Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics.

The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative species of the major lineages. Three of the previously recognized families were resolved as independent monophyletic lineages: Ceramiaceae, Wrangeliaceae and Rhodomelaceae. By contrast, our results indicated that the other six families require reclassification. We propose the new order Inkyuleeales, a new circumscription of the Callithamniaceae to include the Spyridiaceae, and a new concept of the Delesseriaceae that includes the Sarcomeniaceae and the Dasyaceae. We also investigated the evolution of the thallus structure, which has been important in the classical delineation of families. The ancestor of the Ceramiales was a monosiphonous filament that evolved into more complex morphologies several times independently during the evolutionary history of this hyperdiverse lineage

Random mutagenesis and precise gene editing technologies: applications in algal crop improvement and functional genomics

© 2017 British Phycological Society. The establishment of a system for gene modification is crucial for the generation of new improved algal strains and elucidation of functional genome organization to enhance our understanding of algal biology. Several gene transfer methods have been developed for stable introduction of transgenes into algae allowing expression of desired foreign proteins. Site-specific gene integration and gene knockdown were achieved through homologous recombination and RNA interference approaches. The nuclease-associated gene editing technologies such as CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-Cas9) could efficiently generate stable targeted gene editing in algae. Although gene modification technologies have been established for algae, there are still practical difficulties that need to be addressed prior to commercialization such as transgene stability, potential risks and public acceptance. Genetic mitigation and containment strategies should be considered for commercial-scale production of transgenic algae. Abbreviations: ALE, adaptive laboratory evolution; AmiRNA, artificial microRNA; BER, base excision repair; CaMV35S, Cauliflower Mosaic Virus 35S; Cas9, CRISPR-associated protein 9; Cas9n, Cas9 mutant nickase; CRISPR, clustered, regularly interspaced, short palindromic repeats; crRNA, CRISPR RNA; dCAS9, nuclease-deficient Cas9, dead Cas9 or inactive Cas9; DSB, double-stranded break; GM, genetically modified; HDR, homology-directed repair; HR, homologous recombination; miRNA, microRNA; mRNA, messenger RNA; NHEJ, non-homologous end joining; NiR, nitrite reductase; NR, nitrate reductase; PAM, Protospacer-Adjacent Motif; RNAi, RNA interference; sgRNA, single guide RNA; siRNA, small interfering RNA; sRNA, small RNA; SV40, Simian vacuolating virus 40 or Simian virus 40; TALEN, transcription-activator like effector nuclease; tracrRNA, transactivating CRISPR RNA; UTR, Untranslated region; ZFN, zinc-finger nuclease

Marine macroalgae and their associated microbiomes as a source of antimicrobial chemical diversity

© 2017 British Phycological Society. This article reviews the role of microbial biofilms in infection, and the antimicrobial chemical diversity of marine macroalgae and their associated microbiomes. Antimicrobial resistance (AMR) represents one of the major health threats faced by humanity over the next few years. To prevent a global epidemic of antimicrobial-resistant infections, the discovery of new antimicrobials and antibiotics, better anti-infection strategies and diagnostics, and changes to our current use of antibiotics have all become of paramount importance. Numerous studies investigating the bioactivities of seaweed extracts as well as their secondary and primary metabolites highlight the vast biochemical diversity of seaweeds, with new modes of action making them ideal sources for the discovery of novel antimicrobial bioactive compounds of pharmaceutical interest. In recent years, researchers have focused on characterizing the endophytic and epiphytic microbiomes of various algal species in an attempt to elucidate host-microbe interactions as well as to understand the function of microbial communities. Although environmental and host-associated factors crucially shape microbial composition, microbial mutualistic and obligate symbionts are often found to play a fundamental role in regulating many aspects of host fitness involving ecophysiology and metabolism. In particular, algal ‘core’ epiphytic bacterial communities play an important role in the protection of surfaces from biofouling, pathogens and grazers through the production of bioactive metabolites. Together, marine macroalgae and their associated microbiomes represent unique biological systems offering great potential for the isolation and identification of novel compounds and strategies to counteract the rise and dissemination of AMR

A new monotypic family for the enigmatic crustose red alga Plagiospora gracilis.

Plagiospora gracilis, a mucilaginous crustose red alga growing on subtidal pebbles on both coasts of the North Atlantic Ocean, forms distinctive tetrasporangia (red algal meiotic structures that release haploid tetraspores) but gametophytes have never been reported. In the absence of gametangia, the taxonomic position of this monotypic genus has always been uncertain; it is currently placed provisionally in the Gloiosiphoniaceae (Gigartinales) by comparison with sporophytes of Gloiosiphonia obtained in culture. Dioecious gametophytic crusts of P. gracilis are now reported for the first time, forming gametangia in inconspicuous superficial sori. There is no evidence that fertilization ever occurs in the field although fertile males and female were collected together. In culture, tetraspores grew into tetrasporophytes for three successive generations, by presumed apomictic sporophyte recycling. The life history of P. gracilis may represent a late stage in the loss of sexual reproduction leading to tetraspore-to-tetrasporophyte life histories such as that in Hildenbrandia. Phylogenetic analysis of sequences of the rbcL, LSU (28S) rDNA and coxI (COI-5P) genes for P. gracilis with other Gigartinales resolved P. gracilis as a distinct lineage in a well-supported clade of the families Sphaerococcaceae, Gloiosiphoniaceae, Endocladiaceae, Nizymeniaceae and Phacelocarpaceae. We here propose the monotypic Plagiosporaceae fam. nov. to accommodate P. gracilis

Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus

Molecular resources and transgenic studies in red algae are lagging behind those for green algae. The Agrobacterium-mediated gene-transfer method routinely used in plant transformation has not been fully utilised in the red algae, which, as an important source of phycocolloids, warrant more studies. In this regard, a stepwise methodology was developed for Agrobacterium-mediated transformation of the carrageenophyte Chondrus crispus using pCAMBIA 1301 and a construct featuring a codon-optimized beta-glucuronidase (GUS) reporter gene driven by the endogenous Chondrus actin promoter. The effects of several factors on transformation efficiency were investigated. An intimate association of Chondrus and bacterial cells was observed using scanning electron microscopy. GUS transient expression within Chondrus cortical and medullary cells with both expression cassettes testified to the amenability of Chondrus to Agrobacterium-mediated transformation. Darker staining, indicative of higher GUS activity, was observed with the Chondrus-specific construct, suggesting its superiority over the pCAMBIA 1301. Presence of acetosyringone, the wounding method and the type of co-cultivation medium significantly affected the transformation outcome and efficiency. The Agrobacterium-mediated transient expression presented here constitutes a first step towards tailoring a transformation strategy for Chondrus, which can serve to facilitate further transgenic studies in this important red alga

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

<p>Abstract</p> <p>Background</p> <p>The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.</p> <p>Results</p> <p>Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 10³to ca. 10⁴nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 10⁵nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches.</p> <p>Conclusions</p> <p>Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.</p

Genetic analysis of the Linnaean Ulva lactuca (Ulvales, Chlorophyta) holotype and related type specimens reveals name misapplications, unexpected origins, and new synonymies.

Current usage of the name Ulva lactuca, the generitype of Ulva, remains uncertain. Genetic analyses were performed on the U. lactuca Linnaean holotype, the U. fasciata epitype, the U. fenestrata holotype, the U. lobata lectotype, and the U. stipitata lectotype. The U. lactuca holotype is nearly identical in rbcL sequence to the U. fasciata epitype, a warm temperate to tropical species, rather than the cold temperate species to which the name U. lactuca has generally been applied. We hypothesize that the holotype specimen of U. lactuca came from the Indo-Pacific rather than northern Europe. Our analyses indicate that U. fasciata and U. lobata are heterotypic synonyms of U. lactuca. Ulva fenestrata is the earliest name for northern hemisphere, cold temperate Atlantic and Pacific species, with U. stipitata a junior synonym. DNA sequences from type specimens provide an unequivocal method for applying names to Ulva species. This article is protected by copyright. All rights reserved