Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

Chaoyang Liu,Aiping Luan,Jianmei Long,Yehua He,Tao Xie,Yaqi Ding,Chenjie Chen,Chuhao Li

doi:10.1186/s12864-017-3896-y

Chaoyang Liu, Aiping Luan + Show 6 more

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https://doi.org/10.1186/s12864-017-3896-y

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Abstract

BackgroundThe MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level.ResultsIn the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization.ConclusionsIn this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

Highlights

The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes
Identification of 94 Pineapple R2R3-MYB (AcMYB) genes and their sequence feature The amino acid sequence of HMM profile of the Pfam MYB domain (PF00249) was used as a query in BLASTP searches to identify MYB encoding genes presented in pineapple genome
Collinearity analysis indicated that the segmental duplication events contributed to the expansion of pineapple MYB gene family

Summary

Introduction

The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Transcription factors play an important role in the regulation of gene transcription, and control many aspects of plant growth and development through activating or suppressing their target genes [1]. The MYB transcription factors are broadly dispersed in higher plants genomes, and comprise one of the largest transcription factor families in plants [2]. The MYB gene family members bear a characteristic N-terminal MYB DNA-binding domain, which is highly conserved among plants. Since the first plant MYB gene, C1, was isolated, research concerning the identification and functional characterization of the R2R3-MYB gene family has been widely conducted in plants [2, 8].

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