title: Defense peptide repertoire of Stellaria media predicted by high throughput next generation sequencing.
abstract: Being perfectly adapted to diverse environments, chickweed (Stellaria media (L.) Vill), a ubiquitous garden weed, grows widely in Europe and North America. As opposed to the model plants, many weeds, and S. media in particular, have been poorly studied, although they are likely to contain promising components of immunity and novel resistance genes. In this study, for the first time RNA-seq analysis of healthy and infected with Fusarium oxysporum chickweed seedlings, as well as de novo transcriptome assembly and annotation, are presented. Note, this research is focused on antimicrobial peptides (AMPs), the major components of plant immune system. Using custom software developed earlier, 145 unique putative AMPs (pAMPs) including defensins, thionins, hevein-like peptides, snakins, alpha-hairpinins, LTPs, and cysteine-rich peptides with novel cysteine motifs were predicted. Furthermore, changes in AMP expression profile in response to fungal infection were traced. In addition, the comparison of chickweed AMP repertoire with those of other Caryophyllaceae plants whose transcriptomes are presently available is made. As a result, alpha-hairpinins and hevein-like peptides which display characteristic modular structure appear to be specific AMPs distinguishing S. media from Dianthus caryophyllus, Silene vulgaris, and Silene latifolia. Finally, revealing several AMPs with proven antimicrobial activity gives opportunity to conclude that the presented method of AMP repertoire analysis reveals highly active AMPs playing vital role in plant immunity.
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russian Federation. Electronic address: 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., 119991 Moscow, Russian Federation. Electronic address: fallandar@gmail.com.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Shelenkov
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russian Federation. Electronic address: tatko@hotbox.ru.
authors.forename: Tatyana V
authors.initials: TV
authors.lastname: Korostyleva
authors.affiliation: Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russian Federation. Electronic address: rea21@list.ru.
authors.forename: Eugene A
authors.initials: EA
authors.lastname: Rogozhin
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova Str., Moscow 119991, Russian Federation. Electronic address: mnv-4529264@yandex.ru.
authors.forename: Nataliya V
authors.initials: NV
authors.lastname: Melnikova
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova Str., Moscow 119991, Russian Federation. Electronic address: rhizamoeba@mail.ru.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Kudryavtseva
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., 119991 Moscow, Russian Federation. Electronic address: odintsova2005@rambler.ru.
authors.forename: Tatyana I
authors.initials: TI
authors.lastname: Odintsova
mesh_terms: D023181:Antimicrobial Cationic Peptides / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D057865:Plant Immunity; D010940:Plant Proteins / Q000378:metabolism; D029752:Stellaria / Q000378:metabolism*
chemical_list: D023181:Antimicrobial Cationic Peptides; D010940:Plant Proteins
keywords: AMP prediction; Antimicrobial peptides; Chickweed; RNA-seq; Stellaria media; Weeds