Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.cytoskeleton | calcium-signaling | carbohydrate-active enzymes | stress tolerance | vitamin B 12T he red algae are one of the founding groups of photosynthetic eukaryotes (Archaeplastida) and among the few multicellular lineages within Eukarya. A red algal plastid, acquired through secondary endosymbiosis, supports carbon fixation, fatty acid synthesis, and other metabolic needs in many other algal groups in ways that are consequential. For example, diatoms and haptophytes have strong biogeochemical effects; apicomplexans cause human disease (e.g., malaria); and dinoflagellates include both coral symbionts and toxin-producing "red tides" (1). The evolutionary processes that produced the Archaeplastida and secondary algal lineages remain under investigation (2-5), but it is clear that both nuclear and plastid genes from the ancestral red algae have contributed dramatically to broader eukaryotic evolution and diversity. Consequently, the imprint of red algal metabolism on the Earth's climate system, aquatic foodwebs, and

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The marine red alga Porphyra umbilicalis has high tolerance toward various abiotic stresses. In this study, the contents of floridoside, isofloridoside, and trehalose were measured using gas chromatography mass spectrometry (GC-MS) in response to desiccation and rehydration treatments; these conditions are similar to the tidal cycles that P. umbilicalis experiences in its natural habitats. The GC-MS analysis showed that the concentration of floridoside and isofloridoside did not change in response to desiccation as expected of compatible solutes. Genes involved in the synthesis of (iso) floridoside and trehalose were identified from the recently completed Porphyra genome, including four putative trehalose-6-phosphate synthase (TPS) genes, two putative trehalose-6-phosphate phosphatase (TPP) genes, and one putative trehalose synthase/amylase (TreS) gene. Based on the phylogenetic, conserved domain, and gene expression analyses, it is suggested that the Pum4785 and Pum5014 genes are related to floridoside and isofloridoside synthesis, respectively, and that the Pum4637 gene is probably involved in trehalose synthesis. Our study verifies the occurrences of nanomolar concentrations trehalose in P. umbilicalis for the first time and identifies additional genes possibly encoding trehalose phosphate synthases.

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.

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