De novo transcriptome analysis of the gametophyte of Undaria pinnatifida (Phaeophyceae)

Abstract

Undaria pinnatifida has received increasingly more attention worldwide in recent years because, on one hand, it is of high economic importance in East Asian countries and, on the other hand, it is listed as an invasive species in many other countries. Unfortunately, fundamental research has been hindered by the lack of available genomic information on this species. In this study, the transcriptome of the gametophyte of U. pinnatifida was sequenced and de novo assembly was conducted. Using an Illumina sequencing platform, 129 million clean reads were acquired. After assembly, a total of 44,264 unigenes were obtained and the average and N50 length of them were 1,321 and 2,059 nucleotides (nt), respectively. It was predicted that 44,183 (99.8 %) unigenes had the open reading frames (ORF). Twenty-two thousand six hundred fifty-nine unigenes shared homology to existing protein sequences in non-redundant (Nr) database. Fifteen thousand ninety-eight unigenes had significant similarity with the deposited sequences in SwissProt database. A total of 13,282 unigenes were assigned at least one gene ontology (GO) term, and 6,683 unigenes were classified into 25 Cluster of Orthologous Groups (COG) categories. Functional annotation with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database assigned 4,200 unigenes to 114 pathways. Putative genes coding for the key enzymes involved in biosynthetic pathway of fucoidan, alginate, mannitol, and laminarin, as well as those encoding different kinds of heat shock protein families, were identified. Moreover, a total of 14,955 SSR loci were identified in the unigenes longer than 1,000 nt, and tentative primers were designed for 7,405 simple sequence repeat (SSR) loci. To our knowledge, this is the first data set for U. pinnatifida transcriptome and will lay the foundation for further studies on this species.