Genome-wide analysis, annotation and expression profile analysis of VDAC gene family in Rosa chinensis

Document Type : scientific research article

Authors

1 M.Sc. Student, Dept. of Horticultural Science and Landscape, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Gorgan, Iran

2 Corresponding Author, Associate Prof., Dept. of Horticultural Science and Landscape, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Gorgan, Iran.

3 Assistant Prof., Dept. of Horticultural Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China

Abstract

Abstract
Background and objectives:
Rosa chinensis is an everflowering diploid plant originated from China. The diploid level of the cell in these plant facilities its breeding program. The objectives of the present work were to analyse the phylogenetic relationship, promoter analysis, prediction of protein interaction and structure. Moreover RNA seq analysis of 7 R. chinensis VDAC genes has also been conducted.

Material and methods:
VDAC homologues were detected from https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/ via BLAST search program. Two pair of primers was design to isolate RcVDAC1 and 2 from R. chinensis cDNA. The PCR amplified segments inserted into PENTER vector and cloned in E-Coli cell and subsequently sequenced. 1500 pb of upstream of seven RcVDAC genes were isolated from lipm-browsers for analyzing by PlantCare software. Phylogenetic tree was laied out by OMEGA 7.0 and all the inputs collected from NCBI and Tair websites. RcVDACs protein interaction predicted via STRING website. RcVDACs proteins structure prediction laied out via Pymole software and R. chinensis transcriptome analysed through RNAseq data by Mev. software.
Results:
Isolation and sequencing results of RcVDAC1-2 indicated that their sequence is as exact as Rosa data bank information. The separation of the RcVDACs in different cluster by phylogenetic tree suggests the formation of highly divergent paralogues in RcVDACs. Research results gained by PlantCare showed different light, PGR and stress responsive cis-regulatory element in different RcVDACs promoter region. The presence of high amount of transcription factor binding site related to MYB and MYC TF as well as having regions responsive to phytohormones such as jasmonic acid, abscisic acids, auxin, gibberellic acid and also drought and cold stress likely suggesting the regulatory role of RcVAC genes under abiotic stress. In fact the results gained by RNAseq data confirmed the regulatory role that RcVDAC2 and 5 may play during biotic and abiotic stress condition.
Conclusion:
Generally, the analysis of transcriptome by RNAseq, promoter analysis, prediction of 7 of RcVDAC proteins, and their interacting protein and phylogenetic study shed light on the presence of different RcVDAC orthologes and indicates this difference on protein structure; govern their different biological function in different developmental stage and different stress condition. In fact the results gained by RNAseq data confirmed the regulatory role that RcVDAC2 and 5 may play during biotic and abiotic stress condition. In fact the results gained by RNAseq data confirmed the regulatory role that RcVDAC2 and 5 may play during biotic and abiotic stress condition.

Key words: Bioinformatics, cDNA, PENTER, BLAST, PlantCare, RNA seq

Keywords

References

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Journal of Plant Production Research
Volume 29, Issue 1
June 2022
Pages 111-132

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