Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)
Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)
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DOI：
10.1007/s00438-014-0912-7
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发表时间：
2015-02-01
影响因子：
3.1
通讯作者：
Li, Ying
中科院分区：
文献类型：
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作者：
Duan, Weike;Song, Xiaoming;Li, Ying
MADS-box基因家族是一个古老的、被广泛研究的转录因子家族，它几乎在植物的所有发育过程中发挥作用。关于MADS-box家族在不同植物中的表达已有不少报道，但对白菜MADS-box转录因子家族的系统研究还很少。本研究从大白菜全基因组中鉴定了160个MADS-box转录因子，并与其他21种代表性植物的MADS-box转录因子进行了比较。对这22个物种的MADS蛋白的详细列表进行了排序。BrMADS基因与拟南芥和水稻同源基因的系统发育分析表明，BrMADS基因分为I类(Mα、Mβ、M Gamma)和II类(MIKCC、MIKC*)，MIKCC蛋白进一步分为13个亚家族。大白菜类型II组有95个成员，是拟南芥类型II组的两倍，这表明大白菜类型II基因比类型I基因保留得更频繁。最后，RNA-seq转录组数据和实时定量聚合酶链式反应分析表明，BrMADS基因以与拟南芥相似的组织特异性方式表达。有趣的是，许多BrMIKC基因对不同的非生物胁迫处理表现出反应，这表明这些过程中的一些基因也有功能。综上所述，白菜MADS-box家族的特征将有助于选择合适的候选基因，并进一步促进大白菜的功能研究。
The MADS-box gene family is an ancient and well-studied transcription factor family that functions in almost every developmental process in plants. There are a number of reports about the MADS-box family in different plant species, but systematic analysis of the MADS-box transcription factor family in Brassica rapa (Chinese cabbage) is still lacking. In this study, 160 MADS-box transcription factors were identified from the entire Chinese cabbage genome and compared with the MADS-box factors from 21 other representative plant species. A detailed list of MADS proteins from these 22 species was sorted. Phylogenetic analysis of the BrMADS genes, together with their Arabidopsis and rice counterparts, showed that the BrMADS genes were categorised into type I (M alpha, M beta, M gamma) and type II (MIKCC, MIKC*) groups, and the MIKCC proteins were further divided into 13 subfamilies. The Chinese cabbage type II group has 95 members, which is twice as much as the Arabidopsis type II group, indicating that the Chinese cabbage type II genes have been retained more frequently than the type I genes. Finally, RNA-seq transcriptome data and quantitative real-time PCR analysis revealed that BrMADS genes are expressed in a tissue-specific manner similar to Arabidopsis. Interestingly, a number of BrMIKC genes showed responses to different abiotic stress treatments, suggesting a function for some of the genes in these processes as well. Taken together, the characterization of the B. rapa MADS-box family presented here, will certainly help in the selection of appropriate candidate genes and further facilitate functional studies in Chinese cabbage.