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Korea is one of the most advanced countries in kelp aquaculture. The brown algae, Undaria pinnatifida and Saccharina japonica are major aquaculture species and have been principally utilized for human food and abalone feed in Korea. This review discusses the diversity, population structure and genomics of kelps. In addition, we have introduced new cultivar development efforts considering climate change, and potential carbon sequestration of kelp aquaculture in Korea. U. pinnatifida showed high diversity within the natural populations but reduced genetic diversity in cultivars. However, very few studies of S. japonica have been conducted in terms of population structure. Since studies on cultivar development began in early 2000s, five U. pinnatifida and one S. japonica varieties have been registered to the International Union for the Protection of New Varieties of Plants (UPOV). To meet the demands for seaweed biomass in various industries, more cultivars should be developed with specific traits to meet application demands. Additionally, cultivation technologies should be diversified, such as integrated multi-trophic aquaculture (IMTA) and offshore aquaculture, to achieve environmental and economic sustainability. These kelps are anticipated to be important sources of blue carbon in Korea.

A special‐purpose Committee on DNA Sequences as Types was established at the XIX International Botanical Congress (IBC) in Shenzhen, China, in 2017, with a mandate to report to the XX IBC in Madrid in 2024 with recommendations on a preferred course of action with respect to potential amendments of the International Code of Nomenclature for algae, fungi, and plants to allow DNA sequences as types. This is the first in an expected series of papers from the Special‐purpose Committee on this issue. We set out the background to the establishment of the Committee, explore key issues around typification that are pertinent to the question of DNA sequences as types, enumerate pros and cons of allowing DNA sequences as types, and foreshadow options for future discussion and potential recommendations.

Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA.

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier—a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.

We compared the cultivation performance and genetic characteristics of Korean (Sugwawon No. 301) and Chinese strains (Huangguan No. 1) of the brown alga Saccharina japonica at an aquaculture farm in Korea. The number of cortical layer cells and the area of the cortical cells were measured for different size groups (5, 15, 30, 50, 100, 150 cm) of the two strains in a Korean culture farm from January to June 2018. We found better performance of the Sugwawon No. 301 strain in Korean waters, possibly due to increased flexibility as a result of the different cell arrangement of the two strains. The differences in cell shape (spherical or rectangular) and arrangement (irregular or constant layered) of the two strains began to appear at lengths of 50 cm where the Sugwawon No. 301 strain had greater numbers of smaller cells than Huangguan No. 1. In addition we established six sequence simple repeats (SSR) genetic markers that clearly distinguish these two strains of S. japonica. Based on our observations, we speculate that differences in the cell arrangement between strains of S. japonica were determined by genetic variation and morphological properties of the two kelp strains.

Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.

ABCG subfamily proteins are highly enriched in terrestrial plants. Many of these proteins secrete secondary metabolites that repel or inhibit pathogens. To establish why the ABCG subfamily proteins proliferated extensively during evolution, we constructed phylogenetic trees from a broad range of eukaryotic organisms. ABCG proteins were massively duplicated in land plants and in oomycetes, a group of agronomically important plant pathogens, which prompted us to hypothesize that plant and pathogen ABCGs coevolved. Supporting this hypothesis, full-size ABCGs in host plants (Arabidopsis thaliana and Glycine max) and their pathogens (Hyaloperonospora arabidopsidis and Phytophthora sojae, respectively) had similar divergence times and patterns. Furthermore, generalist pathogens with broad ranges of host plants have diversified more ABCGs than their specialist counterparts. The hypothesis was further tested using an example pair of ABCGs that first diverged during multiplication in a host plant and its pathogen: AtABCG31 of A. thaliana and HpaP802307 of H. arabidopsidis. AtABCG31 expression was activated following infection with H. arabidopsidis, and disrupting AtABCG31 led to increased susceptibility to H. arabidopsidis. Together, our results suggest that ABCG genes in plants and their oomycete pathogens coevolved in an arms race, to extrude secondary metabolites involved in the plant's defense response against pathogens.

Genome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodop...

Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-...

Red algae (Rhodophyta) putatively diverged from the eukaryote tree of life >1.2 billion years ago and are the source of plastids in the ecologically important diatoms, haptophytes, and dinoflagellates. In general, red algae contain the largest plastid gene inventory among all such organelles derived from primary, secondary, or additional rounds of endosymbiosis. In contrast, their nuclear gene inventory is reduced when compared to their putative sister lineage, the Viridiplantae, and other photosynthetic lineages. The latter is thought to have resulted from a phase of genome reduction that occurred in the stem lineage of Rhodophyta. A recent comparative analysis of a taxonomically broad collection of red algal and Viridiplantae plastid genomes demonstrates that the red algal ancestor encoded ~1.5× more plastid genes than Viridiplantae. This difference is primarily explained by more extensive endosymbiotic gene transfer (EGT) in the stem lineage of Viridiplantae, when compared to red algae. We postulate that limited EGT in Rhodophytes resulted from the countervailing force of ancient, and likely recurrent, nuclear genome reduction. In other words, the propensity for nuclear gene loss led to the retention of red algal plastid genes that would otherwise have undergone intracellular gene transfer to the nucleus. This hypothesis recognizes the primacy of nuclear genome evolution over that of plastids, which have no inherent control of their gene inventory and can change dramatically (e.g., secondarily non-photosynthetic eukaryotes, dinoflagellates) in response to selection acting on the host lineage.

The taxonomic placement of strains belonging to the extremophilic red alga Galdieria maxima has been controversial due to the inconsistent phylogenetic position inferred from molecular phylogenetic analyses. Galdieria maxima nom. inval. was classified in this genus based on morphology and molecular data in the early work, but some subsequent molecular phylogenetic analyses have inferred strains of G. maxima to be closely related to the genus Cyanidioschyzon. To address this controversy, an isolated strain identified as G. maxima using the rbcL gene sequence as the genetic barcode was examined using a comprehensive analysis across morphological, physiological, and genomic traits. Herein are reported the chloroplast-, mitochondrion-, and chromosome-level nuclear genome assemblies. Comparative analysis of orthologous gene clusters and genome arrangements suggested that the genome structure of this strain was more similar to that of the generitype of Cyanidioschyzon, C. merolae than to the generitype of Galdieria, G. sulphuraria. While the ability to uptake various forms of organic carbon for growth is an important physiological trait of Galdieria, this strain was identified as an ecologically obligate photoautotroph (i.e., the inability to utilize the natural concentrations of organic carbons) and lacked various gene models predicted as sugar transporters. Based on the genomic, morphological, and physiological traits, we propose this strain to be a new genus and species, Cyanidiococcus yangmingshanensis. Re-evaluation of the 18S rRNA and rbcL gene sequences of the authentic strain of G. maxima, IPPAS-P507, with those of C. yangmingshanensis suggests that the rbcL sequences of "G. maxima" deposited in GenBank correspond to misidentified isolates.

We examined 12 strains representing eight species classified in the algal class Phaeothamniophyceae (Heterokontophyta). Based upon a five-gene molecular phylogeny (nuclear-encoded SSU rRNA and plastid-encoded psaA, psbA, psbC, and rbcL) and light microscopic observations, we describe five new species: Phaeoschizochlamys santosii sp. nov., Phaeoschizochlamys siveri sp. nov., Phaeothamnion wetherbeei sp. nov., Stichogloea dopii sp. nov. and Stichogloea fawleyi sp. nov. The Phaeothamniophyceae, as delimited here, form a natural group that is sister to the Aurearenophyceae. Molecular phylogenetic analyses proved more reliable than morphological characters for distinguishing species. Evolutionary trends with the SI clade of the heterokont algae are discussed.

Phlegrean Fields is a large volcanic area situated southwest of Naples (Italy), including both cave and thermoacidic habitats. These extreme environments host the genus Cyanidium; the species C. chilense represents a common phototrophic micro- organism living in anthropogenic caves. With a view to provide a comprehensive characterization for a correct taxonomic classification, morpho-ultrastructural investigations ofC. chilense from Syb’s cave (Phlegren Fields) was herein car-ried out and compared with the thermoacidophilic C. caldarium. The biofilm was also analyzed to define the roleofC. chilensein the establishment of a bio film within caveenvironments. Despite the peculiar ecological and molecular divergences,C. chilenseandC. caldariumshared all the maindiacritic features, suggesting morphological convergence within the genus; cytological identity was found amongC. chilensestrains geographically distant and adapted to different substrates, such as the porous yellow tuff of Sybil cave and calcyte, magnesite and basaltic rocks from other caves. C. chilense is generally dominant in all biofilms, developing monospecific islets, developing both super ficially or betweenfungal hyphae and coccoid cyanobacteria. Extracellular polymeric substances (EPS) were recorded in C. chilense bio filmsfrom Sybil cave, confirming the role of EPS in facilitating cellsadhesion to the surface, creating a cohesive network of inter-connecting biofilm cells

The Cyanidiophyceae are a group of unicellular organisms that diverged from ancestral red algae around 1.3 billion years ago. Present-day species are restricted to hot springs and geothermal habitats from around the world. Because of discontinuous geothermal environments, the distribution patterns and dispersal modes of the cyanidiophycean species are poorly understood. Iceland is the third largest island in the Atlantic Ocean and has intense underground volcanic activity that generates broad hydrothermal areas with different ecological conditions that are excellent for thermoacidophilic microfloral development. We analyzed populations to address the Icelandic cyanidiophycean biodiversity and dispersal. A global rbcL phylogeny showed two main populations inhabiting Iceland, Galdieria sulphuraria and G. maxima. Their areas of distribution are not completely superimposed because they coexisted only in New Zealand, Kamchatka (Russia), Japan, and Iceland. Because of the strong monophyly of Icelandic species with Japanese and Russian species, we hypothesized an origin and dispersion of Icelandic G. suphuraria and G. maxima from northeastern Asia. On the basis of network analysis of rbcL haplotypes, it is likely that the southwestern region of Iceland is the diversity center of both G. sulphuraria and G. maxima.

We characterized the complete sequence of the mitochondrial genome of the freshwater green algal strain YC001, known as ‘Ettlia sp.', which is of great interest for biofuel production. The size of the mitogenome was 52,489 base pairs (bp), with 49.0% GC content. It consisted of 49 mitochondrial genes typical of the Chlorophyceae, including 16 protein-coding genes, 27 transfer RNA genes and six ribosomal RNA genes as well as three introns within cox1 (6832 bp), rnl4 (1805 bp) and cob (1107 bp). We determined that YC001 is a species of Coelastrella on the basis of molecular phylogenetic analyses and microscopic observations. A unique feature of this mitogenome is the presence of three different types of inverted repeats between trnL and trnI and between nad4 and cox1 as well as the presence of orf215, orf755 and one additional copy of the trnM gene, all of which enable a comparison with an available sister taxon, Acutodesmus obliquus.

Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.

Prunus ×yedoensis Matsum. ‘Somei-yoshino’ is the most common and widespread cultivar of the ornamental flowering cherries. We hereby report its complete chloroplast (cp) genome sequences generated by whole-genome next-generation sequencing approach. The cp genome size was 157,792 bp in length consisting of four regions; large single-copy region (85,914 bp), small single-copy region (19,120 bp), and a pair of inverted repeat regions (26,379 bp). The genome contained a total of 131 genes, including 86 coding genes, 8 rRNA genes, and 37 tRNA genes. A total of 92 simple sequence repeats (SSRs) were detected within the cp genome. Its molecular features were compared with the complete cp genome of wild P. yedoensis, which occurs rarely in natural habitats of Mt. Halla in Jeju Island, Korea, displaying nearly indistinguishable morphology as P. ×yedoensis ‘Somei-yoshino’. Although both cp genomes were structured highly alike, the sequence variations between them were revealed in several single-nucleotide polymorphisms (SNPs). Using additional individuals of wild and cultivated flowering cherries, PCR amplification confirmed that those SNPs were phylogenetically informative, providing distinction between wild and cultivated flowering cherries. In future study, the SNPs and SSRs reported in this study could be used to identify wild individuals from morphologically identical cultivars of flowering cherries and also to conserve the genetic diversity of wild flowering cherries in Jeju Island.

Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi-gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.

We described the complete mitochondrial genome of Gracilaria chilensis (Gracilariales), an economically important agarophyte alga. The genome was a 26,898 bp circular DNA with 27.6% guanine-cytosine (GC) content, and it encoded 25 protein-coding genes, two ribosomal RNAs (rRNAs), 26 transfer RNAs (tRNAs), and an intron (499 bp) in trnI. The gene composition was similar to that of the published mitogenome of G. salicornia; however, one inverted and several direct repeat sequences occurred between secY and orf148 genes, resulting in duplicated trnR and trnS tRNA sequences. The mitochondrial genome also contained three integrated partial plasmid sequences, which were reported for G. robusta (Gro4059).

Coccophora langsdorfii (Turner) Greville (Fucales) is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that should be tested in a large survey of populations of C. langsdorfii.

In many eukaryotes, endoplasmic reticulum (ER) stress activates the unfolded protein response (UPR) via the transmembrane endoribonuclease IRE1 to maintain ER homeostasis. The ER stress response in microalgae has not been studied in detail. Here, we identified Chlamydomonas reinhardtii IRE1 (CrIRE1) and characterized two independent knock-down alleles of this gene. CrIRE1 is similar to IRE1s identified in budding yeast, plants, and humans, in terms of conserved domains, but differs in having the tandem zinc-finger domain at the C terminus. CrIRE1 was highly induced under ER stress conditions, and the expression of a chimeric protein consisting of the luminal N-terminal region of CrIRE1 fused to the cytosolic C-terminal region of yeast Ire1p rescued the yeast ∆ire1 mutant. Both allelic ire1 knock-down mutants ire1-1 and ire1-2 were much more sensitive than their parental strain CC-4533 to the ER stress inducers tunicamycin, dithiothreitol and brefeldin A. Treatment with a low concentration of tunicamycin resulted in growth arrest and cytolysis in ire1 mutants, but not in CC-4533 cells. Furthermore, in the mutants, ER stress marker gene expression was reduced, and reactive oxygen species (ROS) marker gene expression was increased. The survival of ire1 mutants treated with tunicamycin improved in the presence of the ROS scavenger glutathione, suggesting that ire1 mutants failed to maintain ROS levels under ER stress. Together, these results indicate that CrIRE1 functions as an important component of the ER stress response in Chlamydomonas, and suggest that the ER stress sensor IRE1 is highly conserved during the evolutionary history.

Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.

Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. This review highlights a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high- throughput 'omic' and reverse genetic methods. It covers the origin and diversification of algal groups, explores advances in understanding the link between phenotype and genotype, considers algal sex determination, and reviews progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest such as biofuel precursors, nutraceuticals, or therapeutics., This manuscript is an outcome of a symposium hosted in June 2016 by The Royal Society entitled ‘Into the genome: advances in the world of algal genomics’, at Chicheley Hall, Buckinghamshire, UK. The symposium organizers, J.B. and D.B., are grateful to the Royal Society for supporting this event. We thank Dr. Doris Gangl for designing Figure 2. The University of Dundee is a registered Scottish charity, No. 015096.

We isolated 17 strains of Chrysotila stipitata and 10 strains of Chrysotila lamellosa from samples collected at exposed chalk surfaces, Westgate, Kent, England, which is the type locality for C. stipitata (generitype) and C. lamellosa. The nuclear-encoded small subunit and large subunit rRNA were used in a molecular phylogenetic analysis. We also examined the cells using light microscopy. Chrysotila stipitata had two chloroplasts per cell, as originally described, and it was positioned within the Coccolithales (Prymnesiophyceae) in a RAxML tree. Chrysotila stipitata gene sequences formed a clade with Pleurochrysis, and because Chrysotila has priority, Pleurochrysis was placed in synonymy. New nomenclatural combinations were also made. Chrysotila lamellosa was located within the order Isochrysidales, and like other members of the order, C. lamellosa had one chloroplast per cell. We reinstated the generic name Ruttnera to accommodate this species (Ruttnera lamellosa comb. nov.). We also showed that several ...

The red alga Pachymeniopsis lanceolata, formerly known as Grateloupia lanceolata, is a component of the native algal flora of northeast Asia and has been introduced to European and North American waters. It has been confused with a cryptic species collected from Korea and Italy. Our analyses of rbcL, cox3 and ITS from P. lanceolata and this cryptic species has revealed two distinct entities, forming a clade, which were clearly separated from its congeners and positioned with other Asian species. Here, we describe the cryptic species as P. gargiuli sp. nov., a species that differs from others by molecular sequence and subtle anatomical characters. We hypothesize that P. gargiuli may have been recently dispersed by anthropogenic vectors, possibly at or near the same time as was P. lanceolata. Our cox3 data set revealed that one haplotype of P. gargiuli, shared between Korea and Italy, and two haplotypes of P. lanceolata, commonly occurring in Korea and USA, are invasive haplotypes. This is the first report of the utility of the mitochondrial coding cox3 sequences in red algae.

Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.

Terrestrial plants have two to four times more ATP-binding cassette (ABC) transporter genes than other organisms, including their ancestral microalgae. Recent studies found that plants harboring mutations in these transporters exhibit dramatic phenotypes, many of which are related to developmental processes and functions necessary for life on dry land. These results suggest that ABC transporters multiplied during evolution and assumed novel functions that allowed plants to adapt to terrestrial environmental conditions. Examining the literature on plant ABC transporters from this viewpoint led us to propose that diverse ABC transporters enabled many unique and essential aspects of a terrestrial plant's lifestyle, by transporting various compounds across specific membranes of the plant.

Kim K.M., Hwang I.K., Yoon H.S. and Boo S.M. 2012. Four novel Gelidium species (Gelidiales, Rhodophyta) isolated from Korea: G. coreanum, G. jejuensis, G. minimum and G. prostratum. Phycologia 51: ...

E-mail: hsyoon2011@skku.edu, jwest@unimelb.edu.auTel: +82-31-290-5915, Fax: +82-31-290-7015This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://cre-ativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The unicellular marine red alga Erythrolobus australicus sp. nov. (Porphyridiophyceae) was isolated into laboratory culture from mangroves in Queensland and New South Wales, Australia. The single multi-lobed red to rose-red plastid has more than one pyrenoid and lacks a peripheral thylakoid. Arrays of small electron dense globules occur along the thylakoids. The nucleus is peripheral with a central to eccentric nucleolus. Each Golgi body is associated with a mitochondrion. The spherical cells are positively phototactic with slow gliding movement. The psaA + psbA phylogeny clearly showed that E. australicus is a distinct species, which is closely related to E. coxiae. The chemotaxonomically relevant and most abundant low molecular weight carbohydrate in E. australicus is floridoside with concentrations between 209 and 231 dry weight. Traces of digeneaside were also detected. These various approaches help to understand the taxonomic diversity of unicellular red algae.

The phylogeny of morphologically simple algae is problematic due to insufficient morphological characters to aid in distinguishing species and relationships. The problem is further compounded because multiple evolutionary lineages of morphologically similar species occur in most well-sampled biogeographic locations; therefore, location cannot be used as a proxy for species. The phylogeny of the upright members of the Erythropeltidales is partially clarified by combining molecular data, unialgal culture observations, and worldwide sampling. Our results show that there are several well-supported lineages within the Erythropeltidales with only two morphologically recognizable taxa at present. The first is the genus Porphyrostromium, with a well-developed basal crust, which includes two Erythrotrichia species (Porphyrostromium ligulatum comb. nov. and Porphyrostromium pulvinatum comb. nov.). The second is the branched species Erythrotrichia welwitschii (Rupr.) Batters. There are also six strongly supported Erythrotrichia carnea-like lineages. While not completely satisfactory, we propose that one lineage (lineage 2) with samples close to the type locality be designated as E. carnea with a specific isolate as an epitype. The lack of morphology to differentiate the other lineages leads to a taxonomy based solely on gene sequencing and molecular phylogeny, with rbcL sequences differentiating the lineages proposed. We hold off on proposing more species and genera until more data and samples can be gathered.

Algae are defined by their photosynthetic organelles (plastids) that have had multiple independent origins in different phyla. These instances of organelle transfer significantly complicate inference of the tree of life for eukaryotes because the intracellular gene transfer (endosymbiotic gene transfer [EGT]) associated with each round of endosymbiosis generates highly chimeric algal nuclear genomes. In this Update we review the current state in the field of endosymbiosis research with a focus on the use of the photosynthetic amoeba Paulinella to advance our knowledge of plastid evolution and current ideas about the origin of the plastid translocons. These research areas have been revolutionized by the advent of modern genomic approaches.

Yang E.C., Scott J. West J.A., Orlova E., Gauthier, D., Kupper F.C., Yoon H.S. and Ulf Karsten U. 2010. New taxa of the Porphyridiophyceae (Rhodophyta): Timspurckia oligopyrenoides gen. et sp. nov. and Erythrolobus madagascarensis sp. nov. Phycologia 49: 604–616. DOI: 10.2216/09-105.1 Two new marine unicellular red algae are described: Timspurckia oligopyrenoides gen. et sp. nov. isolated from southeastern Australia and Erythrolobus madagascarensis sp. nov. isolated from Madagascar. Timspurckia oligopyrenoides cells are spherical, 7–11 µm in diameter, greyish red to reddish brown and surrounded by a conspicuous fibrillar matrix about 2 µm thick. Cells exhibit positive phototaxis. In the single chloroplast the lobes extend from several pyrenoids to occupy most of the cell. A peripheral thylakoid is absent. The pyrenoid matrices are filled with tubular thylakoids and are usually surrounded by starch sheaths in the adjacent cytoplasm. The nucleus is peripheral with a nucleolus appressed to the nucle...

The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.

Accounting for the diversity of photosynthetic eukaryotes is an important challenge in microbial biology. It has now become clear that endosymbiosis explains the origin of the photosynthetic organelle (plastid) in different algal groups. The first plastid originated from a primary endosymbiosis, whereby a previously non-photosynthetic protist engulfed and enslaved a cyanobacterium. This alga then gave rise to the red, green, and glaucophyte lineages. Algae such as the chlorophyll c-containing chromists gained their plastid through secondary endosymbiosis, in which an existing eukaryotic alga (in this case, a rhodophyte) was engulfed. Another chlorophyll c-containing algal group, the dinoflagellates, is a member of the alveolates that is postulated to be sister to chromists. The plastid in these algae has followed a radically different path of evolution. The peridinin-containing dinoflagellates underwent an unprecedented level of plastid genome reduction with the ca. 16 remaining genes encoded on 1–3 gene minicircles. In this short review, we examine algal plastid diversity using phylogenetic and genomic methods and show endosymbiosis to be a major force in algal evolution. In particular, we focus on the evolution of targeting signals that facilitate the import of nuclear-encoded photosynthetic proteins into the plastid.

Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1‐3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella ,a ndErythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora ,a ndRufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). Key index words: Bangiophyceae; Compsopogonophyceae; Cyanidiophyceae; Florideophyceae; Porphyridiophycae; red algal lineages; Rhodellophyceae; Rhodophyta; Stylonematophyceae Abbreviations: BPP, Bayesian posterior probabilities; ML, maximum likelihood; MP, maximum parsimony; PsaA, PSI P700 chlorophyll a apoprotein A1; PsaB, PSI P700 chlorophyll a apoprotein A2; PsbA, PSII reaction center protein D1; PsbC, PSII 44 KD apoprotein; PsbD, PSII D2 reaction center protein; TBR, tree bisection-reconnection

Genomic data is accumulating in public database at an unprecedented rate. Although presently dominated by the sequences of metazoan, plant, parasitic, and picoeukaryotic taxa, both expressed sequence tag (EST) and complete genomes of free-living algae are also slowly appearing. This wealth of information offers the opportunity to clarify many long-standing issues in algal and plant evolution such as the contribution of the plastid endosymbiont to nuclear genome evolution using the tools of comparative genomics and multi-gene phylogenetics. A particularly powerful approach for the automated analysis of genome data from multiple taxa is termed phylogenomics. Phylogenomics is the convergence of genomics science (the study of the function and structure of genes and genomes) and molecular phylogenetics (the study of the hierarchical evolutionary relationships among organisms, their genes and genomes). The use of phylogenetics to drive comparative genome analyses has facilitated the reconstruction of the evolutionary history of genes, gene families, and organisms. Here we survey the available genome data, introduce phylogenomic pipelines, and review some initial results of phylogenomic analyses of algal genome data.

Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.

Photosynthetic members of the genus Dinophysis Ehrenberg contain a plastid of uncertain origin. Ultrastructure and pigment analyses suggest that the twomembrane-bound plastid of Dinophysis spp. has been acquired through endosymbiosis from a cryptophyte. However, these organisms do not survive in culture, raising the possibility that Dinophysis spp. have a transient kleptoplast. To test the origin and permanence of the plastid of Dinophysis , we sequenced plastidencoded psb A and small subunit rDNA from singlecell isolates of D. acuminata Claparede et Lachman, D. acuta Ehrenberg, and D. norvegica Claparede et Lachman. Phylogenetic analyses confirm the cryptophyte origin of the plastid. Plastid sequences from different populations isolated at different times are monophyletic with robust support and show limited polymorphism. DNA sequencing also revealed plastid sequences of florideophyte origin, indicating that Dinophysis may be feeding on red algae.

blue.weeg.uiowa.edu The ceramiaceous red algal genus Campylaephora J. Agardh includes three species that occur exclusively in the northwest Pacific Ocean. We studied the morphology, basiphyte range, and molecular phylogeny of Campylaephora borealis, considered a variety of the C. crassa complex, using material collected over its geographic range. Samples of C. borealis, C. crassa, C. hypnaeoids, and putative relatives were taken from 43 locations in Korea, Japan, and Far-East Russia, including the type localities of the first two of these species. Campylaephora borealis is distinguished by proliferous branchlets on all sides of the main branches and an alternate branching pattern. It is characteristically epiphytic on diverse plants, such as Prionitis divaricata, and occurs mostly in exposed sites. It is distributed from Maengbang, Korea to Nakhodka, Far-East Russia. Based on pairwise divergences of the plastid RuBisCo spacer region and psbA sequences, C. borealis is more closely related to C. hypnaeoides than to C. crassa. The topology of the tree constructed using the combined data shows the monophyly of C. borealis, which is clearly separated from other Campylaephora species and putative relatives. Our molecular data together with the basiphyte range and a morphological reappraisal point to the independent taxonomic position of C. borealis, isolated from Campylaephora crassa. Therefore, we propose to raise Campylaephora crassa f. borealis to the rank of species: Campylaephora borealis (Nakamura) Seo et al., stat. nov. The phylogeny of Campylaephora is also discussed.

Algae include a diverse array of photosynthetic eukaryotes excluding land plants. Explaining the origin of algal plastids continues to be a major challenge in evolutionary biology. Current knowledge suggests that plastid primary endosymbiosis, in which a single-celled protist engulfs and “enslaves” a cyanobacterium, likely occurred once and resulted in the primordial alga. This eukaryote then gave rise through vertical evolution to the red, green, and glaucophyte algae. However, some modern algal lineages have a more complicated evolutionary history involving a secondary endosymbiotic event, in which a protist engulfed an existing eukaryotic alga (rather than a cyanobacterium), which was then reduced to a secondary plastid. Secondary endosymbiosis explains the majority of algal biodiversity, yet the number and timing of these events is unresolved. Here we analyzed a five-gene plastid data set to show that a taxonomically diverse group of chlorophyll c 2 -containing protists comprising cryptophyte, haptophyte, and stramenopiles algae (Chromista) share a common plastid that most likely arose from a single, ancient (≈1,260 million years ago) secondary endosymbiosis involving a red alga. This finding is consistent with Chromista monophyly and implicates secondary endosymbiosis as an important force in generating eukaryotic biodiversity.

As a basis for inferring phylogenetic relationships between Pelvetia and Pelvetiopsis in the family Fucaceae, the complete sequences of the plastid-encoded RuBisCo spacer region were determined for all four species of Pelvetia, for the type species of Pelvetiopsis, P. limitata, and for three other fucacean species (Ascophyllum nodosum, Fucus gardneri and F. vesiculosus). All trees based on the sequences of the RuBisCo spacer region showed that Pelvetia is not monophyletic and consists of two clades, one including P. babingtonii, P. compressa, and P. siliquosa, the other comprising only the type species, P. canaliculata. P. canaliculata is not closely related to any of the other Fucaceae studied, and it may represent a monotypic genus. RuBisCo spacer sequences support the establishment of a new genus for the three Pacific Pelvetia species: P. babingtonii, P. compressa and P. siliquosa. The congruence of the RuBisCo spacer data with reported nuclear rDNA 18S and ITS sequences, and with biogeographical and m...

SUMMARY In order to elucidate the molecular phylogeny of the order Laminariales, complete small subunit (SSU) rDNA sequences were determined for 11 species, including representatives from all the families of the order: Pseudochorda gracilis Kawai et Nabata and P. nagaii (Tokida) Inagaki of the Pseudochordaceae, Chorda fiium (L,) Stackhouse of the Chordaceae, Alaria fistulosa Postels et Ruprecht, Ecklonia cava Kjellman and Egregia menziesii (Turner) Areschoug of the Alariaceae, Agarum clathratum f, yakishiriense, I, Yamada, Kjelimanieila crassifolia Miyabe and Laminaria japonica Areschoug of the Laminariaceae and Lessonia nigrescens Bory and Postelsia palmaeformis Ruprecht of the Lessoniaceae, The published data of Halosiphon tomentosus (Lyngbye) Jaasund and Saccorhiza polyschides (Lightfoot) Batters were included for tree construction. Our SSU rDNA sequences show that the Pseudochordaceae and Chordaceae are clearly separated from the strongly monophyletic group consisting of the Alariaceae, Laminariaceae and Lessoniaceae, The sequence data also show that the Pseudochordaceae is monophyletic and is distant from H. tomentosus and S, polyschides. Considering our molecular data and the reported morphology, life history and sex pheromones of the family, it appears likely that the Pseudochordaceae might have branched off first from the laminarialean lineage that leads, through the Chordaceae, to the advanced Laminariales (i,e, the Alariaceae, Laminariaceae and Lessoniaceae), The limited resolution that results from the close similarities among the SSU rDNA sequences gives a need for more informative molecular markers in order to resolve the circumscription and phylogeny of the Laminariales