De novo transcriptome analysis of Fraxinus velutina using Illumina platform and development of EST-SSR markers

Abstract

To facilitate functional genomic analysis and molecular breeding of velvet ash (Fraxinus velutina Torr), the de novo sequencing was carried out by Illumina sequencing technology. The cDNA samples were prepared from eleven different tissues of velvet ash and sequenced by using the Illumina genome analyzer. Subsequently, de novo assemebly, functional annotation databases, and the screening of expressed sequence tag-simple sequence repeats (EST-SSRs) were performed by comparing with corresponding databases using BLASTx and software tools. We obtained 51 698 unigenes with an average length of 661 bp and an N50 length of 980 bp. Among all these unigenes, 41 267 (79.8 %) were annotated in the NCBI non-redundant protein database and 25 236 (48.8 %) were annotated in the Swiss-Prot database. A total of 31 546 (61.0 %) and 13 281 (25.7 %) unigenes were successfully categorized to 59 and 25 functional groups, respectively, by gene ontology categories and clusters of orthologous group categories. A total of 22 323 (43.2 %) unigenes were assigned to 128 pathways using the Kyoto encyclopedia of genes and genomes pathway database. Additionally, 3 249 EST-SSRs markers were detected in 51 698 unigenes from velvet ash. Based on 3 249 EST-SSRs markers, 1 800 primer pairs were successfully designed using Primer 3. In the 50 randomly selected primers, 48 successfully amplified fragments, and 42 showed polymorphisms. We completed a successful application of the Illumina platform to de novo transcriptome assembly of velvet ash, which has the potential to be used for discovering novel genes and further characterization of gene expression profiles.

Keywords

• rna-seq
• simple sequence repeats
• velvet ash