Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)

Abstract

Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.

Serine Hydroxymethyltransferase (SHMT) Gene Family in Wheat (Triticum aestivum L.): Identification, Evolution, and Expression Analysis

“…Phylogenetic analysis showed that SHMT genes in land plants were classified into four groups: Ia, Ib, IIa, and IIb, which is consistent with previous studies. SHMT genes were also divided into four groups in soybean and tomato [8,12]. However, group IIa members were absent in monocotyledon, e.g., wheat (Figures 1 and 4A), rice, and maize (Zea mays L.), whereas it existed in dicotyledon, e.g., Arabidopsis, soybean, and tomato (Table S1) [8,12], probably due to the absence of chloroplast-targeted SHMTs in monocotyledon [8,24].…”

“…SHMT genes have been identified in different species, such as Arabidopsis (7 members), rice (5 members), soybean (18 members), and tomato (7 members) [7][8][9]12,21]. However, SHMT genes have not been genome-wide-identified in the wheat genome.…”

“…The phylogenetic tree was constructed by the Maximum Likelihood (ML) method with 1000 bootstrap replicates using TBtools software and Evolview online service [13,15]. The amino acid sequences of SHMT in Arabidopsis (AtSHMT), soybean (GmSHMT), and tomato (SlSHMT) were obtained from a previous report [12]. The exon-intron structures were identified by comparing CDS and genomic DNA sequences using TBtools [13].…”

“…SHMT genes have been identified in diverse plants, such as Arabidopsis, rice (Oryza sativa L.), soybean (Glycine max (L.) Merr. ), and tomato (Solanum lycopersicum L.) [7][8][9]12]; however, a genome-wide identification of SHMT genes in wheat has not been performed. In this study, a genome-wide analysis of SHMT genes was performed in wheat to characterize their sequences, evolutionary relationships, expression patterns, and stress tolerance in yeast cells under various abiotic stress treatments.…”

Genome-wide identification and expression analysis of fibrillin (FBN) gene family in tomato (Solanum lycopersicum L.)

“…Three biological replicates and the 2 −ΔΔCT method were used to calculate the relative expression level ( Livak & Schmittgen, 2001 ). The tomato ACTIN gene (Solyc04g011500.3.1) was used as internal reference gene ( Liu et al, 2022 ). The t -test was used to analyze the significance of the difference.…”