Genome-wide identification, characterization, and expression analysis of MIPS family genes in legume species

• Published in: BMC genomics 2024-01, Vol.25 (1), p.95-13, Article 95
• Main Authors: Jacob, Feba, Hamid, Rasmieh, Ghorbanzadeh, Zahra, Valsalan, Ravisankar, Ajinath, Lavale Shivaji, Mathew, Deepu
• Format: Article
• Language: English
• Subjects: Alfalfa; Amino acids; Annotations; Antinutritional factor; Arabidopsis; Arachis hypogaea; Beans; Biofortification; Biosynthesis; Cajanus; Cajanus cajan; Cell division; Chromosomes; Cicer; Cicer arietinum; Crops; DNA sequencing; Drought; Evolutionary genetics; Expression analysis; Fabaceae; Gene expression; Gene sequencing; Genes; Genetic aspects; Genetic research; Genome annotation; Genomes; Glycine max; Identification and classification; Inositol-3-phosphate synthase; Inositols; Lablab purpureus; Legumes; Localization; Medicago truncatula; Methods; Mimosaceae; Nitrogen; Nucleotide sequencing; Peptides; Phaseolus; Phaseolus vulgaris; Phosphates; Phylogenetics; Physiological aspects; Phytic acid; Pisum sativum; Plant growth; Proteins; Pulses; Seeds; Stress response; Trifolium pratense; Vegetables; Vigna unguiculata
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09937-7

Evolutionarily conserved in plants, the enzyme D-myo-inositol-3-phosphate synthase (MIPS; EC 5.5.1.4) regulates the initial, rate-limiting reaction in the phytic acid biosynthetic pathway. They are reported to be transcriptional regulators involved in various physiological functions in the plants, growth, and biotic/abiotic stress responses. Even though the genomes of most legumes are fully sequenced and available, an all-inclusive study of the MIPS family members in legumes is still ongoing. We found 24 MIPS genes in ten legumes: Arachis hypogea, Cicer arietinum, Cajanus cajan, Glycine max, Lablab purpureus, Medicago truncatula, Pisum sativum, Phaseolus vulgaris, Trifolium pratense and Vigna unguiculata. The total number of MIPS genes found in each species ranged from two to three. The MIPS genes were classified into five clades based on their evolutionary relationships with Arabidopsis genes. The structural patterns of intron/exon and the protein motifs that were conserved in each gene were highly group-specific. In legumes, MIPS genes were inconsistently distributed across their genomes. A comparison of genomes and gene sequences showed that this family was subjected to purifying selection and the gene expansion in MIPS family in legumes was mainly caused by segmental duplication. Through quantitative PCR, expression patterns of MIPS in response to various abiotic stresses, in the vegetative tissues of various legumes were studied. Expression pattern shows that MIPS genes control the development and differentiation of various organs, and have significant responses to salinity and drought stress. The MIPS genes in the genomes of legumes have been identified, characterized and their expression was analysed. The findings pave way for understanding their molecular functions and evolution, and lead to identify the putative MIPS genes associated with different cell and tissue development.