Genome-wide in silico characterization and expression analysis of Thaumatin-like gene family during salt and drought stress in watermelon

Abstract

Watermelon is the important eudicot of cucurbitaceous family which contributes 7% of the vegetable production worldwide. Thaumatin-like protein (TLP) is the well known sweetest protein which plays important role to protect the plants against various environmental factors. The TLPs were identified and characterized in various plant species and animal systems. However, the detailed description of TLPs is not known in watermelon till date. Therefore, in the present investigation, we explored the watermelon genome and identified 31 TLP gene families which were designated as Citrullus lanatus TLP genes (ClaTLPs). ClaTLP genes were randomly distributed on some chromosomes rather than covering of whole genome of watermelon. Based on exon-intron distribution, the ClaTLP gene families were clustered into 3 groups. Out of 31 ClaTLPs, twenty five ClaTLP genes exhibited conserved 16 Cys residues whereas 6 ClaTLP genes represented less than 16 Cys.The phylogenetic analysis of ClaTLP proteins classified them into 4 major groups. To depict the possible biological function of the ClaTLP genes, one hundred and one cis-regulatory elements in promoter region of the ClaTLP genes were predicted and analyzed. The in silico expression analysis of ClaTLP genes revealed the relative expression of ClaTLP genes across the tissues. Tissue-specific ESTs count corresponding to the ClaTLP genes revealed the root-specific expression by majority of the genes. The semi-qRT-PCR analysis of the ClaTLP genes during salt stress in watermelon showed the differential expression of theClaTLP gene family. During salt stress, twelve genes (ClaTLP02, ClaTLP06, ClaTLP07, ClaTLP09, ClaTLP15, ClaTLP16, ClaTLP21, ClaTLP22, ClaTLP23, ClaTLP24, ClaTLP26 and ClaTLP29) were gradually up-regulated at 0, 100 and 200mM salt treatment. Similarly, six ClaTLP genes (ClaTLP4, ClaTLP5, ClaTLP6, ClaTLP7, ClaTLP10 and ClaTLP14) revealed a gradual up-regulation during drought stress in watermelon.The identified ClaTLP genes can be utilized for fundamental and applied research in watermelon.