Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange

PLoS One. 2014 Nov 6;9(11):e112375. doi: 10.1371/journal.pone.0112375. eCollection 2014.

Abstract

MYB family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few MYB genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange MYB gene (CsMYB) family in terms of their genomic gene structures and similarity to their putative Arabidopsis orthologs. According to these analyses, these CsMYBs were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these CsMYBs are distributed across nine chromosomes. Sweet orange includes a relatively small number of MYB genes compared with the 198 members in Arabidopsis, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of CsMYBs and Arabidopsis showed that CsMYBs had fewer gene duplication events. Expression analysis revealed that the MYB gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 CsMYBs. These results provide a useful reference for the selection of candidate MYB genes for cloning and further functional analysis forcitrus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Citrus sinensis* / genetics
  • Citrus sinensis* / metabolism
  • Gene Expression Regulation, Plant / physiology*
  • Genome-Wide Association Study
  • Multigene Family / physiology*
  • Plant Proteins* / biosynthesis
  • Plant Proteins* / classification
  • Plant Proteins* / genetics
  • Transcription Factors* / biosynthesis
  • Transcription Factors* / classification
  • Transcription Factors* / genetics

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

This research was supported financially by the National Natural Science Foundation of China (grant nos. 31130046, 31372046, 31221062, 31471863 and 31360469) and the Fundamental Research Funds for the Central Universities (2013PY083). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.