Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour

Abstract Background: CCCH Zinc finger ( Znf ) transcription factors ( TF ), as a novel type Znf genes, regulate genes expression by binding on their mRNA and play important roles in plant abiotic stress, growth and development. However, no overall genome-wide analysis or expression profiling of CCCH ( C3H ) gene family in Dimocarpous longan , especially during the early stages of somatic embryo in longan has been studied. Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia,and longan embryogenesis is the main factor affecting fruit quality and yield. Results: In this study, a comprehensive analysis of longan C3H （ DlC3H ）gene family was carried out. 49 DlC3H genes were identified from longan genome database,which divided into 3 clades. Besides, genes characteristics, phylogenetic tree, gene structure, motif composition were comprehensively analyzed. The analysis of alternative splicing events (AS) suggested that AS events of DlC3H genes were related to longan non-embryonic and embryonic callus transformation. Promoter analysis indicted that most of DlC3H genes included cis -elements associated with hormones and stress response. Quantitative real-time PCR analysis indicated that 26 DlC3Hs ,which possess MeJA and ABA responsive cis -elements, showed different expression patterns and may involved into ABA and MeJA signaling pathway. The expression profiles of 17 DlC3Hs were performed in four stages of longan, the results showed that only DlC3H01/07/14/16/38 was consistent with the data in the transcriptome. DlC3H 07/14/16/36/49 were highly expressed in EC and only DlC3H 04/38 was in GE , suggesting that they have different functions in embryonic development. Finally, sRNAs were verified involved into regulating 6 DlC3Hs . Conclusion: This study provides the first systematic analysis of CCCH protein in longan somatic embryo. Particularly, CCCH genes may be involved in hormone and stress respond, and somatic embryogenesis. Our results presented here may provide a insight into the characteristics and functions of this family in somatic embryogenesis.

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Genome-wide analysis and expression characterization of zinc finger homeodomain (ZHD) family genes responsed to different abiotic stresses and hormonal treatments in grape (Vitis vinifera L.)

10.21203/rs.3.rs-29270/v1 ◽

2020 ◽

Author(s):

Guojie Nai ◽

Juan Mao ◽

Shixiong Lu ◽

Yanmei Li ◽

Zonghuan Ma ◽

...

Keyword(s):

Gene Family ◽

Zinc Finger ◽

Defense Mechanisms ◽

Treatment Time ◽

Expression Profiles ◽

Vitis Vinifera L ◽

Genome Wide Analysis ◽

Genome Wide ◽

Expression Characterization

Abstract Background Zinc finger homeodomain (ZHD) proteins transcription factors (TFs) family occupy a crucial role in regulating plant growth and development. The ZHD TFs family had been studied in diverse organisms such as humans, Drosophila, nematode worms and plants. Especially in plants there is an extensive exploration involved in photosynthesis, defense mechanisms and responses to stress. In this further research, we will provide a better understanding of the ZHD gene family in grape. Results In this study, a total of 12 VvZHD genes were identified from the Grape Genome. The exploration of detailed bioinformatics found that the full length of VvZHD genes ranges from 150 bp (base pair) to 26706 bp, isoelectric points (pIs) were 6.25–9.68, molecular weights (MWs) ranged from 10.28 kilodaltons (KDa) to 97.93 kDa. Also, analysis of phylogenetic evolution showed there existed a common ancestor between Arabidopsis and grape. Ka (Nonsynonymous) / Ks (Synonymous) was lower than 1 and strong collinearity showed there were tandem duplications of genes between Arabidopsis and grape. Codon bias levels of ZHD gene family were relatively higher overall. Gene chip data analysis of cabernet sauvignon seedlings showed VvZHD genes had different expression under different time of different treatments, and with the prolongation of treatment time, most of VvZHD genes were slightly downregulated. The qRT-PCR was carried out under different hormones and stresses to verify expression profiles in grape roots and leaves. Results revealed that most VvZHD genes had higher expressions in roots but lower expressions in leaves. Also, most of the VvZHD gene members were responsed with high expressions after the treatment of ABA, IAA and MeJA in roots. However, VvZHD9, VvZHD11 and VvZHD12 were highly expressed by inducing of PEG in leaves. Conclusions Through genome-wide analysis and expression characterization of ZHD family genes, results showed 12 members had the diversity of function, structure and unique expression characterization under various abiotic stress and hormone treatments. This study will provide us with a newer insight on ZHD gene family of grape and promote to explore the biological functions of ZHD genes in other plants.

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