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Plant Science Today (PST)

Research Articles

Early Access

Identification and annotation of Tm-1 gene in tomato plant

DOI
https://doi.org/10.14719/pst.14489
Submitted
10 March 2026
Published
02-07-2026
Versions

Abstract

This paper reports for genome level analysis of Tm-1 gene which provides resistance against various Tobamo viruses in tomato plant by in silico approach. The Tm-1 gene is present in chromosome no. 2 that is derived from the Solanum habrochaites and halts the virus multiplication. Hidden Markov Model (HMM) were used to search the tomato protein sequences which includes specific domain. Existence of Tm-1 isoform X1 protein domains was verified using Pfam and Batch CDD-search. Many sequences of the Tm-1 isoform X1 protein were obtained from the NCBI. The physiochemical properties and subcellular localisation of Tm-1 isoform X1 protein is determined with the help of web-based applications i.e. EXPASY (http://www.expasy.org/)and Deep LOC 2.0. The instability index shows that every sequence is a stable protein. The subcellular localisation prediction shows that majority of Tm-1 proteins found inside cells, in cytoplasm and peroxisome. MEGA 11 software was used, the Tm-1 protein was divided into discrete clades using a 500-replicate bootstrap test and phylogenetic tree topology with the help of maximum likelihood approach. By Plant CARE database various cis- elements were predicted. The length of amino acids in Tm-1 protein lies between 621 to 869 amino acid with average lengths is 821 AAs. The MW ranged from 79967.45Da to 85518.51Da, while the pI ranged from 5.29 to 6.24. According to the GRAVY test for hydropathicity, SolyTm-1-58, SolyTm-1-61, SolyTm-1-63, SolyTm-1-69, SolyTm-1-72, SolyTm-1-75, SolyTm-1-79, SolyTm-1-84, SolyTm-1-83, SolyTm-1-94, SolyTm-1-97 and SolyTm-1-99 are hydrophilic in nature whereas the others were hydrophobic. The instability index's concludes that every sequence is a stable protein. Subcellular localisation prediction, the majority of Tm-1 proteins found inside cells, in cytoplasm and peroxisome.

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