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Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

View Article: PubMed Central - PubMed

ABSTRACT

Background: MYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution. Previously, few studies have been conducted in upland cotton, Gossypium hirsutum. The recent release of the G. hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family.

Results: In this study, we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development. A total of 524 non-redundant cotton MYB genes, among 1986 MYB and MYB-related putative proteins, were identified and classified into four subfamilies including 1R-MYB, 2R-MYB, 3R-MYB, and 4R-MYB. Based on phylogenetic tree analysis, MYB transcription factors were divided into 16 subgroups. The results showed that the majority (69.1 %) of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton.

Conclusion: Our comparative genomics analysis has provided novel insights into the roles of MYB transcription factors in cotton fiber development. These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development.

Electronic supplementary material: The online version of this article (doi:10.1186/s12863-016-0436-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Expression levels of 20 GhMYB genes measured by qRT-PCR analysis of Ligon-lintless1 mutant and wild-type at different stages of cotton fiber development. Black and grey represent the expression levels of Li1 mutant and wild-type, respectively
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Fig3: Expression levels of 20 GhMYB genes measured by qRT-PCR analysis of Ligon-lintless1 mutant and wild-type at different stages of cotton fiber development. Black and grey represent the expression levels of Li1 mutant and wild-type, respectively

Mentions: MYB transcription factors play roles in many plant specific processes, such as primary and secondary metabolism, cell shape, anthers development, cellular proliferation, differentiation, and stress responses [53, 54]. We randomly selected 20 MYB genes to undergo expression verification using qRT-PCR (Fig. 3). The GhMYB genes MYB25, MYB2, MYB109, MYB5, and MYB3 were highly expressed in wild-type G. hirsutum, and exhibited lower expression levels in G. hirsutum Ligon-lintless1 (Li1) mutants after 5DPA. Previously, it found that 8DPA was the critical point for the Ligon-lintless1 mutant [32]. In addition, MYB109 and CotAD_02818 (GL1) promoted cotton fiber development [29]. MYB25 was expressed in ovules (initiation) and fiber development [26]. Our results indicate these genes may play an essential in maintaining normal cotton fiber development. In contrast, some selected GhMYB genes such as CotAD_29631 (CPC-like), CotAD_47467 (MYB103), CotAD_11820 (CPC-3R-MYB), CotAD_64719 (MYB1), CotAD_42115 (MYB83), and CotAD_21852 (MYB69) were significantly expressed in theLigon-lintless1 mutant, but not in wild-type. A previous study reported that CPC-3R-MYB negatively controlled cotton fiber development [28], consistent with this the genes that are up-regulated in the Ligon-lintless1 mutant could be responsible for the short fiber phenotype observed. Other groups of genes such as CotAD_04154 (MYB_255), CotAD_02811 (MYB52), CotAD_41041 (MYB_198), CotAD_64081 (MYBML5), CotAD_71681 (MYB42), CotAD_13600 (MYB46), and CotAD_27106 (MYB20) were expressed at different levels in the Li1 mutant and wild-type which may indicate functional divergence of GhMYB genes during cotton fiber development. Previous reports mentioned that MYB genes showed significant expression differences between Ligon-lintless2 and wild-type expression during the later stage of cotton fiber development at 20DPA [55]. Several MYB transcription factors were readjusted by the Ligon-lintless1 mutant at 5 DPA [56], 6 DPA [31], 1 DPA, 3 DPA, and 8 DPA ovules [33]. Overall, it can be seen that our RNA-seq data is consistent with qRT-PCR results. In addition, a comparative expression profile analysis of MYBs in upland cotton revealed that GhMYB might have diverse functions at different stages of cell fiber development. Taken together, the RNA-seq and qRT-PCR expression analyses in G. hirsutum support the hypothesis that GhMYBs are involved in fiber development during different developmental stages, and may have diverse functions in Arabidopsis and other species. The functions of most MYBs in higher plants remain unclear, and further investigation is required to elucidate their exact functions. Our results provide a comprehensive understanding of GhMYBs and provide the foundation for future functional analyses of MYB genes and their roles in cotton fiber development.Fig. 3


Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum
Expression levels of 20 GhMYB genes measured by qRT-PCR analysis of Ligon-lintless1 mutant and wild-type at different stages of cotton fiber development. Black and grey represent the expression levels of Li1 mutant and wild-type, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC5017022&req=5

Fig3: Expression levels of 20 GhMYB genes measured by qRT-PCR analysis of Ligon-lintless1 mutant and wild-type at different stages of cotton fiber development. Black and grey represent the expression levels of Li1 mutant and wild-type, respectively
Mentions: MYB transcription factors play roles in many plant specific processes, such as primary and secondary metabolism, cell shape, anthers development, cellular proliferation, differentiation, and stress responses [53, 54]. We randomly selected 20 MYB genes to undergo expression verification using qRT-PCR (Fig. 3). The GhMYB genes MYB25, MYB2, MYB109, MYB5, and MYB3 were highly expressed in wild-type G. hirsutum, and exhibited lower expression levels in G. hirsutum Ligon-lintless1 (Li1) mutants after 5DPA. Previously, it found that 8DPA was the critical point for the Ligon-lintless1 mutant [32]. In addition, MYB109 and CotAD_02818 (GL1) promoted cotton fiber development [29]. MYB25 was expressed in ovules (initiation) and fiber development [26]. Our results indicate these genes may play an essential in maintaining normal cotton fiber development. In contrast, some selected GhMYB genes such as CotAD_29631 (CPC-like), CotAD_47467 (MYB103), CotAD_11820 (CPC-3R-MYB), CotAD_64719 (MYB1), CotAD_42115 (MYB83), and CotAD_21852 (MYB69) were significantly expressed in theLigon-lintless1 mutant, but not in wild-type. A previous study reported that CPC-3R-MYB negatively controlled cotton fiber development [28], consistent with this the genes that are up-regulated in the Ligon-lintless1 mutant could be responsible for the short fiber phenotype observed. Other groups of genes such as CotAD_04154 (MYB_255), CotAD_02811 (MYB52), CotAD_41041 (MYB_198), CotAD_64081 (MYBML5), CotAD_71681 (MYB42), CotAD_13600 (MYB46), and CotAD_27106 (MYB20) were expressed at different levels in the Li1 mutant and wild-type which may indicate functional divergence of GhMYB genes during cotton fiber development. Previous reports mentioned that MYB genes showed significant expression differences between Ligon-lintless2 and wild-type expression during the later stage of cotton fiber development at 20DPA [55]. Several MYB transcription factors were readjusted by the Ligon-lintless1 mutant at 5 DPA [56], 6 DPA [31], 1 DPA, 3 DPA, and 8 DPA ovules [33]. Overall, it can be seen that our RNA-seq data is consistent with qRT-PCR results. In addition, a comparative expression profile analysis of MYBs in upland cotton revealed that GhMYB might have diverse functions at different stages of cell fiber development. Taken together, the RNA-seq and qRT-PCR expression analyses in G. hirsutum support the hypothesis that GhMYBs are involved in fiber development during different developmental stages, and may have diverse functions in Arabidopsis and other species. The functions of most MYBs in higher plants remain unclear, and further investigation is required to elucidate their exact functions. Our results provide a comprehensive understanding of GhMYBs and provide the foundation for future functional analyses of MYB genes and their roles in cotton fiber development.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: MYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution. Previously, few studies have been conducted in upland cotton, Gossypium hirsutum. The recent release of the G. hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family.

Results: In this study, we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development. A total of 524 non-redundant cotton MYB genes, among 1986 MYB and MYB-related putative proteins, were identified and classified into four subfamilies including 1R-MYB, 2R-MYB, 3R-MYB, and 4R-MYB. Based on phylogenetic tree analysis, MYB transcription factors were divided into 16 subgroups. The results showed that the majority (69.1 %) of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton.

Conclusion: Our comparative genomics analysis has provided novel insights into the roles of MYB transcription factors in cotton fiber development. These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development.

Electronic supplementary material: The online version of this article (doi:10.1186/s12863-016-0436-8) contains supplementary material, which is available to authorized users.

No MeSH data available.