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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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See detailStreptomyces from Moonmilk, an Untapped Source of New Bioactive Compounds
Martinet, Loïc ULiege; Maciejewska, Marta; Adam, Delphine ULiege et al

Poster (2017, May 24)

Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical ... [more ▼]

Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical properties, thereby suggesting that its filamentous endemic actinobacterial population might be a source of natural products useful in human treatment. In this work, a screening approach was undertaken in order to isolate cultivable Actinobacteria from moonmilk of the Grotte des Collemboles in Belgium, to evaluate their taxonomic profile, and to assess their potential in biosynthesis of antimicrobials. Phylogenetic analysis revealed that all 78 isolates were exclusively affiliated to the genus Streptomyces and clustered into 31 distinct phylotypes displaying various pigmentation patterns and morphological features. Phylotype representatives were tested for antibacterial and antifungal activities and their genomes were mined for secondary metabolite biosynthetic genes coding for non-ribosomal peptide synthetases (NRPSs), and polyketide synthases (PKS). The moonmilk Streptomyces collection was found to display strong inhibitory activities against a wide range of reference organisms, as 94, 71, and 94% of the isolates inhibited or impaired the growth of Gram-positive, Gram-negative bacteria, and fungi, respectively. Interestingly, 90% of the cave strains induced strong growth suppression against the multi-drug resistant Rasamsonia argillacea, a causative agent of invasive mycosis in cystic fibrosis and chronic granulomatous diseases. We are currently identifying molecules responsible for the observed antimicrobial activities which, next to few known bioactive compounds, also reveals many active compounds with molecular masses that do not correspond to known antibiotic deposited in web biomolecules databases such as KNapSAcK, Pubchem, Chemspider. The challenge is to increase the production yields of these unknown compounds, and purify them to further characterize their structure by NMR. Overall, our work supports the common belief that moonmilk might effectively treat various infectious diseases thanks to the presence of a highly diverse population of prolific antimicrobial producing Streptomyces, and thus may indeed constitute a promising reservoir of potentially novel active natural compounds. [less ▲]

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See detailToRQuEMaDA: Tool for retrieving queried eubacteria, metadata and dereplicating assemblie
Léonard, Raphaël ULiege; Sirjacobs, Damien ULiege; Sauvage, Eric ULiege et al

Poster (2017, May 11)

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a problem when trying to assemble broadly sampled genome sets for phylogenomics and comparative ... [more ▼]

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a problem when trying to assemble broadly sampled genome sets for phylogenomics and comparative genomics. Indeed, most of the new genomes belong to the same subset of hyper-sampled phyla, such as Proteobacteria and Firmicutes, or even to single species, such as Escherichia coli (>3000 genomes as of March 2017), while the continuous flow of newly discovered phyla prompts for regular updates of in-house databases. This situation makes it difficult to maintain sets of representative genomes combining lesser known phyla, for which only few species are available, and sound subsets of highly abundant phyla. An automated method is required but none are publicly available. In this work, the kmer composition of DNA sequences, in conjunction with quality metrics for publicly available assemblies, was used to develop an automated approach for selecting a high-quality subset of representative genomes without redundancy by using our hybrid divide-and-conquer / greedy clustering method. [less ▲]

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See detailDraft Genome of the Axenic Strain Phormidesmis priestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)
Lara, Yannick ULiege; Durieu, Benoit ULiege; Cornet, Luc ULiege et al

in Genome Announcements (2017)

Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacte- rium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein- encoding genes, of which 22.2% have no clear ... [more ▼]

Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacte- rium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein- encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica. [less ▲]

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See detailPhylotranscriptomic consolidation of the jawed vertebrate timetree.
Irisarri, Iker; Baurain, Denis ULiege; Brinkmann, Henner et al

in Nature ecology & evolution (2017), 1(9), 1370-1378

Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model ... [more ▼]

Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates. [less ▲]

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See detailInferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.
Rodriguez, Ariel; Burgon, James D.; Lyra, Mariana et al

in Molecular Phylogenetics & Evolution (2017), 115

The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduces a risk of being ... [more ▼]

The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduces a risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra, a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity. For all six species of the genus Salamandra, and two outgroup species from its sister genus Lyciasalamandra, we used RNA sequencing (RNAseq) and restriction site associated DNA sequencing (RADseq) to obtain data for: (1) 3070 nuclear protein-coding genes from RNAseq; (2) 7440 loci obtained by RADseq; and (3) full mitochondrial genomes. The RNAseq and RADseq data sets retrieved fully congruent topologies when each of them was analyzed in a concatenation approach, with high support for: (1) S. infraimmaculata being sister group to all other Salamandra species; (2) S. algira being sister to S. salamandra; (3) these two species being the sister group to a clade containing S. atra, S. corsica and S. lanzai; and (4) the alpine species S. atra and S. lanzai being sister taxa. The phylogeny inferred from the mitochondrial genome sequences differed from these results, most notably by strongly supporting a clade containing S. atra and S. corsica as sister taxa. A different placement of S. corsica was also retrieved when analysing the RNAseq and RADseq data under species tree approaches. Closer examination of gene trees derived from RNAseq revealed that only a low number of them supported each of the alternative placements of S. atra. Furthermore, gene jackknife support for the S. atra - S. lanzai node stabilized only with very large concatenated data sets. The phylogeny of true salamanders thus provides a compelling example of how classical node support metrics such as bootstrap and Bayesian posterior probability can provide high confidence values in a phylogenomic topology even if the phylogenetic signal for some nodes is spurious, highlighting the importance of complementary approaches such as gene jackknifing. Yet, the general congruence among the topologies recovered from the RNAseq and RADseq data sets increases our confidence in the results, and validates the use of phylotranscriptomic approaches for reconstructing shallow relationships among closely related taxa. We hypothesize that the evolution of Salamandra has been characterized by episodes of introgressive hybridization, which would explain the difficulties of fully reconstructing their evolutionary relationships. [less ▲]

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See detailAssessment of the Potential Role of Streptomyces in Cave Moonmilk Formation
Maciejewska, Marta; Adam, Delphine; Naomé, Aymeric ULiege et al

in Frontiers in Microbiology (2017), 8

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See detailHigh-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication
Mauroy, Axel ULiege; Taminiau, Bernard ULiege; Nezer, Carine et al

in Archives of Virology (2017), 16(4), 1019-1023

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in ... [more ▼]

In this study, we report the genetic diversity and nucleotide mutation rates of five representative regions of the murine norovirus genome during in vitro passages. The mutation rates were similar in genomic regions encompassing partial coding sequences for non-structural (NS) 1-2, NS5, NS6, NS7 proteins within open reading frame (ORF) 1. In a region encoding a portion of the major capsid protein (VP1) within ORF2 (also including the ORF4 region) and a portion of the minor structural protein (VP2), the mutation rates were estimated to be at least one order of magnitude higher. The VP2 coding region was found to have the highest mutation rate. [less ▲]

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See detailA Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals.
Simion, Paul; Philippe, Herve; Baurain, Denis ULiege et al

in Current Biology (2017)

Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera ... [more ▼]

Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals ("Porifera-sister" hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The "Ctenophora-sister" hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged. [less ▲]

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See detailPitfalls in supermatrix phylogenomics
Philippe, Hervé; Vienne, Damien M. De; Ranwez, Vincent et al

in European Journal of Taxonomy (2017), 283

In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then ... [more ▼]

In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted “the end of incongruence”, it soon appeared that analysing large amounts of sequence data without an adequate model of sequence evolution amplifies systematic error and leads to phylogenetic artefacts. With the increasing flood of (sometimes low-quality) genomic data resulting from the rise of high-throughput sequencing, a new type of error has emerged. Termed here “data errors”, it lumps together several kinds of issues affecting the construction of phylogenomic supermatrices (e.g., sequencing and annotation errors, contaminant sequences). While easy to deal with at a single-gene scale, such errors become very difficult to avoid at the genomic scale, both because hand curating thousands of sequences is prohibitively time-consuming and because the suitable automated bioinformatics tools are still in their infancy. In this paper, we first review the pitfalls affecting the construction of supermatrices and the strategies to limit their adverse effects on phylogenomic inference. Then, after discussing the relative non-issue of missing data in supermatrices, we briefly present the approaches commonly used to reduce systematic error. [less ▲]

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

Poster (2016, November 16)

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

In the Polar Regions, Cyanobacteria are the key primary producers and main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in lakes and soil crusts. Their success in these harsh cold conditions can probably be explained by particular adaptations to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other environmental stresses. The BCCM/ULC public collection is funded by the Belgian Science Policy Office since 2011. It has obtained the ISO9001 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 polar 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 226 cyanobacterial strains, of which 119 are of Antarctic origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). As shown by morphological identification, the strains belong to five orders (Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales). The 16S rRNA and ITS sequences of the strains are being characterized. The first 85 Antarctic strains already studied are distributed into 25 Operational Taxonomic Units (OTUs = groups of sequences with > 97,5% 16S rRNA similarity), and thus, represent a quite large diversity. Moreover, strains identified as members of the genera Leptolyngbya or Phormidium appear in several lineages. This supports the idea that there is a need to revise the taxonomy of these polyphyletic genera with a simple filamentous morphology. To better understand the functioning, metabolism and adaptative strategies of cyanobacteria in the extreme Antarctic environment, the genome sequencing of 11 strains has been started. 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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See detailPREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool
Tocquin, Pierre ULiege; Naomé, Aymeric ULiege; Jourdan, Samuel ULiege et al

E-print/Working paper (2016)

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their ... [more ▼]

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/. [less ▲]

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See detailThe BCCM/ULC collection to conserve the biodiversity and explore the applied potential of Polar cyanobacteria
Becker, Pierre; SZTERNFELD, P; ANDJELKOVIC, M et al

Poster (2016, October 28)

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. For example, they build benthic microbial ... [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. For example, 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 226 cyanobacterial strains, with 119 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 being characterized. Our results show that the Antarctic strains are positioned into 25 OTUs (sequences with > 97,5% 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. Among these bioactive metabolites, some display antibiotic, anticancer or antifungal effects. In collaboration with the BCCM/IHEM collection of biomedical fungi, a screening of cyanobacterial strains from BCCM/ULC was performed in order to discover potential new antifungal drugs. The analysis of a first set of methanol extracts from 15 different strains put in evidence the antifungal activity of a Phormidium priestleyi isolate. The latter remains active up to 0.5% (v/v) of fungal culture and was able to inhibit the growth of various fungal species among Candida, Cryptococcus, Aspergillus, and Penicillium. The raw extract was subjected to HPLC and a fraction containing the active molecule was obtained. This molecule appeared to be a thermostable hydrophobic compound. Moreover, in vitro toxicological analyses suggest that the compound has a general cytotoxic effect that could be inhibited by the mammalian metabolism. Further analyses are needed to identify the molecule and to determine if it could be a candidate for a new antifungal drug. 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 detailThe BCCM/ULC collection to conserve and study the biodiversity of Polar cyanobacteria
Wilmotte, Annick ULiege; Renard, Marine ULiege; Lara, Yannick ULiege et al

Poster (2016, September)

The BCCM/ULC public collection of Cyanobacteria has been funded since 2011 by the Belgian Science Policy Office. BCCM/ULC is currently holding 226 cyanobacterial strains, with 119 being of Antarctic ... [more ▼]

The BCCM/ULC public collection of Cyanobacteria has been funded since 2011 by the Belgian Science Policy Office. BCCM/ULC is currently holding 226 cyanobacterial strains, with 119 being of Antarctic origin (including 3 from the sub-Antarctic). The cyanobacteria constitute the bacterial phylum with the largest morphological diversity and their taxonomy is still a work in progress. In Polar Regions, Cyanobacteria represent key primary producers and are important drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build extensive benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They have adapted to their environment, and may present interesting features to survive freeze/thaw cycles, seasonally contrasted light intensities, high UV radiations, dessication and other stresses. In this poster, we present the results of the 16S rRNA phylogenetic analysis for 76 Antarctic strains. This allows us to illustrate the diversity present in the collection, to detect lineages for which no genome has yet been sequenced, and to pinpoint taxonomic problems that should be addressed in a more comprehensive study. [less ▲]

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See detailThe BCCM/ULC collection: a Biological Ressource Center to give access to the Antarctic cyanobacterial diversity
Wilmotte, Annick ULiege; Renard, Marine ULiege; Lara, Yannick ULiege et al

Poster (2016, August)

On the Antarctic continent, Cyanobacteria represent the key primary producers and the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic ... [more ▼]

On the Antarctic continent, Cyanobacteria represent the key primary producers and the main drivers of the food webs in a wide range of aquatic to terrestrial habitats. For example, they build benthic microbial mats in lakes and soil crusts in terrestrial biotopes. They may present interesting features to survive freeze/thaw cycles, sea-sonally 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 microbial mats, soil crusts, cryoconites, endoliths, etc.). It makes it available for researchers to study the taxonomy, evolu-tion, adaptations to harsh environmental conditions, and genomic make-up. It pres-ently includes 226 cyanobacterial strains, with 119 being of Antarctic origin (cata-logue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The morphological identification shows that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. We present here the molecular datasets showing the diversity of the BCCM/ULC strains, studied on the basis of the 16S rRNA gene. A selection of strains was also characterized by sequencing of rpoC1, recA, and gyrA genes after amplification with newly designed primers. Our results mainly show that 25 OTUs included strains of Antarctic origin. Moreo-ver, strains identified as members of the genera Leptolyngbya or Phormidium ap-pear in several lineages. This supports the need to revise these polyphyletic genera with a simple filamentous morphology. A certain divergence of some Antarctic strains from related strains isolated from other regions can also be observed. It suggests that a portion of the Antarctic cyanobacterial flora may have evolved in-dependently from the cyanobacteria in other continents. [less ▲]

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See detailHTC Bayesian Phylogenomics on the Zenobe Tier-1 supercomputer
Baurain, Denis ULiege

Conference (2016, April 22)

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See detailCoding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle.
Kadri, Naveen Kumar ULiege; Harland, Chad ULiege; Faux, Pierre ULiege et al

in Genome Research (2016)

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events ... [more ▼]

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for approximately 10% of the genetic variance in males. [less ▲]

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See detailUsing Next Generation Sequencing to characterize species diets: a study case with faeces of wild boar in the Spanish Pyrenees
Mouton, Alice ULiege; Espelta, Jose Maria; Baurain, Denis ULiege et al

Poster (2016)

The genomic era offer an exciting opportunity to establish biodiversity assessment for plants and animals. More specifically, DNA metabarcoding can be used as a proxy for the biodiversity existing in a ... [more ▼]

The genomic era offer an exciting opportunity to establish biodiversity assessment for plants and animals. More specifically, DNA metabarcoding can be used as a proxy for the biodiversity existing in a sample (soil, water, faeces,..) and therefore it represents a powerful and a non invasive tool to answer concerns regarding ecological questions (conservation, restoration). To illustrate such prospect, we conducted a study on the expanding wild boar populations in the Spanish Pyrenees. Over the last decades, the populations of wild boar are growing in the Iberian peninsula mainly due to their high adaptability to new environments, new climates, varied diets and high reproduction rates. Despite the economic interest of the species in the Peninsula, this expansion cause many damage on ecosystems, humans and farming practices. By moving higher in altitude, it has been suggested that the wild boar populations might be responsible for the rapid decline of the endangered capercaillie (Tetrao urogallus) populations in the Pyrenees. By searching for food, they come accross the ground nesting bird nest and gobble the eggs. The aim of this study was therefore to analyze the diet of the wild boar populations in higher altitude in the Spanish Pyrenees. 81 faecal samples collected during summer and autumn 2014 in the Aigues Tortes National Park have been extracted, amplified and sequenced using the Illumina Technology. With this method, a precise estimation of the animal prey existing in the wild boar faeces was possible and will eventually allow wild life managers to apply concrete management measures for this expanding species. [less ▲]

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See detailGram-Negative Bacteria: "Inner" vs. "Cytoplasmic" or "Plasma Membrane": A Question of Clarity rather than Vocabulary
Baurain, Denis ULiege; Wilmotte, Annick ULiege; Frère, Jean-Marie ULiege

in Journal of Microbial and Biochemical Technology (2016), 8(4), 325-326

In this short commentary, we show that the utilisation of the term “inner membrane” to characterize the cytoplasmic or plasma membrane of Gram-negative bacteria can be a source of confusion and we propose ... [more ▼]

In this short commentary, we show that the utilisation of the term “inner membrane” to characterize the cytoplasmic or plasma membrane of Gram-negative bacteria can be a source of confusion and we propose that it should be completely abandoned. [less ▲]

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