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

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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.


Distribution of GhMYB genes on cotton chromosomes. The chromosomal position of each GhMYB was mapped to the upland cotton genome
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Fig1: Distribution of GhMYB genes on cotton chromosomes. The chromosomal position of each GhMYB was mapped to the upland cotton genome

Mentions: Analysis of the G. hirsutum genome sequence revealed 524 possible members of the GhMYB gene family. Of these genes, 114 had been annotated previously. Three hundred and seventy three (373) GhMYB transcription factor genes were mapped onto upland cotton chromosomes and named according to their chromosomal order (from chromosome 1 to 26) as GhMYB1 to GhMYB373. One hundred and fifty one (151) GhMYB genes were not obviously mapped to any chromosome (scaffolds), and named GhMYB374 to GhMYB524, respectively (Additional file 4: Table S3). The distribution and density of MYB transcription factor genes on chromosomes was not uniform. Some chromosomes, and chromosomal regions, have a high density of MYB transcription factor genes while others do not (Fig. 1). The highest density of MYB genes was observed on chromosome At 9 and its homolog chromosome Dt 9 (23) with 58 genes, and the lowest density of MYB genes was observed on chromosome At 3 and its homolog chromosome Dt 3 (17), with 11 genes. In addition, the majority of MYB transcription factor genes were found at the upper and centromeric regions of the chromosomes. In addition, a greater number of MYB genes were located on Dt chromosomes (tetraploid D) than on At chromosomes (tetraploid A) with 201 and 172 genes, respectively (Table 1).Fig. 1


Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum
Distribution of GhMYB genes on cotton chromosomes. The chromosomal position of each GhMYB was mapped to the upland cotton genome
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Distribution of GhMYB genes on cotton chromosomes. The chromosomal position of each GhMYB was mapped to the upland cotton genome
Mentions: Analysis of the G. hirsutum genome sequence revealed 524 possible members of the GhMYB gene family. Of these genes, 114 had been annotated previously. Three hundred and seventy three (373) GhMYB transcription factor genes were mapped onto upland cotton chromosomes and named according to their chromosomal order (from chromosome 1 to 26) as GhMYB1 to GhMYB373. One hundred and fifty one (151) GhMYB genes were not obviously mapped to any chromosome (scaffolds), and named GhMYB374 to GhMYB524, respectively (Additional file 4: Table S3). The distribution and density of MYB transcription factor genes on chromosomes was not uniform. Some chromosomes, and chromosomal regions, have a high density of MYB transcription factor genes while others do not (Fig. 1). The highest density of MYB genes was observed on chromosome At 9 and its homolog chromosome Dt 9 (23) with 58 genes, and the lowest density of MYB genes was observed on chromosome At 3 and its homolog chromosome Dt 3 (17), with 11 genes. In addition, the majority of MYB transcription factor genes were found at the upper and centromeric regions of the chromosomes. In addition, a greater number of MYB genes were located on Dt chromosomes (tetraploid D) than on At chromosomes (tetraploid A) with 201 and 172 genes, respectively (Table 1).Fig. 1

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.