Prediction of Leymus arenarius (L.) antimicrobial peptides based on de novo transcriptome assembly

• Published in: Plant molecular biology 2015-10, Vol.89 (3), p.203-214
• Main Authors: Slavokhotova, Anna A, Shelenkov, Andrey A, Odintsova, Tatyana I
• Format: Article
• Language: English
• Subjects: Antimicrobial agents; Antimicrobial Cationic Peptides - genetics; Antimicrobial Cationic Peptides - metabolism; antimicrobial peptides; Biochemistry; Biomedical and Life Sciences; computer software; cysteine; Environmental conditions; environmental factors; Gene Expression Regulation, Plant - immunology; Genomics; innate immunity; Leymus arenarius; Life Sciences; Peptides; Plant biology; Plant Pathology; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Sciences; Plant species; Plant tolerance; Poaceae; Poaceae - chemistry; prediction; reverse transcriptase polymerase chain reaction; RNA, Plant - genetics; screening; Seedlings; sequence homology; Transcriptome
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-015-0346-6

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.