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

Content Provider	Springer Nature Link
Author	Slavokhotova, Anna A. Shelenkov, Andrey A. Odintsova, Tatyana I.
Copyright Year	2015
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.
Starting Page	203
Ending Page	214
Page Count	12
File Format	PDF
ISSN	01674412
Journal	Plant Molecular Biology
Volume Number	89
Issue Number	3
e-ISSN	15735028
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-09-14
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Antimicrobial peptides Cysteine-rich peptides Next generation sequencing Leymus arenarius Plant immunity De novo transcriptome assembly Plant Sciences Biochemistry Plant Pathology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Medicine Agronomy and Crop Science

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