title: Massive Analysis of cDNA Ends (MACE) for transcript-based marker design in pea (Pisum sativumL.).
abstract: Aimed at gene-based markers design, we generated and analyzed transcriptome sequencing datasets for six pea (Pisum sativumL.) genetic lines that have not previously been massively genotyped. Five cDNA libraries obtained from nodules or nodulated roots of genetic lines Finale, Frisson, Sparkle, Sprint-2 and NGB1238 were sequenced using a versatile 3'-RNA-seq protocol called MACE (Massive Analysis of cDNA Ends). MACE delivers a single next-generation sequence from the 3'-end of each individual cDNA molecule that precisely quantifies the respective transcripts. Since the contig generated from the 3'-end of the cDNA by assembling all sequences encompasses the highly polymorphic 3'-untranslated region (3'-UTR), MACE efficiently detects single nucleotide variants (SNVs). Mapping MACE reads to the reference nodule transcriptome assembly of the pea line SGE (Transcriptome Shotgun Assembly GDTM00000000.1) resulted in characterization of over 34,000 polymorphic sites in more than 9700 contigs. Several of these SNVs were located within recognition sequences of restriction endonucleases which allowed the design of co-dominant CAPS markers for the particular transcript. Cleaned reads of sequenced libraries are available from European Nucleotide Archive (http://www.ebi.ac.uk/) under accessions PRJEB18101, PRJEB18102, PRJEB18103, PRJEB18104, PRJEB17691.
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, 196608 Saint-Petersburg - Pushkin, Russia.
authors.forename: Aleksandr
authors.initials: A
authors.lastname: Zhernakov
authors.affiliation: GenXPro GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Rotter
authors.affiliation: GenXPro GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Winter
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, 196608 Saint-Petersburg - Pushkin, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Borisov
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, 196608 Saint-Petersburg - Pushkin, Russia; Saint-Petersburg State University, Universitetskaya embankment, 7/9, 199034 Saint-Petersburg, Russia.
authors.forename: Igor
authors.initials: I
authors.lastname: Tikhonovich
authors.affiliation: All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, 196608 Saint-Petersburg - Pushkin, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Zhukov
keywords: CAPS markers; Gene-based markers; MACE (Massive Analysis of cDNA Ends); Pisum sativum L.; SNVs; Transcriptome sequencing