De Novo Assembly and Characterization of Developing Spikes Transcriptome of Finger Millet (Eleusine coracana): a Minor Crop Having Nutraceutical Properties

Abstract

Finger millet (Eleusine coracana), a minor crop, is a rich source of micronutrients especially calcium and protein. In the present study, developing spikes transcriptome of two finger millet genotypes differing in grain calcium content was sequenced using Illumina HiSeq 2000 Genome analyser. A total of 72.44 and 64.84 million reads of high and low grain calcium genotype were assembled using Trinity into a non-redundant set of 120,130 and 109,218 transcripts (≥200 bp). The average lengths of transcripts were 921 and 789 bp and N50 lengths of 1,450 and 1,191 bp with coverage of 60,911.1 and 59,969.9 FPKM, respectively. At the protein level, 74.32 and 75.39 % finger millet transcripts showed significant similarity with the proteins of rice followed by sorghum. A total of 44,255 (36.8 %) and 43,780 (40 %) transcripts were assigned to 106 gene ontology (GO) terms for three main categories: biological function, cellular component and molecular function. Further, functional characterization of transcripts led to the identification of nutritionally important genes encoding calcium transporters and seed storage proteins. In addition, simple sequence repeat (SSR) motifs in the transcripts were also identified. The transcriptome data generated here provides a rich resource for discovery of genes expressed throughout the spike development and development of functional molecular markers.