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Journal of Integrative Agriculture  2022, Vol. 21 Issue (1): 113-130     DOI: 10.1016/S2095-3119(20)63460-8
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour
SU Li-yao*, XIAO Xue-chen*, JIANG Meng-qi, HUANG Shu-qi, XUE Xiao-dong, LI Xue, LAI Zhong-xiong, LIN Yu-ling  
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R.China

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摘要  

CCCHC3H)锌指转录因子(Zinc finger, Znf)是一种新型的Znf基因,其通过绑定于基因的mRNA上调控基因的表达,并在植物生长发育和抗非生物胁迫中发挥重要作用。龙眼是一种具有重要的经济价值热带、亚热带果树。然而,龙眼C3H的基因组信息及功能仍不清楚。本研究对龙眼C3H (DlC3H)基因家族进行了全基因组鉴定及表达分析。从龙眼基因组数据库中共鉴定出分布于3个进化枝中的49DlC3H基因,并对其基因结构、motif组成、系统发育树和潜在功能等方面进行了基因特征分析。可变剪接事件(alternative splicing, AS)分析表明,DlC3H基因AS事件可能参与龙眼非胚性培养物向胚性培养物的转换。启动子分析显示,大多数DlC3H基因包含与激素和胁迫响应相关的顺式作用元件。实时荧光定量PCRqRT-PCR)分析显示,26个具有MeJAABA响应顺式作用元件的DlC3Hs,在ABAMeJA及其内源性抑制剂的作用下表现出不同的表达模式,提示DlC3Hs可能参与了ABAMeJA信号通路。同时,在龙眼非胚性愈伤组织和3个胚胎培养阶段的表达谱显示,17DlC3Hs成员中只有5DlC3Hs的表达模式与转录组数据FPKM相同;DlC3H07/14/16/36/49在胚性愈伤组织中表达较高,而DlC3H04/38在球形胚中表达较高,说明它们在胚胎发育中具有不同的作用。通过改良RLM-RACE验证了DlC3H01/03/05/11/19/39sRNAs调控。本研究首次对龙眼的C3H基因进行了系统分析,特别是C3H基因可能参与激素、胁迫反应以及体细胞胚胎形态建成有关。本试验的初步结果以期为进一步研究龙眼C3H基因家族的特征和功能提供线索。



Abstract  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´ 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.
Keywords:  Dimocarpus longan Lour       CCCH Zinc finger        characteristic identification        expression profile  
Received: 08 June 2020   Accepted: 19 September 2020
Fund: This work was funded by the National Natural Science Foundation of China (31672127 and 31572088), the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University, China (2018S02), the Construction of Plateau Discipline of Fujian Province, China (102/71201801101) and the Project of Fujian Academy of Agricultural Sciences, China (AB2017-4).  
About author:  SU Li-yao, E-mail: 591341454@qq.com; XIAO Xue-chen, E-mail: 1103885400@qq.com; Correspondence LIN Yu-ling, E-mail: buliang84@163.com * These authors contributed equally to this study.

Cite this article: 

SU Li-yao, XIAO Xue-chen, JIANG Meng-qi, HUANG Shu-qi, XUE Xiao-dong, LI Xue, LAI Zhong-xiong, LIN Yu-ling . 2022. Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour. Journal of Integrative Agriculture, 21(1): 113-130 .

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