Molecular Biology Reports

, Volume 39, Issue 3, pp 3327–3335

Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68

Article

Abstract

Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.

Keywords

Transcriptome Red pepper (Capsicum annuumTF68 FunCat SSR SNP 

Supplementary material

11033_2011_1102_MOESM1_ESM.xls (11.4 mb)
Supplementary material 1: Annotation and FunCat results of all contigs and singletons in Capsicum annuum L. TF68 by BLAST against UniProt (XLS 11.632 kb)
11033_2011_1102_MOESM2_ESM.xls (892 kb)
Supplementary material 2: SNP discovery by mapping Capsicum annuum L. TF68 reads to NCBI Bukang cDNA library (XLS 892 kb)
11033_2011_1102_MOESM3_ESM.xls (219 kb)
Supplementary material 3: SSR discovery and primer information revealed by ARGOS program from Capsicum annuum L. TF68 contigs (XLS 219 kb)

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Plant Resources, College of Industrial SciencesKongju National UniversityYesanRepublic of Korea
  2. 2.Vegetable Research DivisionNational Institute of Horticultural & Herbal Science, Rural Development AdministrationSuwonKorea
  3. 3.Legume Bio-Resource Center of Green Manure (LBRCGM)Kongju National UniversityYesanRepublic of Korea

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