Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus.
Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus.
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Brassica Napus中SBP-box基因家族的基因组鉴定，表征和差异表达分析。
DOI：
10.1186/s12870-016-0852-y
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发表时间：
2016-09-08
影响因子：
5.3
通讯作者：
Hu Q
中科院分区：
文献类型：
--
作者：
Cheng H;Hao M;Wang W;Mei D;Tong C;Wang H;Liu J;Fu L;Hu Q
SBP-box基因属于转录因子中最大的家族之一。尽管该家族的成员已经被认为是多种生物学过程的重要调节者，但在第三大油料作物甘蓝型油菜中SBP-box基因的信息很大程度上是未知的。本研究通过全基因组生物信息学分析和转录图谱分析，对甘蓝型油菜(Brassica napus L.)并对其在不同组织中的表达模式以及可能与miRNAs的相互作用进行了分析。此外，还利用不同分枝角度的甘蓝型油菜品系研究了SBP-box基因在植物结构调控中的作用。详细的基因信息，包括基因组组织、结构特征、保守结构域和系统发育关系等都得到了系统的描述。通过系统发育分析，将Bna SBP蛋白分为8个不同的类群，它们代表了拟南芥和水稻中与其家族成员明显的同源关系。在包括营养器官和生殖器官在内的12个组织中的表达分析表明，SBP-box基因在不同组织中的表达模式不同，其中一些基因具有组织特异性表达，表明它们在发育过程中具有不同的功能。44个SBP-box基因被确定含有可能的miR156结合位点，其中30个基因定位于编码区，14个基因定位于3‘非编码区。MiR156的相对表达水平在不同组织中是不同的。在不同分枝角度的品系中，部分Bna SBP基因的表达模式不同，miR156与其靶基因Bna SBP的转录水平呈负相关。综上所述，本研究首次对甘蓝型油菜SBP-box基因家族进行了系统分析。这些数据为理解Bna SBP基因在植物发育和其他生物过程中的重要作用提供了基础。本文的在线版本(doi：10.1186/s12870-0160852-y)包含补充材料，授权用户可以使用。
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. 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. 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. The online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.
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