Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour
Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour
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DOI：
10.1016/s2095-3119(20)63460-8
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发表时间：
2022-01-04
影响因子：
4.8
通讯作者：
Lin Yu-ling
中科院分区：
文献类型：
--
作者：
Su Li-yao;Xiao Xue-chen;Lin Yu-ling
CCCH(C3H)锌指转录因子作为一种新型的锌指基因，通过与基因的mRNAs结合来调控基因的表达，在植物生长发育和非生物胁迫抗性中发挥着重要作用。龙眼又称龙眼，是东南亚重要的热带/亚热带果树。然而，关于C3H的基因组信息及其在龙眼中的功能仍不清楚。本研究对龙眼C3H(DlC3H)基因家族进行了全面分析。从龙眼基因组数据库中鉴定出三个分支中的49个DlC3H基因。从基因结构、基序组成、系统发育树和潜在功能等方面分析了这些基因的特征。对选择性剪接(AS)事件的分析表明，DlC3H基因中的AS事件与龙眼非胚性培养向胚性培养的转化有关。启动子分析表明，大多数DlC3H基因含有与激素和胁迫反应相关的顺式作用元件。实时定量聚合酶链式反应(qRT-PCR)分析表明，49个DlC3H中有26个具有茉莉酸甲酯(MeJA)和脱落酸(ABA)顺式作用元件，在ABA、MeJA及其内源抑制剂处理下表现出不同的表达模式，提示DlC3H可能参与了ABA和MeJA信号转导途径。49个DlC3H中的17个在非胚性愈伤组织和胚胎培养的3个组织中的表达谱显示，17个DlC3H中只有5个在转录组数据中具有与FPKM相同的表达趋势，DlC3H07/14/16/36/49在胚性愈伤组织中的表达水平较高，DlC3H04/38在球形胚胎中的表达水平较高，表明它们在胚胎发育中具有不同的功能。进一步，我们验证了DlC3H01/03/05/11/19/39是通过改进的5个急性口音RLM-RACE方法受sRNA调控的。本研究首次对龙眼C3H基因进行了系统分析，发现C3H基因可能参与了激素和胁迫反应以及体细胞胚胎的发生。我们的初步调查可能会为进一步研究龙眼中该科的特征和功能提供线索。
CCCH (C3H) Zinc finger (Znf) transcription factors (TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance. Longan (Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. However, genomic information on C3H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3H (DlC3H) gene family was carried out. A total of 49 DlC3H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure, motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing (AS) events suggested that AS events in DlC3H genes were related to the transformation from longan non-embryonic to embryonic cultures. Promoter analysis indicated that most of the DlC3H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that 26 of the 49 DlC3Hs, which possess methyl jasmonate (MeJA) and abscisic acid (ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3Hs had the same expression trends as the FPKM trends in transcriptome data; the expression levels of DlC3H07/14/16/36/49 in embryogenic callus and DlC3H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3H01/03/05/11/19/39 were regulated by sRNAs by a modified 5 acute accent RLM-RACE method. This study provides the first systematic analysis of C3H genes in longan, and found that C3H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.