The pyruvate kinase gene family in soybean: genome-wide investigation and expression profiling

Abstract

Pyruvate kinase (PK) catalyzes the last glycolytic reaction to produce ATP and pyruvate, providing energy and intermediates for numerous biological processes. While the functions of Arabidopsis and rice PKs have been reported, little is known about this gene family in soybean (Glycine max). Herein, an in-silico genome wide scan revealed the presence of 21 PK genes in soybean, which were distributed in 11 chromosomes, and were classified into cytosolic and plastidial subfamilies (PKc and PKp) based on phylogenetic analysis. Collinearity analysis indicated that gene duplication contributed largely to the expansion of GmPK gene family and further Ka/Ks calculation suggested that this family experienced strong purifying selection during evolution. All GmPKs contain the conserved PK domain but the two subfamilies show distinct conserved motif composition and exon–intron organization. Gene ontology analysis and subcellular localization implied that seven GmPKs might function in plastid, while the rest function in cytoplasm. According to expression profile analysis, different GmPKcs were found highly expressed in seed, roots, or leaves, but GmPKps were mainly expressed in soybean seed. Abiotic stress responsive cis-acting elements were discovered on the promoters of GmPKs. Correspondingly, different GmPKs were found responsive to abiotic stresses, especially submergence stress. All these findings facilitated our understanding of soybean PK gene family, and established a foundation for further studies on the biological functions of GmPKs.