Deciphering late embryogenesis abundant (LEA) genes in Phaseolus Vulgaris L. through bioinformatics

Year 2024, Volume: 33 Issue: 2, 81 - 108, 25.12.2024

Darya Farhoomand Aksoy , Simay Ezgi Akbulut , İlker Büyük

https://doi.org/10.53447/communc.1440742

Abstract

The Late Embryogenesis Abundant (LEA) gene family is considered vital for plant's ability to survive freezing and desiccation, affecting important developmental and growth processes. These proteins possess notable hydrophilicity and thermal stability, which are essential for preserving cell membrane integrity, forming molecular barriers, aiding in ionic binding, and mitigating oxidative damage during extended periods of exposure to abiotic stress conditions. Although LEA proteins have been extensively studied in numerous plant species, this study represents the initial comprehensive exploration and characterization of LEA proteins in Phaseolus vulgaris L. In this context, the biochemical/physicochemical properties of the LEA family at both the gene and protein level have been deeply characterized and defined using various bioinformatics tools. Through comprehensive bioinformatics analyzes, we identified 80 LEA genes in common bean and phylogenetically categorized their proteins into eight major groups. Investigating gene duplications, we uncovered 28 events, including 24 segmental and 4 tandem duplications, significantly influencing the evolutionary trajectory of this gene family. In silico micro-RNA (miRNA) target analyzes revealed that 21 PvLEA genes were targeted by various miRNAs, with miRN2588 and miR164 being the most prevalent. PvLEA-63 emerged as the most highly expressed gene across tissues, followed by PvLEA-27, PvLEA-35, PvLEA-41, PvLEA-49 and PvLEA-52 genes, demonstrating their ubiquitous expression patterns. Moreover, using publicly available RNAseq data, a comparative expression study of PvLEA genes was carried out, and expression alterations in PvLEA-02, -08, -20, -21, -40, -42, -50 and -51 genes were detected under both salt and drought stress conditions. These results constitute a substantial resource for future researchers interested in unravelling the functional intricacies of PvLEA genes.

Keywords

LEA gene family, Phaseolus vulgaris L., bioinformatics, RNAseq

Thanks

SEA was supported by 100/2000 YÖK (The Council of Higher Education in Türkiye) PhD Scholarship.

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