The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass ( Pennisetum purpureum )

Pennisetum purpureum belongs to the Pennisetum Rich genus in the family Poaceae. It is widely grown in subtropical and tropical regions as one of the most economically important cereal crops. Despite its importance, there is limited genomic data available for P. purpureum , which restricts genetic and breeding studies in this species. In the present study, the transcriptome of P. purpureum was assembled de novo and used to characterize two important P. purpureum cultivars: P. purpureum Schumab cv. Purple and P. purpureum cv. Mott. After assembly, a total of 197,466 unigenes were obtained for ‘Purple’ and ‘Mott’ and 103,454 of these unigenes were successfully annotated. From ‘Purple’ and ‘Mott,’ 214,648 SNPs and 21,213 EST-SSRs were identified in 40,259 unigenes and 18,587 unigenes respectively. Moreover, 50 EST-SSR primers and 6 SNP primers were designed to validate the identified markers. The transcriptomic data of present study from the two P. purpureum cultivars provides an abundant amount of available genomic information for Pennisetum . In addition, the identified SNPs and EST-SSRs will facilitate genetic and molecular studies within the Pennisetum genus.