Biology subjects

Cornet, L.

Publications and source records attributed to Cornet, L..

18 recordsLinked to original sources

bioRxiv2026

An endolithic Gloeobacter and other novel cyanobacterial diversity in alpine dolomites of Piora Valley

Background: Cyanobacteria are the major phototrophs in many endolithic ecosystems, yet their genomic diversity and metabolic adaptations remain poorly characterized. Here, we investigated cyanobacterial diversity in endolithic dolomite rocks from the Piora Valley in the southern Swiss Alps using genome-resolved metagenomics. Results: We reconstructed 138 medium-quality metagenome-assembled genomes (MAGs) from four neighboring endolithic rock communities, including 15 cyanobacterial MAGs distributed across six order-level lineages. The cyanobacterial communities showed limited taxonomic overlap among rocks, and most recovered MAGs represented potentially novel species. Only one Gloeobacter lineage occurred in all sampled rocks, which we propose as Gloeobacter dolomitensis sp. nov., representing the first Gloeobacter genome recovered from an endolithic environment. Comparative genomic analyses identified a cynS gene encoding cyanase unique to G. dolomitensis among the Gloeobacter. Phylogenetic analyses support its horizontal acquisition from Pseudomonadota. Interestingly, the genome of G. dolomitensis lacks a canonical CynABD cyanate transporter and instead contains a distinct ATP-synthase binding cassette (ABC) transporter adjacent to cynS. Although the available genomic and structural evidence does not establish cyanate transport, its genomic association with cynS suggests a potentially non-canonical mechanism. We further show that horizontal gene transfer was unevenly distributed among cyanobacterial lineages, with Acaryochloridales acting predominantly as donors, Chroococcidiopsidales as recipients, and Gloeobacterales showing a comparatively high frequency of interphylum gene exchange. Conclusions: The Piora Valley dolomite environment represents an underexplored reservoir of cyanobacterial diversity, including basal and previously undescribed lineages. The discovery of G. dolomitensis and its unusual cyanate-associated genomic architecture expands our understanding of Gloeobacterales diversity and highlights the potential importance of horizontal gene acquisition and metabolic innovation in endolithic microbial communities.

evolutionary biology↗

bioRxiv2026

A new automated pipeline for whole genome shotgun sequencing analysis and hazard characterization of microbial pesticides

Microbial pesticides are increasingly important for sustainable crop protection, yet hazard analysis and risk assessment remain challenging and require specific characterization of properties relevant to both safety and biological activity. Whole-genome sequencing (WGS) can support the identification of microorganisms at high resolution and characterize potential hazards associated with infectivity, pathogenicity, antimicrobial resistance, and toxic metabolite production. However, the routine use of WGS in this context requires accessible, reproducible, and interpretable workflows. Here, we present a publicly available web-based workflow for WGS-supported hazard analysis of microbial biocontrol agents. The workflow accepts assembled genomes as well as short-read, long-read and hybrid sequencing data, and performs genome quality assessment, taxonomic assignment, genome annotation, AMR detection, mobile-element screening, pathogenicity prediction and secondary-metabolite analysis, and compiles the results into an HTML report. For bacterial agents, we implement a transparent rule-based risk-classification module integrating taxonomic identity, PathogenFinder2 predictions, CARD/RGI resistance evidence, WHO priority taxa, and medically important antimicrobial categories. Secondary-metabolite assessment combines antiSMASH with local BLAST searches and EFSA-aligned identity/coverage thresholds to support product-level interpretation of biosynthetic gene clusters. Comparison with the currently used MOpS workflow developed by EFSA demonstrates the added benefits of the proposed workflow for a guided hazard analysis of microbial pesticides. The workflow is intended as a community-accessible pre-assessment tool that complements regulatory platforms by improving transparency, reproducibility, and early identification of potential hazards in microbial biocontrol candidates, envisioned to make WGS an integral part of the risk assessment of microbial pesticides. Key pointsO_LIThe RATION-GUI provides a public, reproducible workflow for whole-genome sequencing- supported hazard characterization of bacterial and fungal microbial pesticides. C_LIO_LIThe workflow integrates genome quality, taxonomy, annotation, antimicrobial resistance, pathogenicity-related evidence, mobile elements, and secondary-metabolite potential. C_LIO_LIDomain-specific outputs are translated into structured hazard indicators, evidence summaries, and recommended follow-up actions without replacing expert regulatory judgment. C_LIO_LICase studies demonstrate how the workflow improves transparency, traceability, and interpretation of genomic evidence for microbial pesticide risk assessment. C_LI

bioinformatics↗

bioRxiv2026

Taxonomic Description of Uncultured Cyanobacteria from Extreme Habitats through Genome-Based Classification

Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy. Analysis of 46 steam vent associated samples from Hawai i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes. This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material. These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.

genomics↗

bioRxiv2025

Out of Antarctica: new insights into Antarctic Subcluster 5.2 picocyanobacteria based on high-quality genomes

2.Synechococcus-like cyanobacteria are cosmopolitan unicellular picocyanobacteria that have colonized diverse aquatic and terrestrial habitats. The so-called subcluster 5.2 represents a particularly diversified subgroup, including marine and freshwater organisms adapted to extreme conditions, notably polar environments. We increased the genomic representation of polar taxa in this subcluster by reconstructing new high-quality genomes from five Antarctic lacustrine strains and one Arctic freshwater isolate using a combination of small Illumina and long Nanopore reads. A maximum likelihood (ML) phylogenomic analysis of these new assemblies combined with all publicly available good quality assemblies of the subcluster 5.2 suggests evidence of a dispersal process from Antarctica. Indeed, the topology of the phylogenomic tree indicates one basal Antarctic lineage followed by the emergence of two lineages, one Antarctic and one non-Antarctic (Spain). This finding is further supported by a 16S rRNA ML phylogenetic and a pangenomic analysis. Although secondary colonization of Antarctica by cyanobacteria following the cooling of the continent 34 million years ago has been reported, this study is the first to support an Out-of-Antarctica scenario inside subcluster 5.2. 3. Impact statementThis study provides novel insights into the evolutionary history and biogeography of Synechococcus-like picocyanobacteria. By expanding the genomic sampling of polar subcluster 5.2, we reveal that Antarctic taxa are not monophyletic and are intermixed with non-Antarctic lineages, suggesting an unprecedented Out-of-Antarctica dispersal scenario. Our results, supported by 16S rRNA, phylogenomic and pangenomic analyses, highlight the role of polar regions as both a refuge and a source of microbial diversity. This work advances our understanding of cyanobacterial adaptation, radiation and genome evolution in extreme environments. 4. Data summaryRaw sequencing reads and genome assemblies from this study have been deposited in the European Nucleotide Archive (ENA) under Project accession number PRJEB103944. Raw sequencing reads are available under accession numbers ERR15933635 to ERR15933638, ERR15933641 to ERR15933644, ERR15903357, ERR15903358, ERR15905256 and ERR15905257. The assemblies can be accessed under accession numbers GCA_977927515, GCA_977927525, GCA_977927535, GCA_977927545, GCA_977927555 and GCA_977929215. The scripts and code as well as large supplementary files generated during this study are available on Figshare and can be downloaded from https://doi.org/10.6084/m9.figshare.30772781 [1]. Supplementary data files are also provided and contains supplementary figures (Fig. S1-S4) and tables (Table S1-S6).

ecology↗

bioRxiv2025

A FAIR Amplicon Sequencing Workflow for Long-term Environmental Monitoring

Antarctica represents one of the last pristine environments on Earth, providing a unique opportunity to to study the effects of climate change and anthropogenic activities. Ice-free areas, such as the inland nunataks of the Sor Rondane Mountains (SRM), host unique terrestrial and lacustrine ecosystems, of which the simplified food webs rely almost exclusively on microbial primary production. Because of their small size, low productivity and hence low biomass, these microbial communities are fragile. Seven SRM sites were selected to be part of the Antarctic Specially Protected Area (ASPA) 179. The MonASPA project has established an environmental monitoring program to evaluate the effectiveness of the management plan approved by the Antarctic Treaty System for these areas. A key component of MonASPA is the long-term monitoring of microbial biodiversity using 16S rRNA amplicon sequencing. To ensure consistent operation over decades, we developed the Reproducible Amplicon Sequencing Pipeline for Antarctic Monitoring (RASPAM), which is built on Apptainer containers and Nextflow workflows. RASPAM implements Amplicon Sequence Variants (ASVs) and Zero-radius Operational Taxonomic Units (ZOTUs) to provide high-resolution taxonomic affiliation. It incorporates, in addition to the SILVA database, a taxonomically curated 16S rRNA database for cyanobacteria and enables comparisons against NCBI databases to facilitate the identification of rare prokaryotic strains in environmental samples. RASPAM is Findable, Accessible, Interoperable, and Reproducible (FAIR) and represents a robust tool for long-term monitoring of microbial communities in Antarctic and other extreme environments.

bioinformatics↗

bioRxiv2025

Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae

Gloeobacterales has long been considered a "living fossil" cyanobacterial order, owing to its lack of thylakoid membranes and basal phylogenetic position. However, our study reveals that Gloeobacterales actively integrate horizontally transferred genes into their core metabolism. In Gloeobacteraceae--one of the two families within the order--these genes encode a complete ribose ATP synthase binding cassette (ABC) importer and downstream enzymes, enabling the heterotrophic uptake of external ribose and its assimilation into central carbon metabolism, along with photosynthesis, indicative of photomixotrophy. Beyond ribose utilization, their central carbon metabolism exhibits a mosaic architecture shaped by the integration of foreign genes into the Calvin-Benson-Bassham cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway. Uniquely, these genes appear to have been acquired through multiple independent transfer events, as reflected by their dispersed genomic locations and diverse bacterial donors, including other cyanobacteria and Pseudomonadota. These findings contradict the long-standing view of Gloeobacterales as metabolically primitive relics. Instead, Gloeobacterales is likely a dynamic lineage that continues to adapt and evolve through metabolic innovation and the assimilation of foreign genes into its genomes.

evolutionary biology↗

bioRxiv2025

From Cytoplasmic Membrane to Thylakoids: Evolution of Membrane Biogenesis and Photosystem II assembly in early diverging Cyanobacteria

O_LIThylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis. Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis in the cytoplasmic membrane, representing an ancestral state relative to other cyanobacteria (Phycobacteria). This study investigates the evolutionary origin of TM. C_LIO_LIPhylogenomic analyses were performed across a phylogenetically diverse set of cyanobacteria, including extensive representation of basal lineages (Gloeobacterales, Thermostichales, Gloeomargaritales and Pseudanabaenales), as well as micro- and macrocyanobacteria, using orthologous proteins involved in membrane dynamics and Photosystem II (PSII) assembly, together with structural modelling using AlphaFold3. C_LIO_LIWe identified two candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH family member Slr1106, proposed to have been acquired by lateral gene transfer. Analysis of 36 PSII assembly factors revealed modifications in late-stage assembly, notably in manganese homeostasis. Structural changes in the YidC translocase may have facilitated relocation of linear electron transfer components from the cytoplasmic membrane to TM. C_LIO_LIAltogether, these phylogenetic and functional prediction analyses provide new insight into the molecular innovations that led to TM emergence, including membrane trafficking systems, PSII assembly changes, and protein targeting adaptations. C_LI

evolutionary biology↗

bioRxiv2025

Early-Diverging SQR Enzyme in Antarctic Gloeobacterales Indicates Sulfide Tolerance in Thylakoid-Lacking Cyanobacteria

Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions--characterized by sulfidic, anoxic oceans--posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of an early-diverging form of the sulfide quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage lacking thylakoids. Phylogenetic analyses reveal that these SQR sequences are the earliest-diverging cyanobacterial SQR known to date, predating the multiple lateral gene transfer events previously observed in the phylum. Additional searches in metagenomic datasets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions. Impact StatementThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic) a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an Antarctic early diverging cyanobacterium lacking thylakoids gives credit on an ancestral evolutionary stage where oxygenic and anoxygenic traits coexisted within cyanobacteria. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.

evolutionary biology↗

bioRxiv2024

Endurance exercise with reduced muscle glycogen content influences substrate utilization and attenuates acute mTORC1- and autophagic signaling in human type I and type II muscle fibers

BackgroundExercising with low muscle glycogen content can improve training adaptation, but the mechanisms underlying the muscular adaptation are still largely unknown. In this study, we measured substrate utilization and cell signaling in different muscle fiber types during exercise and investigated a possible link between these variables. MethodsFive subjects performed a single leg cycling exercise in the evening (day 1) with the purpose of reducing glycogen stores. The following morning (day 2), they performed two-legged cycling at [~]70% of VO2peak for 1h. Muscle biopsies were taken from both legs pre- and post-exercise for enzymatic analyses of glycogen, metabolite concentrations using LC-MS/MS-based quantification, and protein signaling using Western blot in pools of type I or type II fibers. ResultsGlycogen content was 60-65% lower for both fiber types (P<0.01) in the leg that exercised on day 1 (low leg) compared to the other leg with normal level of glycogen (normal leg) before the cycling exercise on day 2. Glycogen utilization during exercise was significantly less in both fiber types in the low compared to the normal leg (P<0.05). In the low leg, there was a 14- and 6-fold increase in long-chain fatty acids conjugated to carnitine in type I and type II fibers, respectively, post-exercise. This increase was 3-4 times larger than in the normal leg (P<0.05). Post-exercise, mTORSer2448 phosphorylation was increased in both fiber types in the normal leg (P<0.05) but remained unchanged in both fiber types in the low leg together with an increase in eEF2Thr56 phosphorylation in type I fibers (P<0.01). Exercise induced a reduction in the autophagy marker LC3B-II in both fiber types and legs, but the post-exercise level was higher in both fiber types in the low leg (P<0.05). Accordingly, the LC3B-II/I ratio decreased only in the normal leg (75% for type I and 87% for type II, P<0.01). ConclusionsStarting an endurance exercise session with low glycogen availability leads to profound changes in substrate utilization in both type I and type II fibers. This may reduce the mTORC1 signaling response, primarily in type I muscle fibers, and attenuate the normally observed reduction in autophagy.

physiology↗

bioRxiv2023

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava

Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging. In the present study, we generated BAC libraries of the CMD- susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identified and sequenced BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequenced and assembled the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps revealed discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC guided approach to assess cassava genome assemblies significantly improved the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identified 81 stress resistance proteins present in the CMD2 region, amongst which 31 were previously not reported in publicly available CMD2 sequences.

genomics↗

bioRxiv2022

CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)

BackgroundGenome contamination is a well-known issue in (meta)genomics. Although it has received a lot of attention, with an increasing number of detection tools made available over the years, no comparison between these tools exists in the literature. ResultsHere, we report the benchmarking of six of the most popular tools using a simulated framework. Our simulations were conducted on six different taxonomic ranks, from phylum to species. The analysis of the estimated contamination levels indicates that the precision of the tools is not good, often due to large overdetection but also underdetection, especially at the genus and species ranks. Furthermore, our results show that only redundant contamination is accurately estimated. ConclusionOur results indicate that using a combination of tools, including Kraken2, is necessary to estimate the contamination level accurately. We also provide a freely available contamination simulation framework, CRACOT, which may be useful for estimating the accuracy of future algorithms.

bioinformatics↗

bioRxiv2022

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics .

BackgroundMicrobial culture collections play a key role in taxonomy by studying the diversity of their accessions and providing well characterized strains to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (i.e. yeasts). FindingsThis public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenetic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. Technical detailsNextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TestingThe toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early-branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. ConclusionThe GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be useful for other applications, as shown by our case study on Gloeobacterales.

bioinformatics↗

bioRxiv2021

Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveals taxonomic and functional diversity

Snodgrassella is a Betaproteobacteria genus found in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole genome sequences of 75 Snodgrassella strains from 4 species of honey bees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early on from the other species in their evolution, that isolates from honeybees and bumblebees were well separated and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees, i.e. Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species or group specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. ImportanceThe microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bees microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species, i.e. Snodgrassella alvi, has been named. Here we demonstrate that this genus is actually composed of at least seven species, two of them (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) being formally described in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus. Data summaryO_LICornet L and Vandamme P, European Nucleotide Archive (ENA), Project accession: PRJEB47378 C_LIO_LICornet L and Vandamme P, European Nucleotide Archive (ENA), Reads accessions: SAMEA9570070 - SAMEA9570078 C_LIO_LICornet L and Vandamme P, European Nucleotide Archive (ENA), Genome accessions: GCA_914768015, GCA_914768025, GCA_914768035, GCA_914768045, GCA_914768055, GCA_914768065, GCA_914768075, GCA_914768085, GCA_914768095. C_LI

genomics↗

bioRxiv2021

AMAW: automated gene annotation for non-model eukaryotic genomes

SummaryTo support small and large-scale genome annotation projects, we present AMAW (Automated MAKER2 Annotation Wrapper), a program devised to annotate non-model unicellular eukaryotic genomes by automating the acquisition of evidence data (transcripts and proteins) and facilitating the use of MAKER2, a widely adopted software suite for the annotation of eukaryotic genomes. Moreover, AMAW exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2. AvailabilityAMAW is released both as a Singularity container recipe and a standalone Perl script (https://bitbucket.org/phylogeno/amaw/). Contactlmeunier@uliege.be or luc.cornet@sciensano.be Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

ORPER: a workflow for constrained SSU rRNA phylogenies

The continuous increase of sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects evermore complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow "ORPER" (containerized in Singularity), which allows determining the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

bioinformatics↗

bioRxiv2018

A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria)

ObjectivesCyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria, the unique bacterial group able to perform oxygenic photosynthesis. This group has been extensively studied by phylogenomics during the last decade, 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.\n\nResultsWe show that only a little fraction the oxyphotobacterial diversity has been sequenced so far. Indeed 31 rRNA clusters on 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 (G, F, E) and the Oscillatoriales clade (A), which have higher fractions of representative genomes. Yet, the very basal 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.

evolutionary biology↗

bioRxiv2018

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

BACKGROUNDPublicly 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.\n\nRESULTSAs 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).\n\nCONCLUSIONSOur 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.

genomics↗

bioRxiv2018

Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

Cyanobacteria form one of the most diversified phylum 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 likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we deploy a metagenomic pipeline that enables the easy recovery of high-quality 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 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria 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.\n\nImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.

genomics↗