rarely, 2 genes, in addition to the CesA-like (CSL) genes (Table 2); thus, the duplication(s) occurred in the ancient cotton genome.

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.


Related in: MedlinePlus