De Novo Transcriptome Analysis of <i>Solanum lycopersicum</i> cv. Super Strain B under Drought Stress

Abstract

Tomato cv. super strain B was widely cultivated in Saudi Arabia under drought stress. Illumina Hiseq-2000 was used to create the transcriptional profile of tomato cultivar super strain B. A total of 98,069 contigs were gathered, with an average length of 766 bp. Most of the genes in the gene ontology (GO) analysis were categorized into molecular function (MF) of ATP binding (1301 genes), metal ion binding (456 genes), protein kinase activity (392 genes), transferase activity (299 genes), Biological process (BP) of DNA-templated genes (366 genes), and regulation of transcription genes (209 genes), while cellular components (CC) of integral component of membrane (436 genes). The most dominant enzymes expressed were transferases (645 sequences). According to the KEGG pathway database, 15,638 transcripts were interpreted in 125 exclusive pathways. The major pathway groups were metabolic pathways (map01100, 315 genes) and biosynthesis of secondary metabolites (map01110, 188 genes). The total number of variants in the twelve chromosomes of super strain B compared with the tomato genome was 5284. The total number of potential SSRs was 5047 in 4806 unigenes. Trinucleotide repeats (3006, 59.5%) were the most found type in the transcriptome. A total of 4541 SNPs and 744 INDELs in tomato super strain B were identified when compared with the tomato genome.

Keywords

• tomato
• super strain B
• assembly
• transcriptome profile
• SSR markers
• phylogeny