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See detailFull-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq.
Mehta, Devang; Cornet, Luc ULiege; Hirsch-Hoffmann, Matthias et al

in Nature Protocols (2020), 15(5), 1673-1689

Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus ... [more ▼]

Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long. [less ▲]

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See detailPalantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects.
Meunier, Loïc ULiege; Tocquin, Pierre ULiege; Cornet, Luc ULiege et al

in Bioinformatics (Oxford, England) (2020)

SUMMARY: To support small and large-scale genome mining projects, we present Palantir (Post-processing Analysis tooLbox for ANTIsmash Reports), a dedicated software suite for handling and refining ... [more ▼]

SUMMARY: To support small and large-scale genome mining projects, we present Palantir (Post-processing Analysis tooLbox for ANTIsmash Reports), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module, domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. AVAILABILITY: Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. [less ▲]

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See detailBiodiversity of Cyanobacteria and associated microbiome in the BCCM/ULC Culture Collection
Ahn, Anne-Catherine ULiege; Cornet, Luc ULiege; Beets, Kim ULiege et al

Poster (2019, October 18)

Cyanobacteria are a phylum of photosynthetic bacteria that played an important role in the evolution of the planet by oxygenating its early atmosphere and provoking the Great Oxydation Event around 2.3 ... [more ▼]

Cyanobacteria are a phylum of photosynthetic bacteria that played an important role in the evolution of the planet by oxygenating its early atmosphere and provoking the Great Oxydation Event around 2.3 billion years ago. Early cyanobacteria were the ancestors of plastids and thus, at the origin of the highly successful algae and plants. Nowadays, they still are the basis of the food chain in many biotopes, as long as there is liquid water, light, air and some minerals. Some cyanobacterial taxa are very resistant to harsh environmental conditions, and thus, grow in polar, hypersaline, alkaline and/or arid biotopes, but also in spatial conditions. Furthermore, they are also a prolific source of secondary compounds with bioactivies. The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 presently includes 224 cyanobacterial strains, with 140 being of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The strains are unicyanobacterial but not axenic, due to the well known difficulties of purifying them. Morphological identification showed that the strains belong to the orders of Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. Furthermore, 16S rRNA and ITS sequences of the strains are being characterized. Recent sequencing efforts increased the amount of available 16S rRNA sequences of BCCM/ULC strains to 190. Those sequences belong to 75 OTUs (groups of sequences with > 99 % 16S rRNA similarity), which represents a quite large diversity. To better characterize the microbiome of the cultures, a metagenomic analysis was performed for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. The design of a specific metagenomic pipeline enabled the easy recovery of the cyanobacterial genomes from the non-axenic cultures. In parallel, 31 genomes of co-cultivated bacteria (12 nearly complete) from the same cultures were determined. They mostly belonged to Bacteroidetes and Proteobacteria, some of them being very closely related, in spite of sometimes geographically distant sampling sites (Cornet et al. 2018). In summary, the BCCM/ULC public collection serves as a Biological Resource Centre to conserve ex situ and document the biodiversity of cyanobacteria and their microbiomes, as well as a repository for discovery of novel bioactive compounds. Cornet, L., Bertrand, A., Hanikenne, M., Javaux, E., Wilmotte, A., & Baurain, D. (2018). Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures. Microbial Genomics.4. DOI 10.1099/mgen.0.000212. [less ▲]

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See detailBCCM/ULC : genomic research on Polar cyanobacteria
Wilmotte, Annick ULiege; Beets, Kim ULiege; Simons, Véronique et al

in European Journal of Phycology (2019, August 27), 54(sup1), 31-117

The BCCM/ULC public collection of cyanobacteria aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins (microbial mats, soil crusts, cryoconites ... [more ▼]

The BCCM/ULC public collection of cyanobacteria aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins (microbial mats, soil crusts, cryoconites, endoliths, etc.) and ensure their ex-situ conservation in a context of global change. These strains are available for researchers to study the biodiversity, taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up of Polar cyanobacteria. Currently, there are 120 unicyanobacterial strains of Polar origin in the collection (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The collection is ISO 9001 certified for depositing and distributing strains, as part of the multi-site certification of the Belgian Co-ordinated Collections of Micro-organisms (BCCM) consortium. Morphological and molecular identification (based on 16S rRNA sequences) indicate that the strains belong to the orders Chroococcales, Chroococcidiopsidales, Nostocales, Oscillatoriales, Pleurocapsales, and Synechococcales. This broad genotypic distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. The first genome of an axenic Antarctic strain, Phormidesmis priestleyi ULC007, was sequenced. To investigate the occurrence of genes involved in the cold stress response, a selection of 42 PEGs (protein encoding genes) linked to cold adaptation was studied in 72 cyanobacterial genomes. By comparing the genes copy numbers as a proxy of adaptation, our results underline the importance of different functions in the adaptation mechanisms to the polar environment (e.g. DNA repair, Heat shock proteins, EPS biosynthesis). We also described a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures, tested on 17 cyanobacterial strains from the BCCM/ULC collection. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria. [less ▲]

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See detailCyanobacteria of Polar Regions: Focus of the BCCM/ULC Culture Collection
Ahn, Anne-Catherine ULiege; Beets, Kim ULiege; Lara, Yannick ULiege et al

Poster (2019, June 13)

In the Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. They build benthic microbial mats in lakes ... [more ▼]

In the Polar Regions, Cyanobacteria represent key primary producers and are the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. They build benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They may present interesting features to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other stresses. The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic mats, soil crusts, cryoconites, endoliths…). It makes it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up. It presently includes 224 cyanobacterial strains, with 140 being of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). An ISO 9001 certificate was obtained for the public deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. The morphological identification shows that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. The 16S rRNA and ITS sequences of the strains are gradually being characterized. The 159 BCCM/ULC strains for which 16S rRNA sequences were analyzed correspond to 69 OTUs (sequences with > 99 % 16S rRNA similarity), and thus, represent a quite large diversity. In addition, cyanobacteria are known to produce a wide range of secondary metabolites (e.g. alkaloids, cyclic and linear peptides, polyketides) with bioactive potential. Genome sequencing was performed for 15 strains (Lara et al. 2017, Cornet et al. 2018). The bioinformatic analysis of the partial genomes of strains ULC007, ULC065 and ULC129 showed the presence of clusters encoding NRPS, PKS, hybrid clusters and other types of secondary metabolites. The comparison of a selection of the PEGs involved in the cold adaptation mechanisms revealed that more copies of PEGs involved in various molecular mechanisms of cold stress responses have been found in polar than in non polar genomes. In summary, the BCCM/ULC public collection serves as a Biological Resource Centre to conserve ex situ and document the biodiversity of polar cyanobacteria, as well as a repository for discovery of novel bioactive compounds. [less ▲]

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See detailCyanobacteria evolution: Insight from the fossil record
Demoulin, Catherine ULiege; Lara, Yannick ULiege; Cornet, Luc ULiege et al

in Free Radical Biology and Medicine (2019), 140

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 ... [more ▼]

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis. © 2019 The Authors [less ▲]

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See detailBCCM/ULC: a collection of cyanobacteria linking Poles to Space
Wilmotte, Annick ULiege; Beets, Kim ULiege; Santoro, Mariano ULiege et al

Conference (2018, December 18)

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the cyanobacterial diversity with a focus on Polar biotopes (e.g. limnetic ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the cyanobacterial diversity with a focus on Polar biotopes (e.g. limnetic microbial mats, soil crusts, cryoconites, endolithes). It represents an exclusive Biological Resource Centre (BRC) where characterized polar cyanobacterial strains are available for researchers to study the taxonomy, biogeography, evolution, synthesis of secondary metabolites, adaptation to harsh environmental conditions, and genomic make-up. It currently holds 190 strains, including over 120 of Polar origin (online catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). Living cultures are regularly transferred, and the majority are also cryopreserved (as back-up), in order to assure their preservation and the rapid delivery of strains to clients for fundamental and applied research in both academia and industry. Genomic DNA is also available on request. The collection has obtained the ISO 9001:2015 certification for deposit and distribution of strains, as part of the multi-site certification for the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. A polyphasic approach based on morphological and molecular identifications (based on SSU rRNA sequences) show that the strains belong to the Synechococcales, Oscillatoriales, Chroococcidiopsidales, Pleurocapsales, and Nostocales orders. This large diversity renders the BCCM/ULC collection particularly interesting for taxonomic, biogeographic and phylogenomic studies. Furthermore, the sequencing of the genomes of several strains has started. The BRC also aims to become a source for researchers to study further applications of cyanobacteria in astrobiology as shown by investigations of the resistance to desiccation and radiation of strains of Chroococcidiopsis sp. dominating rock-dwelling communities in extreme dry environments [1]. In paleontology, cyanobacteria represent model organisms thanks to their fundamental role in the oxygenation of the atmosphere and oceans during the Great Oxidation Event. Lastly, the mat-forming cyanobacterial strains may represent “critical organisms” in the investigation of the factors that determine the boundaries of microbial survival and growth on Earth and in the space environment, by virtue of the fact that they are components of microbial mat model systems which are more and more used to elucidate Earth’s past and the detection of life’s biosignatures. [less ▲]

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See detailA Novel Method of Capturing and Sequencing Rolling Circle-Replicating Helitron Transposons
Syed-Shan-e-Ali, Zaïdi ULiege; Cornet, Luc ULiege; Mehta, Devang et al

Scientific conference (2018, October 28)

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See detailCombining BAC and PacBio sequencing to resolve cassava mosaic disease resistance locus CMD2
Syed-Shan-e-Ali, Zaïdi ULiege; Cornet, Luc ULiege; Comadira, Gloria et al

Scientific conference (2018, October 16)

Cassava provides staple food to an estimated 800 million people worldwide and is the most important source of food in developing countries after maize, rice, and wheat. However, cassava production is ... [more ▼]

Cassava provides staple food to an estimated 800 million people worldwide and is the most important source of food in developing countries after maize, rice, and wheat. However, cassava production is severely affected by virus-borne cassava mosaic disease (CMD) in Africa and the Indian subcontinent. Annual yield losses due to CMD are estimated to be 55 million tones. A milestone in molecular breeding to for CMD was the identification of single dominant disease resistance locus CMD2. But recent studies have shown that CMD2 cultivars lost resistance during early stages of somatic embryogenesis in tissue culture. It is therefore necessary to understand the mechanism of CMD2-mediated resistance for its efficient utilization in the cassava improvement. My research aims at combining BAC sequencing, whole genome PacBio sequencing and mapping population of CMD resistant (TME3) and susceptible (60444) accessions to fully sequence, assemble and compare the CMD2 locus. We have generated BAC libraries for both cassava genotypes and screened these libraries to identify CMD2-associatted BACs. We have used the information available from classical marker-assisted breeding studies to develop high quality probes for BAC hybridization. Using this pipeline, we have selected and sequenced 33 BACs on PacBio platform, that cover ~3MB of estimated 8MB CMD2 locus. Further, we have used the latest whole genome assemblies of TME3 and 60444 (accessible from ETH Zurich), to perform comparative analysis. In summary, our results have shown that BAC sequencing is an efficient approach for resolving CMD2, specially in the highly repetitive regions. These results have important implications in understanding CMD and developing a long term strategy to control CMD in farmer fields. [less ▲]

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See detailThe BCCM/ULC collection of cyanobacteria in the spotlight at ULiège
Santoro, Mariano ULiege; Beets, Kim ULiege; Simons, Véronique et al

Poster (2018, October 11)

The ULC public collection of cyanobacteria belongs since 2011 to the consortium of Belgian Co-Ordinated Collections of Microorganisms (BCCM). It aims to conserve ‘ex situ’ a representative portion of the ... [more ▼]

The ULC public collection of cyanobacteria belongs since 2011 to the consortium of Belgian Co-Ordinated Collections of Microorganisms (BCCM). It aims to conserve ‘ex situ’ a representative portion of the biodiversity of cyanobacterial diversity of different origins, with a focus on Antarctic and Artic cyanobacteria isolated from terrestrial and aquatic ecosystems. BCCM/ULC currently holds 174 cyanobacterial strains that are available for researchers who study taxonomy, evolution, biogeography and the adaptation to harsh environmental conditions. The strains are identified by morphology and molecular characterization (based on rRNA sequences) and belong to the Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales orders. This large taxonomic distribution renders it a suitable reference point for phylogenomic and genomic make-up studies. Regular transfer of living cultures ensures the conservation of strains, whose majority are also cryopreserved in order to limit the genetic drift. BCCM/ULC obtained an ISO 9001:2015 certification for public and safe deposits, and for distribution of living strains and genomic DNA. The BCCM policy continuously aims to guarantee a safe fit-for-use microbiological material and data compliant with the rules on access and utilization of the Nagoya Protocol. In addition, BCCM/ULC provides, to clients from academia & industry, a service of morphological identification and molecular characterization, along with other scientific services as tailor-made trainings and collaborations. The public collection is progressively enriched by public deposits from other geographical areas and by incorporating the most interesting strains from the research collection of the host laboratory. The latter is also involved in the valorisation of the collection and collaborations, aiming to study the molecular mechanisms of adaptation to cold stress in polar strains, their production of potential bioactive compounds, to decipher and analyze their genomes and to determine the usefulness of their pigments as ‘traces of life’ in astrobiology. [less ▲]

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See detailEx-situ conservation and exploration of polar cyanobacteria in the BCCM/ULC Collection
Wilmotte, Annick ULiege; Santoro, Mariano; Beets, Kim ULiege et al

Poster (2018, October)

The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.). It makes it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up. It presently includes 174 cyanobacterial strains, with more than half being of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). [less ▲]

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See detailEx-situ Conservation of Polar Cyanobacteria in the BCCM/ULC Collection
Wilmotte, Annick ULiege; Beets, Kim; Simons, Véronique et al

Poster (2018, June)

The BCCM/ULC public collection is funded by the Belgian Science Policy Office (BELSPO) and aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins ... [more ▼]

The BCCM/ULC public collection is funded by the Belgian Science Policy Office (BELSPO) and aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and ensure their ex-situ conservation in a context of global change. These strains are available for researchers to study the biodiversity, taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up of Polar cyanobacteria. Currently, there are 120 cyanobacterial strains of Polar origin in the collection (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The strains are kept living and their cryopreservation is currently tested. The collection is ISO 9001 certified for depositing and distributing strains, as part of the multi-site certification of the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. Morphological and molecular identification (based on 16S rRNA sequences) indicate that the strains belong to the orders Chroococcales, Chroococcidiopsidales, Nostocales, Oscillatoriales, Pleurocapsales, and Synechococcales. This broad genotypic distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. The genomes of several strains are currently being sequenced and the first genome of an Antarctic cyanobacterial strain, Phormidesmis priestleyi ULC007 was recently published. [less ▲]

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See detailPolar cyanobacteria in the BCCM/ULC collection : diversity and characterization
Lara, Yannick ULiege; Beets, Kim ULiege; Simons, Véronique et al

Poster (2018, March)

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (e.g ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (e.g. limnetic microbial mats, soil crusts, cryoconites, endoliths). It makes it available for researchers to study the taxonomy, evolution, adaptation to harsh environmental conditions, and genomic make-up. It presently includes 177 cyanobacterial strains, including 120 of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). Continuous maintenance of living cultures, most of which are also cryopreserved (as back-up), ensure the preservation and the rapid delivery of strains to clients for fundamental and applied research. Genomic DNA is also available on request. The collection has obtained the ISO 9001 certification for deposition and distribution of strains, as part of the multi-site certification for the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. Morphological and molecular identifications (based on SSU rRNA 16S sequences) show that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, and Nostocales. This broad ordinal distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. Hence, the sequencing of the genomes of several strains is underway. In addition, cyanobacteria produce a range of secondary metabolites (e.g. alkaloides, peptides, polyketides) with different potential bioactivities. Due to their geographic isolation and strong environmental stressors in their habitat, the exploration of Antarctic cyanobacteria metabolites is likely promising for both biotechnology or biomedical applications. [less ▲]

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See detailThe survival toolkit of the Antarctic cyanobacterium Phormidesmis priestleyi ULC007
Lara, Yannick ULiege; Durieu, Benoit ULiege; Pessi, Igor et al

Conference (2018, March)

Extreme seasonality led by rapid changes in day length and harsh environmental conditions make Antarctica a unique habitat. Freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to ... [more ▼]

Extreme seasonality led by rapid changes in day length and harsh environmental conditions make Antarctica a unique habitat. Freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to perennially ice-covered lakes where conspicuous benthic microbial mat communities constitute most of the biomass. In these mats, cyanobacteria form the matrix in which other microorganisms can live, and where they are the key primary producers and main drivers of the carbon and food webs[1].
Narrow filamentous cyanobacteria belonging to the order Pseudanabaenales are especially abundant in polar microbial mats [2]. Despite the dominance of cyanobacteria on the Antarctic continent, there is currently no study available on the genomic evolution of Antarctic cyanobacteria. Here we investigate the genome of a widely distributed Antarctic cyanobacterium, Phormidium priestleyi ULC007. To provide a better understanding of the survival strategies of this taxon, we used high-throughput sequencing technologies to investigate its geographic distribution and genome evolution. More precisely, we investigated the abundance of genes in targeted functional categories based on the RAST subsystems technology, so as to provide a better overview of the genetic mechanisms involved in cold adaptation and circadian oscillation [3]. In Polar regions, low temperatures lead to the success of particular organisms featuring adaptations to molecular and cellular disturbances such as rigidity of membranes, reduction of enzyme-catalyzed reactions, and solute transport. Our main results underline the importance of functional categories of genes involved in the production of key molecules for the survival of polar P. priestleyi (e.g. exopolysaccharides, chaperone proteins, fatty acids and phospholipids). [less ▲]

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See detailGenomics, Metagenomics and Phylogenomics of Cyanobacteria
Cornet, Luc ULiege

Doctoral thesis (2018)

This PhD thesis concerns the genomics, metagenomics and phylogenomics of Cyanobacteria. It is composed of five main parts, of which four are result manuscripts. In the first part (i.e., Introduction), I ... [more ▼]

This PhD thesis concerns the genomics, metagenomics and phylogenomics of Cyanobacteria. It is composed of five main parts, of which four are result manuscripts. In the first part (i.e., Introduction), I review a decade of cyanobacterial phylogeny and molecular dating. I show that, in spite of a considerable literature, the global topology of the cyanobacterial tree is incongruent across 9 of the 12 recent studies. I also raise the issue that cyanobacterial datings are all based on ambiguous fossils, since no genomic data are available for unambiguous fossil calibration points. The second part deals with the problem of public genome contamination. I analyzed 440 genomes of Cyanobacteria with a consensus approach of five methods (two based on ribosomal genes and three based on complete genome analysis), and determined that >5% cyanobacterial genomes are contaminated by foreign DNA. The next two parts are metagenomic analyses. The first metagenomic study is a pipeline for properly assembling complete genomes from non-axenic cultures. To this end, I used 17 cyanobacterial cultures from the BCCM/ULC collection of the ULiège and assembled metagenomic reads into 15 genomes with a very low level of contaminants and a high level of completeness. The second metagenomic study deals with the new field of phylometagenomics. Hence, I developed a new syntenic algorithm designed for metagenomes in mind, and applied it to the study of lichenized Cyanobacteria. I found 90 syntenic and collinear genes shared between 28 Nostocales genomes, including 12 new photobiont metagenomes. The subsequent phylogenetic analysis showed a relatively high level of congruence among these genes. Finally, the last part of the thesis is a large constrained SSU rRNA (16S) tree intended to serve as a guide in organism selection for future sequencing projects. It revealed 31 clusters of Cyanobacteria that are completely devoid of representative genomes (<0.1%). Altogether, the results of this PhD work lay the ground for a better phylogenomic study of the Cyanobacteria, taking advantage of new key organisms. [less ▲]

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See detailHigh-throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits
Maciejewska, Marta ULiege; Całusińska, Magdalena; Cornet, Luc ULiege et al

in Antibiotics (2018), 7(2)(28),

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See detailMetagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.
Cornet, Luc ULiege; Bertrand, Amandine ULiege; Hanikenne, Marc ULiege et al

in Microbial Genomics (2018), 4

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are ... [more ▼]

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites. [less ▲]

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See detailConsensus assessment of the contamination level of publicly available cyanobacterial genomes.
Cornet, Luc ULiege; Meunier, Loïc ULiege; Van Vlierberghe, Mick ULiege et al

in PLoS ONE (2018), 13(7), 0200323

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for ... [more ▼]

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases. [less ▲]

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See detailA constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria).
Cornet, Luc ULiege; Wilmotte, Annick ULiege; Javaux, Emmanuelle ULiege et al

in BMC Research Notes (2018), 11(1), 435

OBJECTIVE: Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria. This group has been extensively studied by phylogenomics notably because it is widely accepted that ... [more ▼]

OBJECTIVE: Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria. This group has been extensively studied by phylogenomics notably because it is widely accepted that Cyanobacteria were responsible for the spread of photosynthesis to the eukaryotic domain. The aim of this study was to evaluate the fraction of the oxyphotobacterial diversity for which sequenced genomes are available for genomic studies. For this, we built a phylogenomic-constrained SSU rRNA (16S) tree to pinpoint unexploited clusters of Oxyphotobacteria that should be targeted for future genome sequencing, so as to improve our understanding of Oxyphotobacteria evolution. RESULTS: We show that only a little fraction of the oxyphotobacterial diversity has been sequenced so far. Indeed 31 rRNA clusters of the 60 composing the photosynthetic Cyanobacteria have a fraction of sequenced genomes < 1%. This fraction remains low (min = 1%, median = 11.1%, IQR = 7.3%) within the remaining "sequenced" clusters that already contain some representative genomes. The "unsequenced" clusters are scattered across the whole Oxyphotobacteria tree, at the exception of very basal clades. Yet, these clades still feature some (sub)clusters without any representative genome. This last result is especially important, as these basal clades are prime candidate for plastid emergence. [less ▲]

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See detailThe BCCM/ULC collection to conserve the biodiversity and study the secondary metabolites of Antarctic cyanobacteria
Lara, Yannick ULiege; Durieu, Benoit ULiege; Renard, Marine et al

in Van de Putte, Anton (Ed.) Book of abstracts: XIIth SCAR Biology Symposium, Leuven, Belgium, 10-14 July 2017. (2017, June)

The BCCM/ULC public collection is funded by the Belgian Science Policy Office since 2011. A Quality Management System ensures that the services of deposits (both public and safe) and distribution are well ... [more ▼]

The BCCM/ULC public collection is funded by the Belgian Science Policy Office since 2011. A Quality Management System ensures that the services of deposits (both public and safe) and distribution are well documented and efficient for the clients’ satisfaction. It has obtained the ISO 9001 certification for deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. This collection aims to gather a representative portion of the Antarctic cyanobacterial diversity with different ecological origins (limnetic mats, soil crusts, cryoconites, endoliths…) and make it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, pigments, and genomic make-up. It presently includes 216 cyanobacterial strains, of which 119 are of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). In addition, cyanobacteria are known to produce a wide range of secondary metabolites (e.g. alkaloids, cyclic and linear peptides, polyketides) with bioactive potential. Genome sequencing of 11 strains has been started to enable genome mining for biosynthetic clusters. Pair-read data from illumina MiSeq runs were obtained and submitted to a bioinformatic pipeline dedicated to the assembly of genomes and search of sequences involved in the biosynthesis of secondary metabolites. Gene cluster prediction analysis allowed to characterize 20 clusters of NRPS, PKS and hybrid NRPS-PKS from 2 to 66kb. Surprisingly, none of the characterized operons had previously been described in the literature. [less ▲]

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