Genome-wide analysis of the MYB transcription factor superfamily in soybean.
Genome-wide analysis of the MYB transcription factor superfamily in soybean.
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大豆 MYB 转录因子超家族的全基因组分析
DOI：
10.1186/1471-2229-12-106
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发表时间：
2012-07-09
影响因子：
5.3
通讯作者：
Tang YX
中科院分区：
文献类型：
--
作者：
Du H;Yang SS;Liang Z;Feng BR;Liu L;Huang YB;Tang YX
背景MYB超家族是植物中最丰富的转录因子家族之一。然而，它们的职能似乎非常多样化，仍然相当不明确。到目前为止，还没有在豆科植物中对该基因家族进行全基因组表征。在这里，我们报告了第一个全基因组分析的整个MYB超家族的豆类物种，大豆（Glycine max）的基因结构、遗传、染色体定位、保守基序和表达模式，并与拟南芥进行了比较基因组分析。通过系统发育分析，发现MYB基因存在缺失和重复现象，并将其进一步划分为48个亚家族。系统发育分析表明，大多数功能相似的MYB基因都聚在同一个亚家族中，通过同线性分析确定的同源基因表明，MYB基因亚群之间具有很强的功能保守性。MYB结构域外高度保守的内含子/外显子结构和基序支持了MYB基因各亚群的系统发育关系。同义核苷酸替换（dN/dS）分析表明，大豆MYB DNA结合结构域是在强烈的负选择。染色体的分布模式强烈表明，全基因组的节段和串联重复有助于大豆MYB基因的扩展。此外，我们发现约4%的大豆R2 R3-MYB基因经历了选择性剪接事件，从单个基因产生多种转录物，这说明了转录组调控的高度复杂性。R2 R3-MYB基因在大豆和拟南芥中的比较表达谱分析表明，MYB基因在植物中发挥保守和各种作用，这是指示在functions.ConclusionsIn这项研究中，我们确定了最大的MYB基因家族在植物中已知的日期。我们的研究结果表明，这个大的基因家族的成员可能参与不同的植物生物学过程，其中一些可能是潜在的参与豆类特异性同化。我们的比较基因组学分析提供了一个坚实的基础，为未来的功能解剖这个家庭的基因。
BackgroundThe 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 withArabidopsis.ResultsA 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 andArabidopsisrevealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function.ConclusionsIn 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.
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针叶树R2R3-MYB转录因子：白云杉（Picea Glauca）的木制组织中的序列分析和基因表达。
影响因子：
5.3
作者：
Bedon, Frank;Grima-Pettenati, Jacqueline;Mackay, John
通讯作者：
Mackay, John
影响因子：
9.4
作者：
Gigolashvili, Tamara;Engqvist, Martin;Fluegge, Ulf-Ingo
通讯作者：
Fluegge, Ulf-Ingo
影响因子：
10.7
作者：
Amoutzias, G. D.;Veron, A. S.;Robertson, D. L.
通讯作者：
Robertson, D. L.
影响因子：
7.2
作者：
Gigolashvili, Tamara;Berger, Bettina;Fluegge, Ulf-Ingo
通讯作者：
Fluegge, Ulf-Ingo
影响因子：
14.9
作者：
CORPET, F
通讯作者：
CORPET, F