De novo assembly of the transcriptome of Neottopteris nidus using Illumina paired-end sequencing and development of EST-SSR markers

Neottopteris nidus is an economically important foliage plant. However, the EST sequence resources available for N. nidus are still very limited. In this study, we present the first transcriptome analysis of N. nidus using the Illumina sequencing technology. More than 53 million reads were generated in transcriptome analysis, and de novo assembly generated 41,173 unigenes with an average length of 969 bp. The similarity search indicated that 24,801 unigenes (60.23 %) had significant similarity with proteins in the NR and Swiss-Prot protein databases. Among these annotated unigenes, 15,683 and 7942 unigenes were assigned to gene ontology categories and Clusters of Orthologous Groups, respectively. A total of 5548 unigenes were mapped into 116 pathways by the Kyoto Encyclopedia of Genes and Genomes Pathway database. Some abundant transcripts related to photomorphogenesis and development, including chlorophyll a–b-binding protein, phototropin, amino acid transporter, ATP-binding protein, expansin, and ribosomal protein, were identified in the N. nidus transcriptome. In total, 5792 potential EST-SSRs were identified among the unigenes. The most abundant type of repeat was dinucleotide (3836, 66.24 %), followed by trinucleotide (1575, 27.19 %) and tetranucleotide (207, 3.57 %) repeats. The dominant repeat motif was CT/GA (1229, 21.22 %), followed by AG/TC (905, 15.63 %), CA/GT (504, 11.32 %), and AC/TG (339, 8.70 %). In addition, a total of 100 potential marker sites were selected to validate the assembly quality and develop EST-SSR markers. This study generated a substantial fraction of N. nidus transcriptome sequences, which were very useful resources for gene discovery and molecular marker development.