Into the genome: advances in the world of algal genomics

The widespread photosynthetic organelle (plastid) originated ca. 1.6 billion years ago in a heterotrophic protist via primary endosymbiosis involving a beta-cyanobacterium. Evidence will be presented that generally supports the single origin of this plastid in the common ancestor of the Archaeplastida, with some recent insights into the putative branching order of the three phyla in this kingdom. The only other known case of primary plastid origin is in the clade comprised of photosynthetic rhizarian amoebae, Paulinella. Members of this genus contain a photosynthetic organelle, referred to as a chromatophore that is derived from an alpha-cyanobacterial endosymbiont. I will present the results of our analysis of Paulinella cultures and of significant genome and transcriptome data that was generated from Paulinella chromatophora and other species in this genus. Our goal was to gain insights into the process of primary plastid establishment. We find that P. chromatophora is light sensitive and has undergone large-scale duplication of EGT-derived HLI genes that are involved in adaptation to high light. Phylogenomic analysis uncovered extensive recruitment of bacterium-derived genes that appear to counteract gene losses from the chromatophore due to Muller’s ratchet. Because nearly all of the genes still encoded on the chromatophore genome are of cyanobacterial affiliation, we postulate that HGTs from non-endosymbiont sources was key to chromatophore survival. This suggests that phagotrophy was likely maintained after plastid origin to facilitate HGT from prey or other symbiotic bacteria. How these insights inform us about the process of organellogenesis will be discussed.

Professor Debashish Bhattacharya, Rutgers University, USA

Professor Debashish Bhattacharya, Rutgers University, USA

Debashish Bhattacharya is an evolutionary biologist who uses the tools of genomics and bioinformatics to study the origin of the photosynthetic organelle, the plastid, in diverse algae to understand how organelles are integrated into host metabolism. Other areas of specialization include single cell genomics and transcriptomics to explore uncultivated biodiversity and algal biofuel research using the green algal lineage Picochlorum spp. The Bhattacharya group and collaborators have also recently embarked on a large-scale study of coral genome evolution, the origin and developmental control of biomineralization in this lineage, and coral interactions with their dinoflagellate symbionts. Teaching interests at Rutgers include courses in fundamental genomics and the evolution of photosynthesis in eukaryotes.

Red algae (Rhodophyta) include more than 7,000 species thrive in marine and freshwater habitats. Red algae play a critical role in the eukaryote tree of life as the donor through secondary endosymbiosis of the plastid that subsequently gave rise to chlorophyll-c containing groups such as diatoms, dinoflagellates, haptophytes, and cryptophytes. However, only limited genome data are available from economically important red algal species. Here, we report the complete nuclear genome of the agarophyte Gracilariopsis chorda and present genome comparisons with other algal species. We also assembled the plastid and mitochondrial genomes from the largest dataset including 45 from the red algae (17 novel plastid genomes) to elucidate the evolution of these organelles. We find extreme conservation of plastid and mitochondrial genome structures in the major lineages of Florideophyceae. Only three minor structural types were detected in this group that are explained by recombination events of the duplicated rRNA operons. A similar high level of structural conservation (however, with different gene content) was found in seed plants. Three major plastid genome structures were identified from representatives of 46 orders of angiosperms and 3 orders of the gymnosperms. Our results provide a comprehensive accounting of plastid gene loss and genome rearrangement events within Archaeplastida and lead to one major conclusion. From a pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display extreme conservation in plastid genome architecture. We speculate that the origin of complex reproductive tissue types in red seaweeds and in seed plants likely set in place developmental pathways linking the nuclear and organelle genomes that constrained evolution of the photosynthetic compartment.

Professor Hwan Su Yoon, Sungkyunkwan University, South Korea

Professor Hwan Su Yoon, Sungkyunkwan University, South Korea

Hwan Su Yoon is an Associate Professor in the Department of Biological Sciences at Sungkyunkwan University, Korea. He received his PhD in biology from Chungnam National University. After research training at the University of Iowa, he worked at the Bigelow Laboratory for Ocean Sciences. His research interests include eukaryotic biodiversity, phylogeny, single cell genomics, and genome evolution, with a focus on red algae and red algal plastid descendants (e.g., the cryptophytes, haptophytes, stramenopiles, dinoflagellates).

Chloroplast genomes, relics of an ancient endosymbiotic cyanobacterial genome, are typically circular, double-stranded DNA molecules. Their size usually ranges between 100-200 kb and they encode 100-200 genes. While multipartite architectures of mitochondrial genomes evolved several times independently during the evolution of eukaryotes, fragmented plastid genomes are only known in dinoflagellates. Here we report on the chloroplast structure of the Cladophorales, an order of green seaweeds. Based on a combination of short NGS reads, long sequencing reads and RNA-seq, we conclude that they do not possess a single circular chloroplast genome but a genome fragmented into multiple molecules, 2-3 kb in size, each containing one protein-coding gene. In that aspect, the chloroplast genome of the Cladophorales somewhat resembles dinoflagellates chloroplast minicircles. However, in Cladophorales the molecules are linear single-stranded molecules that fold onto themselves in a hairpin-like structure due to the presence of extensive inverted repeats. So far we assembled 13 hairpins, each harbouring a distinct full-length chloroplast gene (e.g. atpA, atpB, atpH, atpI, petA, petB, psaA, psaC, psbA, psbB, psbC, psbD, rbcL). RNA-seq analysis confirmed that these genes are transcribed and produce functional transcripts. Phylogenetic analyses indicate that the genes are more rapidly evolving compared to chloroplast genes of other green algae. As far as known such a chloroplast structure is unique among eukaryotes.

Andrea Del Cortona, Ghent University, Belgium

Andrea Del Cortona, Ghent University, Belgium

Andrea Del Cortona is a PhD student at Ghent University, Belgium. He obtained a M.Sc. in Plant Biotechnology from Wageningen University, the Netherlands (2013) and he started his PhD shortly after, under the supervision of Prof. Olivier De Clerck and Prof. Klaas Vandepoele. Beside his training focussed mainly on molecular biology and molecular aspects of bio-interactions, he dived into the fascinating world of green algal genomics. He is actually working on a comparative transcriptomic approach to unravel the evolution of complex morphologies in green seaweeds (Ulvophytes) and to shed light in the evolutionary history of this class.

Dinoflagellates are an important group of primary producers and grazers, predominantly found in the marine environment. Almost all dinoflagellates are free-living (including species that cause harmful algal blooms); Symbiodinium, the only symbiotic lineage, is associated with cnidarian hosts (e.g. corals and jellyfish) and diverse coral reef animals. The origin of plastid in dinoflagellates can be traced back to multiple, serial events of endosymbiosis, during which genetic material could have been transferred from the engulfed endosymbiont (of prokaryote and eukaryote origins) to the host nucleus. The frequency and functional impact of exogenous gene recruitment in dinoflagellates are known to be as great as in prokaryotes, impacting some of the most fundamental traits. Due to its remarkable complexity, evolution of dinoflagellate genomes is sometimes considered as the “worst-case” scenario in microbial eukaryotes. Furthermore, dinoflagellate genomes are huge — often estimated 20–230 Gbp — and they exhibit anomalous characteristics e.g. non‐canonical nucleotides and unusual intron‐exon splice signals; sequencing and assembly of these genomes remain a challenge. Symbiodinium genomes are orders of magnitude smaller (estimated 1.2–3Gbp) than their free-living counterparts, thus providing a practical, initial analysis platform for dinoflagellate genomics. Two genomes of Symbiodinium were recently published, with more dinoflagellate genomes expected to become available. Here I will present our recent findings from the analysis of three Symbiodinium genomes and their biological implications for our understanding of dinoflagellate (and algal) evolution. Technical challenges of sequencing dinoflagellate genomes and future perspectives will also be discussed.

Dr Cheong Xin Chan, University of Queensland, Australia

Dr Cheong Xin Chan, University of Queensland, Australia

Dr Chan, better known as ‘CX’, has a PhD in Genomics and Computational Biology from the University of Queensland (UQ). He underwent postdoctoral training at Rutgers University (USA) in algal genomics and evolution and returned to UQ in late 2011 as one of the inaugural Great Barrier Reef Foundation Bioinformatics Fellows. CX joined UQ's School of Chemistry and Molecular Biosciences in 2020 as a Group Leader at the Australian Centre for Ecogenomics (ACE). His group adopts computational approaches to study genome evolution of microbial eukaryotes and the evolution of symbiosis, and to develop highly scalable phylogenomic approaches using alignment-free methods. At UQ, CX is leading the world’s largest concentrated genome-sequencing effort of dinoflagellates that include essential coral symbionts and harmful bloom-forming species.

Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol.

We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis. In particular, we show that half of the genes encoding enzymes of tryptophan synthesis in Archaeplastida are of chlamydial origin. Tryptophan is known to define an essential cue triggering two alternative modes of replication in Chlamydiales. In addition, sophisticated tryptophan starvation mechanisms are known to have been implemented as antibacterial defences by their eukaryotic hosts. We propose that Chlamydiales have donated their tryptophan operon to the emerging plastid to ensure increased synthesis of tryptophan by the plastid ancestor. This would have allowed massive expression of the tryptophan rich chlamydial transporters responsible for symbiosis. It would also have allowed possible export of this valuable amino-acid in the inclusion of the tryptophan hungry pathogens. Free-living single cell cyanobacteria are devoid of proteins able to transport this amino-acid. We therefore investigated the phylogeny of the E.coli Tyr/Trp transporters and found yet another LGT from Chlamydiales to Archaeplastida thereby considerably strengthening our proposal.

Professor Steven Ball, University of Lille, France

Professor Steven Ball, University of Lille, France

Steven Ball got his PhD from the Agronomy Faculty of Gembloux (Belgium) following work on the molecular genetics of the yeast killer dsRNA virus like particles under the supervision of Reed B Wickner at NIH (Bethesda – Maryland). In 1985 he got a permanent position as assistant professor in Gembloux and got a full professorship at the University of Lille in 1987. Since 1986 he focused all of his experimental work on storage polysaccharide metabolism first in yeast and then very rapidly and predominantly in Chlamydomonas reinhardtii. Steven Ball is internationally recognized for his contribution to the understanding of those functions that distinguish starch from glycogen synthesis. He has recently suggested that storage polysaccharide metabolism acted as a biochemical buffer between unrelated networks at the onset of plastid endosymbiosis. This led him to propose that intracellular Chlamydiales pathogens may have had a major role in this process.

Using powerful bioinformatics tools and comparative genomics is allowing us to identify novel components of photosynthesis. This information will help elucidate new photosynthetic functions and provide opportunities for engineering plants and algae for efficient solar energy utilization, increased agricultural outputs and improved resiliency to changing global environments.  The GreenCut represents an informatics assemblage of nuclear-encoded proteins that are conserved among photosynthetic organisms of the green lineage (Viridiplantae), but that are either not present, or poorly conserved in heterotrophic (nonphotosynthetic) organisms. Many uncharacterized GreenCut proteins (unknown specific functions) appear to have regulatory functions or roles in the biogenesis of the photosynthetic apparatus based on specific domains in their protein sequences. Other GreenCut proteins have no domains that are currently informative with respect to function. Generating insertional mutants of genes encoding GreenCut proteins in Chlamydomonas reinhardtii has allowed for the characterization of mutant phenotypes, suggesting roles for a number of these proteins with respect to photosynthetic activities. One GreenCut protein was recently shown to be involved in stabilizing the assembly of photosystem I (PSI) under oxic conditions, and is potentially involved in protecting oxygen sensitive PSI cofactors (e.g. Fe-S clusters) during the assembly process; as the Earth became oxygenated mechanisms must have evolved that protect existing oxygen sensitive cofactors from disruption. Other novel proteins of the GreenCut appear to be important for the biogenesis/stability of the cytochrome b6f complex. I will discuss the GreenCut and the ways in which it is being used to examine photosynthetic function and evolution.

Professor Arthur Grossman, Carnegie Institution for Science, USA

Professor Arthur Grossman, Carnegie Institution for Science, USA

Dr. Arthur Grossman has spent over thirty years in microalgal research and is widely recognized as an expert in this field, concentrating on algal physiology, genetics and genomics. He received a Ph.D. in Plant Biology from Indiana University, performed postdoctoral research at The Rockefeller University and is currently a Senior Staff Scientist at the Carnegie Institution for Science, a Courtesy Professor at Stanford University and Chief of Genetics for Solazyme Inc. Most of Dr. Grossman's academic research has focused on the ways in which algae perceive and respond to changes in their environment. He has received the prestigious Darbaker Prize from the Botanical Society for algal research in 2002, and in 2009 was awarded the Gilbert Morgan Smith Medal for excellence in published research on marine and/or freshwater algae. The award, which only recognizes one scientist every three years, was established through the Helen P. Smith Fund and is awarded by the National Academy of Sciences USA. 

Marine macroalgae are host to a wide range of prokaryotic and eukaryotic life, creating a dynamic and complex community of specialists or generalists that can be beneficial (mutualistic), neutral (commensal) or harmful (parasitic) organisms. Bacteria are the dominant active group that make up the microbiome, and macroalgal-bacterial studies suggest that there is a core microbiome at the phylum level consisting of the Gammaproteobacteria, Bacteroidetes, Alphaproteobacteria, Firmicutes and Actinobacteria.  Until relatively recently, studies of bacteria associated with various macroalgal hosts were undertaken using cultures and electron microscopy. Next generation sequencing (NGS) is now revolutionising the subject and revealing the extent of bacterial diversity in these microbiomes. This talk will review what is known about microbiomes of marine macroalgae with a particular focus on the red algae.  It will explore the notion of a core microbiome for different host groups and also the spatial and temporal ecological impact on host photosynthesis of different types of epiphytes.  Focussing in particular on the prokaryote component of the microbiome, the nature of the relationships between the bacteria and host and the implications for ecosystem function and environmental change including ocean acidification and increasing sea surface temperatures will be explored.  Drawing upon our results of the microbiome of Corallina officinalis – the first for a geniculate coralline alga – differences in microbiome composition will be compared both within and between fleshy and calcified species. Evidence that the epiphytic bacteria provide important services to hosts that are vital to their health, performance and resilience will be discussed. Ways forward to identify prokaryote and eukaryote diversity, to understand their roles in productivity, and the overall nature of these relationships will be explored.

Professor Juliet Brodie, Natural History Museum, UK

Professor Juliet Brodie, Natural History Museum, UK

Professor Juliet Brodie is a Merit Researcher in Phycology at the Natural History Museum, London. She is an expert in seaweeds, notably in the red algae and specialises in seaweeds in a time of rapid environmental change. Her work includes including genomic approaches to macroalgae and microbiomes, taxonomy, phylogenetics, conservation, seaweed aquaculture and structural colour. She has received several awards including the 2020 Linnean Medal for Botany, the Provasoli Award, Phycological Society of America (PSA), for outstanding paper in Journal of Phycology in 2012, National University of Ireland Professorship, and the Plantlife Award for Outstanding Contribution to Plant Conservation in 2007. She has been President of the British Phycological Society (2009-2011), the Systematics Association (2010-2012), and the International Phycological Society (2016-2018) and is currently the President-elect of the Phycological Society of America. 

Marine viruses that infect marine microorganisms are recognized as major ecological and evolutionary driving forces, shaping community structure and controlling cycling of nutrient energy in the marine environment. A major challenge in our current understanding of host-virus interactions in the marine environment is to decode the wealth of genomic and metagenomic data and translate it into cellular mechanisms that mediate host susceptibility and resistance to viral infection. Nevertheless, the cellular mechanisms that govern these host-virus dynamics are largely underexplored. Recent reports highlighted a novel genomic inventory found in marine viruses which can encode for auxiliary metabolic genes previously thought to be restricted to their host genomes. Thus, these genes can expand the metabolic capabilities of the infected host cell (Virocell) and the flux of the nutrients and metabolites between the cell and its micro-environment.

Emiliania huxleyi is a globally important coccolithophore forming massive algal blooms in the North Atlantic Ocean that are routinely infected and terminated by large DNA viruses (EhVs) belong to the coccolithoviruses. We explore the molecular and metabolic basis for these host-virus dynamics and the signal transduction pathways that mediate host-virus interactions. By combining genome-enabled technologies, analytical chemistry and advance cell imaging approaches, we were able to identify several fundamental metabolic pathways that mediate these host-virus interactions. We revealed the role of viral-encoded sphingolipid biosynthesis, redox and DMS metabolism and their function in determining host cell fate (e.g. PCD and autophagy) and viral replication strategies.

Professor Assaf Vardi, Weizmann Institute of Science, Israel

Professor Assaf Vardi, Weizmann Institute of Science, Israel

Assaf Vardi earned a BSc in biology from the Hebrew University of Jerusalem (1994), from which he also received his MSc in environmental sciences (1999) and PhD in molecular ecology (2004). After conducting postdoctoral research at the École Normale Supérieure in Paris and at Rutgers University, he joined the Weizmann Institute faculty as a senior scientist in 2010. He was also appointed as an Adjunct Scientist at the Woods Hole Oceanographic Institution (USA) during 2011-2014.

His research interests focus on elucidating the molecular mechanism that drives microbial interactions in the marine environment. Specifically he studies marine photosynthetic microorganisms (phytoplankton) which are the basis of marine foodwebs and are responsible for nearly 50% of the global annual carbon-based primary production.

He explores the signal transduction pathways related to the origin of programmed cell death, cell-cell communication, host-virus interactions and chemical-based defense (DMS, sphingolipids, ROS). Our work aims at elucidating the cell signalling pathways that regulate cell fate decisions and uncover the chemical signals (infochemicals) involved in microbial trophic-level interactions in the oceans.

Pythium porphyrae is responsible for devastating outbreaks in seaweed farms of Pyropia, the most valuable seaweed worldwide. While the genus Pythium contains many well studied plant and animal pathogens, the infection strategies and genome content of P. porphyrae remains to be elucidated.  Recent reports also indicated the ability of P.porphyrae to infect, colonize and reproduce on a great variety of land plants, begging the question of its potential land origin, as well as the molecular mechanisms underpinning its host specificity. Here, we used RNA sequencing to provide the first description of P. porphyrae gene repertoire and assess its similarity to fully sequenced Pythiums. Using ab-initio detection strategies, similarity based and manual annotation, we found that the P.porphyrae gene repertoire is strikingly similar to the ones described for classical phytopathogenic Pythium species, including Crinklers, elicitins, cellulases, CBEL-like proteins and a total absence of RxLR effectors. Comparative genomics revealed that 1507 genes, including CBEL-like proteins and elicitins, have orthologs in some plant infecting Pythiums but not in the animal pathogen P.insidiosum. Despite 34% of the P.porphyrae proteome having no orthologs in other sequenced Pythiums, we could not identify any enzyme involved in the degradation of red algal-specific cell wall components. Complementary infection experiments indicated that P.porphyrae is specific of Bangiales, contrasting with the general broad host range observed on land plants, perhaps suggesting a recent adaptation linked with the development of Pyropia cultivation.

Muséum National d'Histoire Naturelle, France

Muséum National d'Histoire Naturelle, France

Originally trained as a molecular plant pathologist, Claire Gachon specialises in establishing model interactions involving eukaryotic pathogens and their algal host(s). She then uses these models to address questions ranging from algal ecology to the physiology and evolution of parasites in aquatic (marine and freshwater) systems, disease management and biosecurity in commercial algal cultivation. Her most recent work investigates the role(s) of bacteria in influencing the outcome of the interaction between a green alga and an aquatic fungus. She is also very active in running infrastructure and networking projects in the UK, the EU and beyond.

Fouling is a paramount phenomenon in the marine environment. However, surfaces of certain seaweeds like the brown alga Fucus vesciculosus, remain relatively free from heavy fouling and are covered by a thin film of epibiotic microorganisms. We found that Fucus in a given habitat harbors a distinct epibacterial community. Fucus also produces defence compounds like fucoxanthin, DMSP reducing bacterial settlement. These compounds have also been found to be strain specific in their action, thus probably assisting Fucus in ‘gardening’ a distinct bacterial community on its surface. This idea was further supported by a study that correlated the surface concentration of the defence compounds with the presence or absence of different bacterial clades. Several bacterial groups were found to be positively or negatively affected by the compounds present on surfaces of Fucus individuals. Seaweeds also account for a substantial proportion of all introduced species. The East Asian red macroalga Gracilaria vermiculophylla has successfully invaded several temperate areas of the Northern hemisphere. Although foulers have the potential to determine invasion success or failure of invasive seaweeds, this perspective has been ignored so far. We tested whether the impressive invasion success of Gracilaria may be enhanced by a rapid adaptation of defence against potentially facultative new target microfoulers in the invaded range. Native and invasive Gracilaria populations were equally well defended against presently co-occurring bacterial foulers. However, native populations were weakly defended against bacteria from the invaded range, while invasive populations were weakly defended against bacteria from the native range. Thus, the invasive populations exhibited an adaptation of their defence capacity to cope with the new foes, but have lost capacity to fend off old foes. These results provide the first evidence that confrontation by new foulers can trigger a rapid defence adaptation of aquatic weeds, which could be necessary for algal invasiveness.

Dr Mahasweta Saha, Plymouth Marine Laboratory, UK

Dr Mahasweta Saha, Plymouth Marine Laboratory, UK

Dr Mahasweta Saha is an expert in chemically mediated interaction between host and microbes under present and future ocean scenarios. Dr Saha has been awarded several prestigious research fellowships to study the chemical ecology of algae and is currently investigating association of pathogenic Vibrio with phytoplanktion in relation to waterborne diseases and nature-based solutions to mitigate the problem of poor water quality. She sits on the editorial board of four international journals, including high rank, and also serves as a reviewer for the German and Belgium research foundation and over twenty international journals. Dr Saha is also a science communicator and has represented the UK at the European Researchers Night. She is deeply committed to the career development of the next generation of scientists, as supervisor and mentor to students and is an advocate of EDI. She is also an active member of the Athena Swan Charter which strives for gender balance and equality in academia. Most recently, in 2021, Mahasweta won the UK’s Asian Women of Achievement Award in the Science category.