Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum

Zahra Hajibarat; Abbas Saidi; Mehrshad Zeinalabedini; Ahmad Mosuapour Gorji; Mohammad Reza Ghaffari; Vahid Shariati; Rahim Ahmadvand

doi:10.1186/s43141-022-00306-7

Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum

J Genet Eng Biotechnol. 2022 Feb 11;20(1):25. doi: 10.1186/s43141-022-00306-7.

Authors

Zahra Hajibarat¹, Abbas Saidi², Mehrshad Zeinalabedini^{3

4}, Ahmad Mosuapour Gorji⁵, Mohammad Reza Ghaffari^{3

4}, Vahid Shariati⁶, Rahim Ahmadvand⁵

Affiliations

¹ Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
² Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. abbas.saidi@gmail.com.
³ Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
⁴ Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
⁵ Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
⁶ NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

Abstract

Background: The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes.

Results: Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. The number of exons in U-box genes ranged from one to sixteen. For most U-box genes, the exon-intron compositions and conserved motifs composition in most proteins in each group were similar. The intron-exon patterns and the composition of conserved motifs validated the U-box genes phylogenetic classification. Based on the results of genome distribution, StU-box genes were distributed unevenly on the 12 S. tuberosum chromosomes. The results showed that gene duplication may possess a significant role in genome expansion of S. tuberosum. Furthermore, genome evolution of S. tuberosum was surveyed using identification of orthologous and paralogous. We identified 40 orthologous gene pairs between S. tuberosum with Solanum lycopersicum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Zea maize, Coriaria mytifolia, and Arabidopsis thaliana as well as eight duplicated genes (paralogous) in S. tuberosum. StU-box 51 gene is one of the important gene among other StU-boxes in S. tuberosum under drought stress which was expressed in tuber and leaf under drought stress. Furthermore, StU-box 51 gene has the highest expression levels in four tissue-specific (stem, root, leaf, and tuber) in potato as well as it had the highest number of TFBS in promoter region. Based on our results, StU-box 51 can introduce to researcher to utilize in breeding program and genetic engineering in potato.

Conclusions: The results of this survey will be useful for further investigation of the probable role and molecular mechanisms of U-box genes in response to different stresses.

Keywords: Phylogenetic; Solanum tuberosum; TFBS; U-box gene.