Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis).
Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis).
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DOI：
10.4238/2015.october.5.11
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发表时间：
2015-10
期刊：
影响因子：
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通讯作者：
P. Tao;W. Guo;B. Y. Li;Wenhui Wang;Z. Yue;J. Lei;X. Zhong
中科院分区：
文献类型：
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作者：
P. Tao;W. Guo;B. Y. Li;Wenhui Wang;Z. Yue;J. Lei;X. Zhong
小分子热激蛋白（Small heat shock proteins，sHSPs）是植物正常生长发育和逆境反应，特别是热胁迫反应所必需的。关于大白菜sHSP基因的信息很少，因此我们进行了全基因组分析，以确定该物种的sHSP基因。我们确定了26个非冗余sHSP基因分布在所有染色体上，除了染色体A7，与一个额外的sHSP基因从表达序列标签库中确定。结果表明，大白菜中sHSP基因的含量高于拟南芥。27个sHSP基因可分为11个亚家族。我们在大白菜和拟南芥中鉴定了22组sHSP同线同源基因。此外，在大白菜中还发现了8组旁系同源基因。利用Phyre2蛋白质组学软件对27个白菜sHSPs蛋白质结构进行了模拟，结果表明，27个白菜sHSPs蛋白质均含有多条不同亚家族的保守β链。除过氧化物酶体sHSP基因外，大白菜和拟南芥各亚家族的基因结构基本保守。启动子序列分析表明，大多数sHSP基因含有热激元件或变异体。我们还发现，在大白菜sHSP亚家族的进化过程中发生了偏向性基因丢失。大白菜sHSP基因在长角果和早期子叶胚中的表达丰度最高。因此，在全基因组范围内鉴定和鉴定sHSP基因是大白菜sHSP研究的第一步，也是重要的一步。
Small heat shock proteins (sHSPs) are essential for the plant's normal development and stress responses, especially the heat stress response. The information regarding sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis) is sparse, hence we performed a genome-wide analysis to identify sHSP genes in this species. We identified 26 non-redundant sHSP genes distributed on all chromosomes, except chromosome A7, with one additional sHSP gene identified from an expressed sequence tag library. Chinese cabbage was found to contain more sHSP genes than Arabidopsis. The 27 sHSP genes were classified into 11 subfamilies. We identified 22 groups of sHSP syntenic orthologous genes between Chinese cabbage and Arabidopsis. In addition, eight groups of paralogous genes were uncovered in Chinese cabbage. Protein structures of the 27 Chinese cabbage sHSPs were modeled using Phyre2, which revealed that all of them contain several conserved β strands across different subfamilies. In general, gene structure was conserved within each subfamily between Chinese cabbage and Arabidopsis, except for peroxisome sHSP. Analysis of promoter motifs showed that most sHSP genes contain heat shock elements or variants. We also found that biased gene loss has occurred during the evolution of the sHSP subfamily in Chinese cabbage. Expression analysis indicated that the greatest transcript abundance of most Chinese cabbage sHSP genes was found in siliques and early cotyledon embryos. Thus, genome-wide identification and characterization of sHSP genes is a first and important step in the investigation of sHSPs in Chinese cabbage.