Genome-wide identification and expression analysis of bHLH transcription factor family in response to cold stress in sweet cherry (Prunus avium L.)
Genome-wide identification and expression analysis of bHLH transcription factor family in response to cold stress in sweet cherry (Prunus avium L.)
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甜樱桃 (Prunus avium L.) 冷胁迫反应中 bHLH 转录因子家族的全基因组鉴定和表达分析
DOI：
10.1016/j.scienta.2021.109905
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发表时间：
2021-01-16
影响因子：
4.3
通讯作者：
Qiao, Guang
中科院分区：
文献类型：
--
作者：
Shen, Tianjiao;Wen, Xiaopeng;Qiao, Guang
基本螺旋-环-螺旋（bHLH）家族是植物中最大的转录因子（TF）家族之一，在调节生长、发育和非生物胁迫反应中发挥着至关重要的作用。然而，迄今为止，对甜樱桃（Prunus avium L.）bHLH TF家族的系统分析尚未见报道。本研究在甜樱桃基因组中鉴定出66个bHLH基因，系统发育分析结果表明，根据拟南芥bHLH的分类，这些PavbHLH可分为17个亚科。 60个PavbHLH基因不均匀地分布在8条染色体上，6个PavbHLH基因无法定位到任何染色体。根据 PavbHLH 的氨基酸序列，鉴定出 10 个基序。基序 1 和基序 2 在几乎所有 PavbHLH 蛋白中高度保守。外显子-内部分析表明，属于同一亚家族的蛋白质表现出相似的基因结构。此外，启动子顺式元件和蛋白质相互作用网络预测分析表明，PavbHLH家族的大多数成员参与了响应冷应激的各种过程。半定量逆转录聚合酶链式反应（RT-PCR）结果显示，62个PavbHLH基因在不同低温处理过程中均有不同程度表达，其中约20个PavbHLH基因在4℃和10℃处理初期表达量快速诱导，随后达到峰值并下降，而在16℃时表达量持续上调。结合定量实时PCR结果(qRT-PCR)初步确定PavbHLH1、-18、-28、-60、-61、-65和-66可能参与调节甜樱桃对冷胁迫的反应。本研究为甜樱桃 bHLH 基因家族及其在冷应激中的反应提供了有用的认识。
The basic helix-loop-helix (bHLH) family is one of the largest families of transcription factors (TFs) in plants and plays crucial roles in regulating growth, development and abiotic stress responses. However, systematic analyses of the bHLH TF family in sweet cherry (Prunus avium L.) have not been reported to date. In our study, 66 bHLH genes were identified in the sweet cherry genome, and the result of phylogenetic analysis indicated that these PavbHLHs could be classified into 17 subfamilies according to the classification of bHLHs in Arabidopsis thaliana. Sixty PavbHLH genes were unevenly distributed on 8 chromosomes, and 6 PavbHLH genes could not be mapped to any chromosome. Based on the PavbHLH's amino acid sequences, 10 motifs were identified. Motif 1 and motif 2 were highly conserved among the almost all PavbHLH proteins. Exon-intmn analysis indicated that proteins belonging to same subfamily exhibited a similar gene structure. Furthermore, promoter cis-element and protein interaction network prediction analysis suggested that most members of the PavbHLH family are involved in various processes in responses to cold stress. The results of semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) showed that 62 PavbHLH genes were all expressed to varying degrees during various low-temperature treatments, of which the expression levels of approximately 20 PavbHLHs were rapidly induced in the early stages of 4 and 10 degrees C treatment, reached a peak and decreasing thereafter, while the expression continued to be upregulated at 16 degrees C. Combined with the results of the quantitative real-time PCR (qRT-PCR), it was preliminarily determined that PavbHLH1, -18, -28, -60, -61, -65 and -66 may be involved in regulating the responses to cold stress in sweet cherry. The present study offers useful perception into the sweet cherry bHLH gene family and its responses in cold stress.