title: De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome.
abstract: The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from "Nodules" and "Root Tips" assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The "Nodules" assembly was compared with the "Root Tips" assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, Russia.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Zhukov
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, Russia.
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Zhernakov
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, Russia.
authors.forename: Olga A
authors.initials: OA
authors.lastname: Kulaeva
authors.affiliation: Institute of Cytology & Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia.
authors.forename: Nikita I
authors.initials: NI
authors.lastname: Ershov
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, Russia.
authors.forename: Alexey Y
authors.initials: AY
authors.lastname: Borisov
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, Russia ; Saint Petersburg State University, Universitetskaya Embankment 7-9, Saint Petersburg 199034, Russia.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Tikhonovich