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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.

Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae/plants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters. [ABSTRACT FROM AUTHOR]

Within the Bangialean red algae the multi-copy small subunit nuclear ribosomal gene (SSU) has been shown to contain group-I introns at positions corresponding to 516 and 1506. Using the polymerase chain reaction (PCR) with primers flanking the 1506 intron we found that this intron was present in some copies of the rDNA in several North Atlantic Porphyra species. However, when the combination of a flanking and internal primer was used to amplify across the intron the percentages of individuals containing the intron increased. The likely explanation for these results was that, when flanking primers were used for PCR, template competition favoured the amplification of the intronless rDNA fragments. A combination of internal and flanking primers used to screen for the 516 intron amplified the intron in every accession of five taxa (Porphyra dioica, P. leucosticta, P. suborbiculata, P. umbilicalis and P. yezoensis) and in most samples of P. amplissima, P. linearis, and P. purpurea. When PCR primers were optimized for the 1506 intron and SSU of P. umbilicalis, the intron was detected in 28/28 samples. Such observations suggest that the 1506 intron is ubiquitous in Porphyra and is present in some, but not all, copies of the ribosomal DNA (rDNA) repeat. Multiple size 1506 introns were detected in individuals of P. umbilicalis. Four of the larger size variants were shown to encode a putative His-Cys box that was associated with mobility of other group-I introns. Our observations suggest that the 1506 group-I intron may still be mobile within the Porphyra lineage. [ABSTRACT FROM AUTHOR]