Genome-wide analysis of the MADS-box gene family in cucumber

Abstract

MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.

Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

“…The locations of all SlPGs were determined. Tandem-duplicated genes and segment-duplicated events were analyzed according to a previous study [47]. CoGe comparative genomics system [31] and Circos [32] were used to conduct the synteny analysis and generate the diagram of genomic distribution and syntenic relationship of SlPGs .…”

Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

“…A pair of genes were identified as tandem duplicates if the genes both shared ≥40% amino acid sequence similarity and separated by fewer than five intervening genes [50]. PGDD [51] was adopted to perform synteny analysis and detect the segment duplications, as described in cucumber MADS gene family [50]. Full-length amino acid sequences were aligned using the ClustalW algorithm [52], and then Ks and Ka were calculated using the Codeml procedure of the PAML program [53].…”

Conservation and Diversification of Floral Homeotic MADS-box Genes in Eustoma grandiflorum

“…The Arabidopsis, grapevine, and cucumber genomes contained 39, 38, and 30 MIKCtype MADS-box genes, respectively (Diaz-Riquelme et al, 2009;Hu and Liu, 2012;Par̆enicová et al, 2003). In this study, we identified 23 MIKC c -type MADSbox genes expressed in the Eustoma flower (Table 2).…”

“…Recent advances in whole-genome sequencing have enabled genome-wide analyses of the MADS-box gene family in economically important crops, such as in grapevine (Diaz-Riquelme et al, 2009), maize, sorghum (Zhao et al, 2011), cucumber (Hu and Liu, 2012), and soybean (Shu et al, 2013). The Arabidopsis, grapevine, and cucumber genomes contained 39, 38, and 30 MIKCtype MADS-box genes, respectively (Diaz-Riquelme et al, 2009;Hu and Liu, 2012;Par̆enicová et al, 2003).…”