Maize Research Institute, Sichuan Agricultural University, Chengdu Sichuan, China.
BMC Plant Biol. 2012 Jul 9;12:106. doi: 10.1186/1471-2229-12-106.
The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no genome-wide characterization of this gene family has been conducted in a legume species. Here we report the first genome-wide analysis of the whole MYB superfamily in a legume species, soybean (Glycine max), including the gene structures, phylogeny, chromosome locations, conserved motifs, and expression patterns, as well as a comparative genomic analysis with Arabidopsis.
A total of 244 R2R3-MYB genes were identified and further classified into 48 subfamilies based on a phylogenetic comparative analysis with their putative orthologs, showed both gene loss and duplication events. The phylogenetic analysis showed that most characterized MYB genes with similar functions are clustered in the same subfamily, together with the identification of orthologs by synteny analysis, functional conservation among subgroups of MYB genes was strongly indicated. The phylogenetic relationships of each subgroup of MYB genes were well supported by the highly conserved intron/exon structures and motifs outside the MYB domain. Synonymous nucleotide substitution (dN/dS) analysis showed that the soybean MYB DNA-binding domain is under strong negative selection. The chromosome distribution pattern strongly indicated that genome-wide segmental and tandem duplication contribute to the expansion of soybean MYB genes. In addition, we found that ~ 4% of soybean R2R3-MYB genes had undergone alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Comparative expression profile analysis of R2R3-MYB genes in soybean and Arabidopsis revealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function.
In this study we identified the largest MYB gene family in plants known to date. Our findings indicate that members of this large gene family may be involved in different plant biological processes, some of which may be potentially involved in legume-specific nodulation. Our comparative genomics analysis provides a solid foundation for future functional dissection of this family gene.
MYB 超家族构成了在植物中描述的最丰富的转录因子之一。然而，它们的功能似乎高度多样化，仍然相当不清楚。迄今为止，在豆科植物中尚未对该基因家族进行全基因组特征描述。在这里，我们报告了在豆科植物大豆中首次对整个 MYB 超家族进行的全基因组分析，包括基因结构、系统发育、染色体定位、保守基序和表达模式，以及与拟南芥的比较基因组分析。
共鉴定出 244 个 R2R3-MYB 基因，并根据与推定的同源物的系统发育比较分析进一步分为 48 个亚家族，显示出基因丢失和复制事件。系统发育分析表明，大多数具有相似功能的已鉴定 MYB 基因聚类在同一亚家族中，通过同线性分析鉴定出同源物，强烈表明 MYB 基因亚群之间存在功能保守性。每个 MYB 基因亚群的系统发育关系得到高度保守的内含子/外显子结构和 MYB 结构域外基序的很好支持。同义核苷酸替换（dN/dS）分析表明，大豆 MYB DNA 结合域受到强烈的负选择。染色体分布模式强烈表明，全基因组片段和串联重复导致大豆 MYB 基因的扩张。此外，我们发现，大豆 R2R3-MYB 基因中约有 4%经历了选择性剪接事件，从单个基因产生多种转录本，这说明了转录组调控的极高复杂性。大豆和拟南芥 R2R3-MYB 基因的比较表达谱分析表明，MYB 基因在植物中发挥保守和多样化的作用，这表明功能上的分化。
在这项研究中，我们鉴定了迄今为止已知的植物中最大的 MYB 基因家族。我们的发现表明，这个庞大基因家族的成员可能参与不同的植物生物学过程，其中一些可能与豆科植物特有的结瘤有关。我们的比较基因组学分析为进一步对该家族基因进行功能解析提供了坚实的基础。
