Using bioinformatic tools to identify new Methylketone Synthase 2 (MKS2) genes in the currant tomato Solanum pimpinellifolium
Keywords:Solanum pimpinellifolium, DNA barcoding, methylketone synthase 2 (MKS2).
2-Methylketone is the organic compound containing a ketone functionality on the second carbon. This group of compounds has been known for their widespread applications in plant protection, fragrance and flavor industry, and biofuel production. Previously, two cDNAs encoding two proteins necessary for methylketone biosynthesis in the wild tomato species Solanum habrochaites subsp. glabratum were identified and designated methylketone synthase 1 (ShMKS1) and methylketone synthase 2 (ShMKS2). In searching of new MKS2 variants that are capable of using substrates of different chain lengths or degree of unsaturation, we used ShMKS2 as a query sequence for TBLASTN searches against the currant tomato (Solanum pimpinellifolium) genome. With the support of other bioinformatics tools for gene prediction, we identified three homologous genes of ShMKS2 on four contigs (contig 3697822, 6568413, 6704221, and 6708991) found in the genomic database of Solanum pimpinellifolium. Three genes encoded proteins with more than 65% identity to previously reported ShMKS2 and more than 98% identity to SlMKS2s; we named these genes as SppMKS2-1, SppMKS2-2, and SppMKS2-3. All three of these Solanum pimpinellifolium MKS2 genes had five exons and four introns (whose positions are conserved in comparison with the exon and intron positions in the homologous S. lycopersicum genes). The protein sequences of the MKS2 homologs from three Solanum species were compared and a phylogenetic tree was constructed.