Characterization of the global transcriptome using Illumina sequencing and novel microsatellite marker information in seashore paspalum

Abstract

Seashore paspalum (Paspalum vaginatum O. Swartz) is a halophytic warm-season perennial grass, which plays an important role in protection of environment. However, very limited transcriptomic and genomic information are currently available for seashore paspalum. In this study, the seashore paspalum transcriptome were sequenced using Illumina paired-end sequencing technology. In total, 32,603 unigenes with an average length of 970 bp were obtained by de novo assembly. Of the unigenes, 25,411 unigenes (77.94 %) had significant similarity with known proteins in the NCBI non-redundant protein and Swiss-Prot databases. Of these annotated unigenes, 20,962 and 10,620 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 4,699 unigenes were mapped into 118 Kyoto Encyclopedia of Genes and Genomes pathways. In addition, 3,010 potential simple sequence repeats (SSRs) were predicted for microsatellite analyse. Tri-nucleotide was the dominant repeat (1,583, 52.58 %), followed by di-nucleotide (975, 32.39 %) and tetra-nucleotide (217, 7.21 %). Fifty SSR sites were randomly selected for validation and development of EST–SSR markers. This study provided the global sequence data for seashore paspalum and demonstrated that the Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development.