Wöhrmann et al. 2015 (Conference Paper) Fosterella

SSR discovery in cDNAs of Fosterella christophii (Pitcairnioideae) using the PacBio third-generation sequencing platform

Author(s):—T. Wöhrmann, B. Huettel, N. Wagner, K. Schubert & K. Weising in Benko-Iseppon, A.M.; Alves, M. & Louzada, R. (2015) An overview and abstracts of the First World Congress on Bromeliaceae Evolution. Rodriguésia 66(2): A1-A66.

Publication:— (2015).

Abstract:—We used the single-molecule real-time (SMRT, Pacific Biosciences) third-generation sequencing system PacBio RS II to generate 1,590 high quality cDNA sequences of one accession of Fosterella christophii. After isoform-level clustering, polishing and trimming of raw data, 971 non-redundant contigs were obtained.These were screened for the presence of microsatellites (simple sequence repeats, SSRs) with motif lengths between one and six bp. Lower thresholds of 15, 7, 6, 5, 4 and 4 repeat units were used to define SSRs of the mono-, di-, tri-, tetra-, penta- and hexanucleotide repeat type, respectively. Based on these criteria, a total of 446 perfect SSRs were identified. Dinucleotide repeats were most abundant (52.9%), followed by trinucleotide(31.6%) and hexanucleotide (6.1%) repeats. Only perfect di- to hexanucleotide repeats were considered as candidates for marker development, resulting in a total of 421 potentially amplifiable SSR loci. Sufficient SSR flanking sequence of appropriate quality and length for primer design was present in 275 contigs, which together contained 335 SSR loci. Similarity searches were conducted on these contigs using Blast2Go software.A total of 20 perfect SSR loci (four di-, eight tri-, two tetra-, three penta- and three hexanucleotide repeats) were selected and tested for marker performance in several populations of the source species as well as for transferability to other Fosterella species. The potential of these markers to cross-amplify and to differentiate between closely related bromeliad species will be discussed.

Keywords:—Transcriptome; Microsatellites; Fosterella.