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

Abstract

The red alga Porphyra umbilicalis Kützing 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 fortynine 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.

Let's talk about sex: Why reproductive systems matter for understanding algae

“…Blouin and Brawley (2012) concluded that there was evidence for apomixis based on the resampling of genotypes using amplified fragment length polymorphisms (AFLPs). Eriksen et al (2016) and Cao et al (2018) also interpreted their results as evidence for apomixis, but both studies were based on a handful of markers only. The former used three microsatellite loci derived from expressed sequence tags (ESTs) and, therefore, the loci were unlikely to be neutral.…”

Review of Presence, Induction and Isolation of Major Cellular Constituents From <em>Porphyra</em> <em>Sensu Lato (Rhodophyceae)</em>, Including Mycosporine-Like Amino Acids (MAA's)

“…Together with its importance in aquaculture, this has led to strain characterization and breeding programs [37,38]. Porphyra has been seen as model organism for red seaweeds and genetic research has been undertaken, including genomic sequencing [16,[39][40][41][42][43][44].…”

“…Proximate ash content for Porphyra.Citation: van Groenigen J, Derksen GCH, Timmermans KR (2022) Review of Presence, Induction and Isolation of Major Cellular Constituents From Porphyra Sensu Lato (Rhodophyceae), Including Mycosporine-Like Amino Acids (MAA's). J Mar Biol Aquaculture Res 4(1):[30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] …”

“…Concentrations are converted to total MAA's (mg g -1 DW).Citation: van Groenigen J, Derksen GCH, Timmermans KR (2022) Review of Presence, Induction and Isolation of Major Cellular Constituents From Porphyra Sensu Lato (Rhodophyceae), Including Mycosporine-Like Amino Acids (MAA's). J Mar Biol Aquaculture Res 4(1):[30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] connected to their specific growth conditions. Mapping the influence of external factors on chemical compositions will, over time, favourably impact cultivation and usages of Porphyra.…”

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Genetic Diversity of Saccharina Cultivars in Shandong, China

“…Previous studies indicated that intensive inbreeding and selection during the domestication process may reduce the genetic diversity (Voisin et al, 2005;Doebley et al, 2006;Veasey et al, 2008;Provan et al, 2013;Cao et al, 2019). Some previous reports have assessed the genetic diversity and population structure of S. japonica populations in China and indicated that intensive selection and inbreeding for multiple generations are likely to have an effect on the genetic diversity of cultivated S. japonica populations (Wang et al, 2005;Shan et al, 2010;Bi et al, 2011;Liu F. et al, 2012).…”