In Silico Identification of Gene Families Encoding Cysteine-Rich Peptides in Solanum lycopersicum L.

Abstract

Plant cysteine-rich peptides (CRP) play a key role in protection of plants from pathogens and abiotic stress, in symbiosis with bacteria, and in plant development and reproduction. The composition and role of CRPs in tomato Solanum lycopersicum, one of the most important vegetable, has not been studied so far. In this paper, using two approaches, hidden Markov models and regular expressions, in silico identification of tomato CRP families was performed. A bioinformatic analysis of NCBI databases revealed 191 CRP precursors. The peptides found belong to the families of antimicrobial and signaling peptides. Among the antimicrobial peptides, defensins and defensin-like peptides, nonspecific lipid-transfer proteins, thionins, snakins, and hevein- and knottin-like peptides were found. Among signaling peptides, the peptides belonging to the RALF, Ole e 1, Ole e 6, and MEG families were discovered. In addition, peptides with new cysteine motifs were identified. All discovered CRPs are synthesized as pre- or preproproteins. The predicted mature peptides were characterized by cysteine motifs, antimicrobial activity, and domain structure. Thus, for the first time, using bioinformatic approaches, systemic data on the arsenal of CRPs in the tomato genome were obtained, which creates a basis for further functional studies of these peptides and their subsequent use in agriculture to develop new strategies for increasing tomato pathogen resistance, as well as in medicine to create next-generation drugs.

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Funding

This study was supported by the Russian Science Foundation (grant no. 16-16-00032).

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Correspondence to T. I. Odintsova.

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Istomina, E.A., Slezina, M.P., Kovtun, A.S. et al. In Silico Identification of Gene Families Encoding Cysteine-Rich Peptides in Solanum lycopersicum L.. Russ J Genet 56, 572–579 (2020). https://doi.org/10.1134/S1022795420050063

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Keywords:

  • plant immunity
  • tomato Solanum lycopersicum
  • cysteine-rich peptides
  • cysteine motifs
  • antimicrobial peptides
  • signaling peptides
  • regular expressions
  • hidden Markov models