Comparative transcriptome analysis of high-growth and wild-type strains of Pyropia yezoensis

Abstract

Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.