Genome-wide identification, characterisation and expression analysis of the MADS-box gene family in Prunus mume

Abstract

MADS-box genes encode transcription factors that play crucial roles in plant development, especially in flower and fruit development. To gain insight into this gene family in Prunus mume, an important ornamental and fruit plant in East Asia, and to elucidate their roles in flower organ determination and fruit development, we performed a genome-wide identification, characterisation and expression analysis of MADS-box genes in this Rosaceae tree. In this study, 80 MADS-box genes were identified in P. mume and categorised into MIKC, Mα, Mβ, Mγ and Mδ groups based on gene structures and phylogenetic relationships. The MIKC group could be further classified into 12 subfamilies. The FLC subfamily was absent in P. mume and the six tandemly arranged DAM genes might experience a species-specific evolution process in P. mume. The MADS-box gene family might experience an evolution process from MIKC genes to Mδ genes to Mα, Mβ and Mγ genes. The expression analysis suggests that P. mume MADS-box genes have diverse functions in P. mume development and the functions of duplicated genes diverged after the duplication events. In addition to its involvement in the development of female gametophytes, type I genes also play roles in male gametophytes development. In conclusion, this study adds to our understanding of the roles that the MADS-box genes played in flower and fruit development and lays a foundation for selecting candidate genes for functional studies in P. mume and other species. Furthermore, this study also provides a basis to study the evolution of the MADS-box family.

Systematic analysis of O -methyltransferase gene family and identification of potential members involved in the formation of O -methylated flavonoids in Citrus

“…Multiple genes of one family were characterized as tandem genes when they were located within the same or a neighboring region (within 100 kb). Segmental duplications were determined using the method of Du et al (2013), Xu et al (2014), and Lu et al (2015). Firstly, BLASTP was used to identify potential anchors (E b 1 e−5 , top 5 matches); subsequently, the homologous regions were determined using software MCscan.…”

SEP-class genes in Prunus mume and their likely role in floral organ development

“…Among these, E class genes play a significant role in flower development. Scientists have already carried out investigations of the MADS-box gene family and the cloning of C class genes in P. mume [10]; however, the molecular mechanisms behind flower organ development and morphology remain unclear. Therefore, an expression and functional analysis of SEP genes is required to uncover these processes.…”

Genome-Wide Identification, Characterization and Expression Analysis of the TCP Gene Family in Prunus mume

“…(Rosaceae, Prunoideae) has been cultivated in China for over 3,000 years for its prominent ornamental and economic value. This species has acquired favorable ornamental characteristics with various types of flowers, colorful corollas, pleasing fragrance, and early blooming in the Prunus genus (Zhang et al, 2012; Xu Z. et al, 2014). The flower development plays a vital role in ornamental value.…”

“…The flower development plays a vital role in ornamental value. In P. mume , the studies of the MADS-box gene family and SBP-box gene family have been performed to gain insights into flower development (Xu Z. et al, 2014; Xu et al, 2015). Nevertheless, the molecular regulation of its flower development are still almost unknown.…”