Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Abstract

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

Identification and Characterization of the HD-Zip Gene Family and Dimerization Analysis of HB7 and HB12 in Brassica napus L.

“…The chromosomal distribution of the HD-Zip genes in the three Brassica species showed that HD-Zip orthologous genes are more similar in the B. rapa AA genome to the B. napus AA genome than in the B. oleracea CC genome to the B. napus CC genome, which may also be associated with more gene domain loss events during the expansion of the HD-Zip gene family in B. oleracea or the location of some genes are unclear. This is consistent with the findings for other gene families in the three species, such as GST [ 41 ], UGTs [ 42 ], and SUV [ 43 ]. A draft genome sequence of B. oleracea , comparing it with that of B. rapa reveals numerous chromosome rearrangements [ 38 ].…”