title: Prediction of Leymus arenarius (L.) antimicrobial peptides based on de novo transcriptome assembly.
abstract: Leymus arenarius is a unique wild growing Poaceae plant exhibiting extreme tolerance to environmental conditions. In this study we for the first time performed whole-transcriptome sequencing of lymegrass seedlings using Illumina platform followed by de novo transcriptome assembly and functional annotation. Our goal was to identify transcripts encoding antimicrobial peptides (AMPs), one of the key components of plant innate immunity. Using the custom software developed for this study that predicted AMPs and classified them into families, we revealed more than 160 putative AMPs in lymegrass seedlings. We classified them into 7 families based on their cysteine motifs and sequence similarity. The families included defensins, thionins, hevein-like peptides, snakins, cyclotide, alfa-hairpinins and LTPs. This is the first communication about the presence of almost all known AMP families in trascriptomic data of a single plant species. Additionally, cysteine-rich peptides that potentially represent novel families of AMPs were revealed. We have confirmed by RT-PCR validation the presence of 30 transcripts encoding selected AMPs in lymegrass seedlings. In summary, the presented method of pAMP prediction developed by us can be applied for relatively fast and simple screening of novel components of plant immunity system and is well suited for whole-transcriptome or genome analysis of uncharacterized plants.
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119991. annslav82@gmail.com.
authors.forename: Anna A
authors.initials: AA
authors.lastname: Slavokhotova
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119991.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Shelenkov
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119991.
authors.forename: Tatyana I
authors.initials: TI
authors.lastname: Odintsova
mesh_terms: D023181:Antimicrobial Cationic Peptides / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000276:immunology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D006109:Poaceae / Q000737:chemistry*; D018749:RNA, Plant / Q000235:genetics*; D059467:Transcriptome
chemical_list: D023181:Antimicrobial Cationic Peptides; D010940:Plant Proteins; D018749:RNA, Plant
keywords: Antimicrobial peptides; Cysteine-rich peptides; De novo transcriptome assembly; Leymus arenarius; Next generation sequencing; Plant immunity