A pilot study of genetic structure of Porphyra umbilicalis Kutzing in the Gulf of Maine using SNP markers from RNA-Seq

The red alga Porphyra umbilicalis Kutzing has a broad distribution within the North Atlantic. In the Northeast Atlantic, P. umbilicalis is dioecious and reproduces both sexually and asexually, while in the Northwest Atlantic, only asexual reproduction has been observed. In this study, transcriptomes were mined to identify putative single nucleotide polymorphisms (SNP) markers. A computational pipeline was developed that accounts for the specific characteristics of transcriptome dataset, filtered against the available red alga Chondrus genome and P. umbilicalis EST library to eliminate microbial contamination. Five hundred forty-nine putative SNPs were detected within a single population (Schoodic Point, ME, USA). Five of the validated SNP markers were applied in a pilot study of genetic diversity and population structure of seven P. umbilicalis populations within the Gulf of Maine. Results of this study revealed the genetic diversity and structure of P. umbilicalis populations in the Gulf of Maine. Novel genotypes were found in the open coastal populations at Reid State Park, Schoodic Point, and the estuarine tidal rapid population at Wiscasset. Our study represents the first attempt to develop suitable bioinformatic pipeline for RNA-seq to detect SNP markers for red alga Porphyra umbilicalis and successfully used these SNP markers for population study.