Genome-wide survey of potato MADS-box genes reveals that StMADS1 and StMADS13 are putative downstream targets of tuberigen StSP6A.
Genome-wide survey of potato MADS-box genes reveals that StMADS1 and StMADS13 are putative downstream targets of tuberigen StSP6A.
复制标题
马铃薯 MADS-box 基因的全基因组调查表明 StMADS1 和 StMADS13 是块茎菌 StSP6A 的假定下游靶标
DOI：
10.1186/s12864-018-5113-z
复制
发表时间：
2018-10-03
期刊：
影响因子：
4.4
通讯作者：
Ma H
中科院分区：
文献类型：
--
作者：
Gao H;Wang Z;Li S;Hou M;Zhou Y;Zhao Y;Li G;Zhao H;Ma H
mads -box基因编码的转录因子参与了植物生长发育的多个方面，特别是花器官的发育。迄今为止，在马铃薯基因组测序完成后，仍缺乏对马铃薯MADS-box基因家族的全面分析。本研究对MADS-box转录因子基因家族进行了全基因组的表征、分类和表达分析。结果根据与拟南芥和水稻MADS-box基因的系统发育关系，共鉴定出153个MADS-box基因，并将其分为MIKC亚家族（mikcca和MIKC*）和m型亚家族（Mα、Mβ和Mγ）。马铃薯m型亚家族有114个成员，几乎是MIKC成员（39个）的3倍，这表明m型MADS-box基因在马铃薯基因组进化过程中具有更高的重复率和/或更低的损失率。马铃薯MADS-box基因全部存在于12条马铃薯染色体上，具有大量聚类，主要由m型成员贡献。马铃薯MADS-box基因的染色体定位表明，MADS-box基因主要位于马铃薯基因组的重复片段上，而串联重复主要促进了m型基因的扩增。马铃薯MIKC亚家族可进一步分为11个亚群，在拟南芥中发现的tt16样、agl17样和flc样亚群在马铃薯中不存在。此外，利用RNA-seq数据分析了马铃薯MADS-box基因在不同组织中的表达，并通过实时荧光定量PCR验证了mikcc基因主要在花器官中表达，部分mikcc基因在匍匐茎和块茎中高表达。StMADS1和StMADS13在StSP6A过表达植物中表达上调，在StSP6A- rnai植物中表达下调，它们在叶片和/或幼块茎中的表达与StSP6A的高表达相关。结论本研究鉴定了马铃薯MADS-box基因家族成员，探讨了MADS-box基因家族的进化历史和功能分化。此外，我们分析了mikcc表达模式并筛选了与结核有关的基因。最后，StMADS1和StMADS13最有可能是StSP6A的下游靶点，参与块茎发育。
BackgroundMADS-box genes encode transcription factors that are known to be involved in several aspects of plant growth and development, especially in floral organ specification. To date, the comprehensive analysis of potato MADS-box gene family is still lacking after the completion of potato genome sequencing. A genome-wide characterization, classification, and expression analysis of MADS-box transcription factor gene family was performed in this study.ResultsA total of 153 MADS-box genes were identified and categorized into MIKC subfamily (MIKCCand MIKC*) and M-type subfamily (Mα, Mβ, and Mγ) based on their phylogenetic relationships to theArabidopsisand rice MADS-box genes. The potato M-type subfamily had 114 members, which is almost three times of the MIKC members (39), indicating that M-type MADS-box genes have a higher duplication rate and/or a lower loss rate during potato genome evolution. Potato MADS-box genes were present on all 12 potato chromosomes with substantial clustering that mainly contributed by the M-type members. Chromosomal localization of potato MADS-box genes revealed that MADS-box genes, mostly MIKC, were located on the duplicated segments of the potato genome whereas tandem duplications mainly contributed to the M-type gene expansion. The potato MIKC subfamily could be further classified into 11 subgroups and the TT16-like, AGL17-like, and FLC-like subgroups found inArabidopsiswere absent in potato. Moreover, the expressions of potato MADS-box genes in various tissues were analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the MIKCCgenes were mainly expressed in flower organs and several of them were highly expressed in stolon and tubers. StMADS1 and StMADS13 were up-regulated in the StSP6A-overexpression plants and down-regulated in the StSP6A-RNAi plant, and their expression in leaves and/or young tubers were associated with high level expression of StSP6A.ConclusionOur study identifies the family members of potato MADS-box genes and investigate the evolution history and functional divergence of MADS-box gene family. Moreover, we analyze the MIKCCexpression patterns and screen for genes involved in tuberization. Finally, the StMADS1 and StMADS13 are most likely to be downstream target of StSP6A and involved in tuber development.
登录
查看更多内容
大米中的MADS-box基因家族：在生殖发育和压力期间，全基因组识别，组织和表达分析。
影响因子：
4.4
作者：
Arora, Rita;Agarwal, Pinky;Ray, Swatismita;Singh, Ashok Kumar;Singh, Vijay Pal;Tyagi, Akhilesh K.;Kapoor, Sanjay
通讯作者：
Kapoor, Sanjay
葡萄枯草杆菌酶基因家族的全基因组和分子进化分析。
影响因子：
4.4
作者：
Cao J;Han X;Zhang T;Yang Y;Huang J;Hu X
通讯作者：
Hu X
大豆 MADS 基因的全基因组表达分析显示在种子发育中的潜在功能
影响因子：
3.7
作者：
Fan, Cheng-Ming;Wang, Xu;Fu, Yong-Fu
通讯作者：
Fu, Yong-Fu
影响因子：
11.4
作者：
Gramzow, Lydia;Ritz, Markus S.;Theissen, Gunter
通讯作者：
Theissen, Gunter
影响因子：
7.2
作者：
Colombo, Monica;Masiero, Simona;Colombo, Lucia
通讯作者：
Colombo, Lucia