Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus

Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.

背景：SBP-box基因属于最大的转录因子（transcription factor）家族之一。尽管该家族成员已被证实是多种生物过程的重要调控因子，但针对第三大重要油料作物甘蓝型油菜（Brassica napus）中SBP-box基因的相关信息仍未得到充分解析。
结果：本研究通过全基因组生物信息学分析与转录组谱分析，在甘蓝型油菜（Brassica napus L.）中鉴定出58个SBP-box基因家族的推定成员，并对其在不同组织中的表达模式以及与microRNA（miRNA）的潜在互作关系进行了分析。此外，本研究利用分枝角度存在显著差异的甘蓝型油菜株系，探究了SBP-box基因在植物株型调控中的作用。研究系统解析了这些基因的详细信息，包括基因组结构、结构特征、保守结构域以及系统发育关系。通过系统发育分析，BnaSBP蛋白被划分为8个独立的类群，这些类群与拟南芥（Arabidopsis）和水稻中的家族成员存在明确的直系同源关系。对包括营养器官与生殖器官在内的12种组织的表达分析显示，不同SBP-box基因的表达模式存在差异，且部分基因呈现组织特异性表达，表明其在植物发育过程中发挥着多样的功能。44个SBP-box基因被证实含有推定的miR156结合位点，其中30个和14个基因分别在编码区和3'非翻译区（3'UTR）被miR156靶向。miR156的相对表达水平在不同组织中存在差异。在分枝角度不同的株系中，部分BnaSBP基因的表达模式存在差异，且miR156与其靶标BnaSBP基因的转录水平呈负相关关系。
结论：综上，本研究是首次对甘蓝型油菜SBP-box基因家族进行的系统性分析。本研究提供的数据为解析BnaSBP基因在植物发育及其他生物过程中的关键作用奠定了基础。