Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton
Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identifie...
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PeerJ Inc.
2017-10-01
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| author | Xueqiang Su Xu Sun Xi Cheng Yanan Wang Muhammad Abdullah Manli Li Dahui Li Junshan Gao Yongping Cai Yi Lin |
| author_facet | Xueqiang Su Xu Sun Xi Cheng Yanan Wang Muhammad Abdullah Manli Li Dahui Li Junshan Gao Yongping Cai Yi Lin |
| author_sort | Xueqiang Su |
| collection | DOAJ |
| description | Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber. |
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| last_indexed | 2024-03-09T06:25:31Z |
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| spelling | doaj.art-09b85ab7620343e18e383a09a333d1f32023-12-03T11:19:38ZengPeerJ Inc.PeerJ2167-83592017-10-015e397410.7717/peerj.3974Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cottonXueqiang Su0Xu Sun1Xi Cheng2Yanan Wang3Muhammad Abdullah4Manli Li5Dahui Li6Junshan Gao7Yongping Cai8Yi Lin9School of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaPlant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.https://peerj.com/articles/3974.pdfUpland cottonPolyketide synthaseProcyanidinsGene expressionGenome-wide analysis |
| spellingShingle | Xueqiang Su Xu Sun Xi Cheng Yanan Wang Muhammad Abdullah Manli Li Dahui Li Junshan Gao Yongping Cai Yi Lin Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton PeerJ Upland cotton Polyketide synthase Procyanidins Gene expression Genome-wide analysis |
| title | Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton |
| title_full | Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton |
| title_fullStr | Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton |
| title_full_unstemmed | Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton |
| title_short | Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton |
| title_sort | comparative genomic analysis of the pks genes in five species and expression analysis in upland cotton |
| topic | Upland cotton Polyketide synthase Procyanidins Gene expression Genome-wide analysis |
| url | https://peerj.com/articles/3974.pdf |
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