Transcriptome analysis and SNP/SSR marker information of red pepper variety YCM334 and Taean

Transcriptome analysis is becoming a powerful tool for the identification and characterization of molecular markers, splicing-specific mRNA mutants, and differentially expressed genes. In this study, we present the first comprehensive characterization of the transcriptomes of the mature fruits of two red pepper (Capsicum annuum) accessions, YCM334 and Taean, using the 454 Genome Sequencer (GS)-FLX Titanium System. For YCM334, sequencing runs yielded 121,152 reads (average length = 409 nucleotides), which were assembled into 11,770 contiguous sequences (contigs) and 13,827 singletons. Sequencing runs for Taean yielded 154,088 reads (average length = 395 nucleotides) assembled into 14,200 contigs and 15,135 singletons. Using a BLAST search against the NCBI non-redundant (NR) and UniProt databases with an arbitrary expectation value of E-5, over 10,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme, and were found to distribute in 18 FunCat categories for YCM334 and 17 for Taean. Expression pattern analysis identified 540 Tentative Consensus (TC) sequences that were specifically detected in YCM334. Most of these differential TCs assigned with specific annotations covered 16 FunCat categories, of which 4 were annotated with resistance terms. Polymorphic marker discovery revealed a total of 1265 and 1436 simple sequence repeat (SSR) motifs for YCM334 and Taean, respectively, and a total of 3218 single nucleotide polymorphisms (SNPs) with high confidence. The information generated in this study provides valuable resources for characterization of some important agronomic traits and identification of molecular mechanism such as phytopathogen resistance.

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► Transcriptome information of two red pepper accessions using 454 pyrosequencing.
► YCM334 and Taean were separately resistance and susceptible against Phytophthora capsici.
► Sequence annotation and classification using FunCat scheme.
► Gene expression pattern analysis and resistance-related sequences mining.
► SNP and SSR information discovery to develop polymorphic DNA markers.