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The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. This research examines the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, it shows that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.

© 2014 Gomez-Valero et al. Background: The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires' disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. Results: We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Conclusions: Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. © 2013 Macmillan Publishers Limited. All rights reserved.

Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of proteincoding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche- and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.

Cylindrospermopsis raciborskii is a filamentous, potentially toxic bloom-forming cyanobacterium in tropical and temperate freshwaters. We compared the cylindrospermopsin (CYN) producing C. raciborskii strain CS-505 (Australia) against a PSP toxin producing strain D9 (Brazil), originally identified as conspecific. Cylindrospermopsis raciborskii forms a monophyletic group comprising identities >99% for the 16S rRNA gene, whereas strains D9 and CS-505 are 99.7% similar. We sequenced the complete genome of these strains, the first for any PSP- or CYN-toxin producing cyanobacterium. The genome sizes are the smallest known for filamentous cyanobacteria (3.3 and 3.9 Mbp for D9 and CS-505, respectively), but exhibit an apparently large size difference. Genome comparison yielded 471 and 801 strain-specific genes for D9 and CS-505, respectively, and revealed remarkable differences between strains. These differences are mainly related to signatures for high genomic plasticity in CS-505, gene loss in D9 (such as the lack of nitrogen fixation genes), and genes for secondary metabolite production, specifically in the STX and CYN clusters. Functional analysis via gene expression studies using microarrays and qPCR have supported the function of the identified toxin-related gene clusters as well as indicating fundamental differences in phenotypic expression between the strains.

Cylindrospermopsis raciborskii is a filamentous, potentially toxic, bloom-forming cyanobacterium in tropical and temperate freshwaters. Its high competition and ability of produce toxins have made of this cyanobacterium one of the most studied in the ecological and public health fields. A clonal culture described as C. raciborskii strain D9 (Brazil), produces Paralytic Shellfish Poisoning (PSP) toxins; however, differed from C. raciborskii due to the presence of anomalous heterocysts (N-fixing specialized cells characteristic of the species). C. raciborskii strain CS-505 (Australia) produces cylindrospermopsin (CYN). In spite of these phenotypic differences, strains D9 and CS-505 present 99.7% of identity at the 16S rRNA gene. We have sequenced the complete genome of these toxic strains; the first for cyanobacteria producing either PSP- or CYN-toxins. The genome sizes, the smallest found for filamentous cyanobacteria, are 3.3 and 3.9 Mbp for D9 and CS-505, respectively, fairly different for so closely related organisms. The genome comparison revealed a large amount of transposition elements and repeated sequences, as well as secondary metabolite pathways in CS-505 genome, demonstrating a high plasticity and signatures of large genome species. In contrast, strain D9 presents a high number of genes involved in DNA modification (protection) and repair and lacks all the nitrogen fixation genes. In summary, it seems the strain D9 have undergone genome reduction and implies a resistance of strain D9 to the acquisition of new functions and also raise the possibility of a misclassification of this strain.

Paralytic shellfish poisoning (PSP) is a syndrome related to consumption of shellfish contaminated by toxigenic microalgae that biosynthesize the tetrahydropurine neurotoxin saxitoxin (STX) and/or various derivatives. Dinoflagellates are the main producers of PSP toxins in marine environments but PSP toxin production is also well described from freshwater cyanobacteria. Although the pathways involved in STX biosynthesis remain poorly known, studies with labeled precursors have suggested that dinoflagellates and cyanobacteria share this biosynthetic pathway. In contrast to the complexity of the dinoflagellate genome (3000215000 Mbp), the simplicity of cyanobacterial genomes (from 1.8 to 13.6 Mb) offers an alternative model for understanding the pathways involved in toxin production and gene regulation. The cyanobacterium Cylindrospermopsis raciborskii (genome size ca. 2.2 Mb) comprises strains able to produce either PSP toxins or the hepatotoxin cylindrospermopsin (CYN), as well as non-toxigenic strains. We have fully sequenced the complete genome of two strains of C. raciborskii that share 99.7% of their 16S rRNA sequences but differ in toxin profile (a CYN- versus a PSP toxin-producer). This project includes a study of: i) comparative genomics to identify the main differences between these strains that could be related to toxin production or regulation; and ii) physiological conditions that modify the toxin profile and its genetic regulation in the CYN- versus PSP toxin-producing strains using whole genome microarrays. The data for the cyanobacterium should be useful to evaluate homology of PSP toxin production among Cyanobacteria and Dinoflagellates and may assist in identifying the key genes responsible for PSP toxin synthesis in Dinoflagellates.

The dinoflagellate Alexandrium ostenfeldii is the only known producer of toxic spirolides. Spirolides are macrocyclic imines that are derived via polyketide biosynthetic pathways production is therefore almost certainly mediated by polyketide synthase (PKS) genes. At the genomic level, studies on the biosynthesis of protist-derived polyketides have been very sparsely reported. For dinoflagellates this is due in part to the pecularities of the dinoflagellate genome in both structural and regulatory respects. Our research focuses on the identification and characterization of genes involved in spirolide biosynthesis, specifically PKS genes. Genomic characterization of A. ostenfeldii was conducted by generating two Expressed Sequence Tag (EST) data banks, based on normalized cDNA libraries of two strains of A. ostenfeldii (AOSH1 and AOSH2) from Nova Scotia, Canada, which produce distinctive spirolide profiles. About 5.300 and 12.287 ESTs were sequenced which yielded in 2.634 and 9.833 unique sequences, respectively. The ESTs were annotated and compared between the two strains. Several genes putatively related to toxin synthesis were detected, including genes encoding PKS. A Fosmid library was also generated to detect and further analyse toxin-related genes. Significant insights into the general genomic organisation of A. ostenfeldii and the relationship with putative toxin-producing genes are expected. The identification of polyketide biosynthetic genes from dinoflagellates provide the first steps for further research on this pharmalogically interesting enzyme group.

Alexandrium minutum is a widely distributed HAB dinoflagellate that typically produces PSP neurotoxins (gonyautoxins 1,2,3,4), as well as poorly characterized allelochemicals. Within the EU-Project ESTTAL (Expressed Sequence Tags of Toxic Algae), we aim to identify candidate genes and processes putatively involved in toxicity and allelochemical interactions, and in growth regulation and stress responses. To obtain RNA samples linked with physiological status, batch cultures of A. minutum were grown under different environmental conditions, yielding differences in growth, PSP toxin production, and allelochemical potency. As a basis for gene expression analysis, we generated a normalized cDNA library, from which about 10,000 expressed sequence tags (ESTs) were generated. Annotation of these data yielded first insights into the genome of A. minutum. Based on the EST library, we designed an oligonucleotide microarray, which will be used to screen for differences in gene expression among the differently treated A. minutum cultures. Here we present the results of the EST library analysis, the design of the microarray, and physiological data of cultures grown for gene expression analysis.

Udgivelsesdato: 2005-May-5, The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.