De Novo Assembly and Characterization of the Transcriptome and Molecular Discovery in Capsicum Annuum L. R597

Abstract

Pepper (Capsicum spp.) is one of the most economically and agriculturally important vegetable crops on the globe. However, the genomic resources of Pepper (Capsicum spp.) were scarcity, and only a few nucleotide sequences could be obtained in public databases. In this study, we examined transcriptome in C.annuum R597. More than 66million of high quality reads were generated using Illumina paired-end sequencing technology. Approximately 6 Gbp of data were generated, and de novo assembled into 96, 340 unigenes, with an N50 of 989 bp. The average length of unigenes was 651 bp. Based on sequence similarity search with known protein database, 51, 053 (53.0%) showed significant similarity to know proteins in Nr database, and 33, 766 (35.0%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 26, 050 of C.annuum R597 unigenes were assigned to GO term annotation, and 28, 428 were found to have COG classification. In addition, a total of 14, 279 unigenes were assigned to 270 KEGG pathways. Moreover, a total 5, 960 SNPs, 5, 426 SSRs, and 2, 199 InDels were detected as potential molecular markers in pepper. Our study enriches the genomic resources of Pepper (Capsicum spp.) and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs, SNPs and InDels in pepper could server as valuable for studies on the agronomic traits and identification of molecular mechanism such plant resistance.