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

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3896-y) contains supplementary material, which is available to authorized users.

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“…Members of such groups are important candidates for species-specific functional investigations (Table 2). The phylogenetic results were consistent with recent reports [26,32,47] showing that various groups included more MYBs from Arabidopsis than M. acuminata, M. balbisiana, and O. sativa. These results are in accordance with the current information that Arabidopsis underwent more duplication events after divergence of the last common ancestor from these three close species.…”

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“…The number of segmental duplications in sea buckthorn was significantly higher than the number of tandem duplications, which had been found in many plants. This suggested that the occurrence of segment duplications might play a more critical role in the expansion of the sea buckthorn R2R3-MYB gene family [29].…”

Anthocyanin Synthesis and the Expression Patterns of bHLH Transcription Factor Family during Development of the Chinese Jujube Fruit (Ziziphus jujuba Mill.)

“…The fragments per kilobase of exon per million mapped reads (FPKM) values were calculated based on RNA-Seq reads. The heatmap was generated with TBTOOLS software (https://github.com/CJ-Chen/ TBtools) [31]. The color scale shown represents FPKM counts, and the ratios were log2 transformed.…”