Abstract
MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKCC, MIKC*) and the MIKCC group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated functional divergence and neo-functionalization or sub-functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.
Highlights
MADS-box transcription factors have been reported in animals, plants and fungi, which initiated transcription of target gene by binding to the CArG-boxes domain in the cis-acting element of the target gene[1]
In order to further understand the differences in the MADS-box gene family between the two Pyrus species, we compared the differences in exon-intron structure between European pear and Chinese pear
In order to better understand the evolutionary relationship of the MADS-box gene family in Rosaceae species, phylogenetic trees of MADS-box genes from Arabidopsis, Prunus mume, Prunus persica, Malus domestica, Fragaria vesca, Pyrus communis and Pyrus bretschneideri were constructed using maximum likelihood (ML) and Maximum Parsimony (MP) method, respectively
Summary
MADS-box transcription factors have been reported in animals, plants and fungi, which initiated transcription of target gene by binding to the CArG-boxes domain in the cis-acting element of the target gene[1]. MADS-box genes play a significant role in the development and signal transduction of various organs, such as fruit development and maturation[12,13]. The completion of whole-genome sequencing of European pear and Chinese pear provides a basis for further study of the MADS-box gene family function. 73 and 74 MADS-box genes were identified from European pear and Chinese pear, respectively, and analyzed their evolutionary relationships and genetic structure. The chromosome localization and microcollinearity analysis have been investigated Both RNA-Seq and qRT-PCR analyses were used to understand the functional divergences of MADS-box transcription factors between European pear and Chinese pear during pear fruit development. This study will provide new ideas for further understanding the similarities and differences between closely related species at the genomic level, and for discovering the mechanisms of species differentiation and biodiversity formation
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