Genomic resources such as ESTs, molecular markers and linkage maps are essential for crop improvement. However, these resources are still limited in important legumes such as lentil (Lens culinaris Medik.), which is valued world wide as a rich source of dietary protein. In this study, the de novo transcriptome assembly of 119 855 798 short reads, generated by Illumina paired-end sequencing, was performed using various assembly programs. This resulted in 42 196 nonredundant high-quality transcripts of average length 810 bases, N50 value of 1 432 and an average expression per transcript of 26.21 rpkm reads per kilobase per million(RPKM). Similarity search with the unigenes and protein sequences of other plants resulted in maximum similarity with soybean. A total of 20 009 nonredundant transcripts showed similarity with the UniProtKB database and of these, 18 064 transcripts were grouped into three main GO categories, that is, biological process (15 126), molecular function (15 505) and cellular component (9 434). Annotated transcripts were mapped to 289 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 8 893 transcripts were classified into 24 functional categories based on Cluster of Orthologous Groups (COG) of proteins. Mining the data set for the presence of SSRs resulted in 8 722 SSRs with a frequency occurrence of one SSR per 3.92 kb. From these, 5 673 SSR primer pairs were designed, and a subset of these were utilized for diversity analysis. This study, which provides a large data set of annotated transcripts and gene-based SSR markers, would serve as a foundation for various applications in lentil breeding and genetics.
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