Luc Cornet, evolution of oxygenic photosynthesis on Luc Cornet

Citizen Science project: the quest for new basal cyanobacteria in caves

Mon, 01 Jan 0001 00:00:00 +0000

Oxygenic photosynthesis is a biochemical process of fundamental importance for life on Earth, as it converts solar energy into chemical energy while releasing oxygen. This process emerged more than 2.4 billion years ago within cyanobacteria, a group of bacteria that subsequently colonized a wide range of terrestrial and aquatic habitats.

Cyanobacteria are responsible for a substantial fraction of global photosynthesis, notably through their presence in marine phytoplankton. Among extant cyanobacteria, there is a very primitive group known as the Gloeobacterales, which is distinguished by the absence of thylakoids, an intracellular structure essential for photosynthesis in most cyanobacteria. This absence makes Gloeobacterales an important source of information for understanding the origin and evolution of oxygenic photosynthesis.

GEN-ERA

Mon, 01 Jan 0001 00:00:00 +0000

The GEN-ERA project, which ran from 2020 to 2022, aimed to establish reproducible genomics practices within the Belgian Coordinated Collections of Microorganisms (BCCM). To achieve this goal, a toolbox consisting of 14 Nextflow workflows, each relying on a dedicated Singularity container, was developed. This toolbox addresses the main needs of scientists working in genomics: downloading data, assembling and binning (meta)genomes from short or long reads, as well as performing orthologous inference and maximum-likelihood phylogenomic analyses with bootstrap and jackknife support. Constrained SSU rRNA phylogenies, guided by ribosomal phylogenomics, can also be inferred. In addition, the toolbox includes workflows for average nucleotide identity calculations, GTDB-based taxonomic identification, and metabolic modelling. Since the end of the initial project, GEN-ERA has been actively maintained and has recently been refinanced for a further four-year period (2026–2030), notably to expand and strengthen its functional genomics component.
https://github.com/Lcornet/GENERA

On the non-oxygenic origins of thylakoids

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet
Thylakoid membranes are the site of oxygenic photosynthesis, one of the most important biochemical processes on earth. The ancestral state of these membranes is represented today in Gloeobacterales, where they are lacking and photosynthesis instead takes place in the cytoplasmic membrane. The evolutionary transition from this ancestral state to the modern thylakoid membranes provided a major advantage, as it increased photosynthetic efficiency. However, how this significant transition occurred remains an understudied question. The biogenesis of modern thylakoid membranes relies on a highly synchronized process involving numerous assembly factors and showing important differences between the two photosystems. Together, these features suggest the existence of intermediate evolutionary states during the emergence of this compartment. Here, I propose a non-oxygenic origin of thylakoid membranes, where these intermediate states were initially dedicated to alternative electron flows. This hypothesis further addresses the paradox of cyanobacterial diversification in an euxinic environment, toxic to photosystem II.
https://www.nature.com/articles/s42003-025-09100-w

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

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Syed Shan-e-Ali Zaidi, Jia Li, Yvan Ngapout, Sara Shakir, Loic Meunier, Caroline Callot, William Marande, Marc Hanikenne, Stephane Rombauts, Yves Van de Peer & Hervé Vanderschuren
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 generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble 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 reveals 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 improves 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 identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences. The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.
https://link.springer.com/article/10.1186/s13059-025-03620-8

Despite their importance, cyanobacteria are underrepresented in evolutionary studies

Mon, 01 Jan 0001 00:00:00 +0000

We retrieved the abstracts of studies involving cyanobacteria published between 2020 and 2024 and analyzed them using the BART large language model, based on a predefined set of keywords (see figure legend). This analysis indicates that the evolutionary aspects of cyanobacteria are the least studied, regardless of the year considered. In contrast, blooms and public health are the most represented research areas. The fundamental importance of cyanobacteria—particularly their role in the emergence of oxygenic photosynthesis, which was essential for the formation of the biosphere as we know it—remains largely overlooked compared to the negative aspects of cyanobacteria, such as toxicity, which is relatively rare from a taxonomic perspective. Beyond providing new strains for isolation, a citizen science project also offers an opportunity to raise awareness of the evolutionary importance of cyanobacteria.

OR-OX-PHOT-IN-CYN

Mon, 01 Jan 0001 00:00:00 +0000

This two-year project (2024–2026) aims to bridge the evolutionary gap between photoautotrophic cyanobacteria and their chemoheterotrophic outgroups. We pursue two interdependent objectives. First, we will investigate the emergence of oxygenic photosynthesis by building on key observations in both groups: (a) the capacity of cyanobacteria to survive under heterotrophic or mixotrophic growth conditions, and (b) the presence in Vampirivibriona of individual genes belonging to four of the five known classes of carbon-concentrating mechanisms (CCMs), which are in principle associated with autotrophy. Second, we will expand the phylogenetic diversity of cyanobacteria and their outgroups by (a) sequencing new strains obtained from culture collections, selected based on the phylogenetic placement of their SSU rRNA genes, and (b) mining public SRA datasets to recover new metagenome-assembled genomes (MAGs) of basal cyanobacteria and related outgroups.

Evol-CM-to-TM

Mon, 01 Jan 0001 00:00:00 +0000

Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis by utilizing two photosystems in their electron transport chain (ETC), with photosystem II (PSII) splitting water molecules. In most cyanobacteria, this process occurs within the membranes of specialized compartments called the thylakoids. The process by which the ETC is integrated into the thylakoids has been studied for certain subunits and involves the coordination of numerous assembly factors, of which only a fraction has been identified so far. In Gloeobacterales, the most basal group of extant cyanobacteria, these photosystems and the ETC are instead integral to the plasma membrane. While recent studies suggest an appearance of oxygenic photosynthesis well before the Great Oxidation Event (GOE), the structural advantages of thylakoids hint to a key role in GOE, though their origin remains unclear. The aim of this project is to test the hypothesis that the emergence of thylakoids is related to anoxygenic photosynthesis and alternative electron flows, conferring an advantage in the photic zone of Proterozoic oceans, where oxic and sulfidic-rich conditions coexisted. In this project, metabolic modelling by flux balance analysis will be used to test hypothetical evolutionary stages of thylakoids in simulated conditions.

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

Mon, 01 Jan 0001 00:00:00 +0000

Louise Hambücken, Denis Baurain, Luc Cornet
Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis which involve a linear electron transfer (LET) chain composed of multi- subunit complexes, including notably Photosystem II (PSII). Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis within specialized regions of the cytoplasmic membrane (CM), thereby representing an ancestral state with respect to other cyanobacteria, all equipped with TM and known as Phycobacteria. The emergence of TM, which increased the membrane surface available for oxygenic photosynthesis, was a key innovation that likely contributed to the Great Oxidation Event. This evolutionary transition involved the formation of a distinct membrane compartment, followed by the relocation of LET components from the CM to TM. Here, we present a phylogenomic analysis identifying three candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH family member Slr1106, which we show was acquired via lateral gene transfer. Moreover, evolutionary analysis of 36 PSII assembly factors indicates key modifications in late-stage PSII assembly, notably in manganese homeostasis, and highlights structural changes in the early-acting YidC translocase that may have facilitated the relocation of LET components from the CM to TM. Altogether, our phylogenetic and functional prediction analyses of proteins involved in membrane dynamics and PSII assembly factors bring new insights into the molecular innovations that led to the emergence of TM.
https://doi.org/10.1101/2025.11.06.686923

How to participate

Mon, 01 Jan 0001 00:00:00 +0000

To receive your sampling kit and project documentation, please contact Luc Cornet (see the contact section). The kits are generally sent by mail with a pre-printed return label. Sampling should be completed within one month to ensure the viability of the samples. We are particularly interested in caves from Western Europe.

A FAIR Amplicon Sequencing Workflow for Long-term Environmental Monitoring

Mon, 01 Jan 0001 00:00:00 +0000

Marie Harmel, Benoit Durieu, Valentina Savaglia, Bjorn Tytgat, Denis Baurain, Annick Wilmotte, Elie Verleyen, Luc Cornet
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 Sør 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.
https://doi.org/10.64898/2025.12.04.692289

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

Mon, 01 Jan 0001 00:00:00 +0000

Louise Hambücken, Edi Sudianto, Jimmy H. Saw, Denis Baurain, Luc Cornet
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.
https://doi.org/10.1101/2025.10.24.684318

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

Mon, 01 Jan 0001 00:00:00 +0000

Edi Sudianto, Denis Baurain, Luc Cornet
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.
https://doi.org/10.1101/2025.11.10.686926

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

Mon, 01 Jan 0001 00:00:00 +0000

Edi Sudianto, Maximillian D. Shlafstein, Benoit Durieu, Marie Harmel, Luc Cornet, Jimmy H. Saw 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.
https://doi.org/10.64898/2026.01.02.697360

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

Mon, 01 Jan 0001 00:00:00 +0000

Benoit Durieu, Valentina Savaglia, Mick Van Vlierberghe, Valérian Lupo, Denis Baurain, Annick Wilmotte, Luc Cornet
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.
https://doi.org/10.64898/2025.12.17.694815

Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria

Mon, 01 Jan 0001 00:00:00 +0000

Carlos J Pardo-De la Hoz , Diane L Haughland , Darcie Thauvette , Sydney Toni , Spencer Goyette , William White , Ian D Medeiros , Luc Cornet , Petr Dvořák , Diego Garfias-Gallegos , Jolanta Miadlikowska , Nicolas Magain , François Lutzoni
Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g. cycads and bryophytes) and fungi (e.g. cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e. when closely related clades of Nostoc co-occur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria.
https://doi.org/10.1093/molbev/msaf244

Melissospora conviva gen. nov., sp. nov., a novel actinobacterial genus isolated from beehive through cross-feeding interactions

Mon, 01 Jan 0001 00:00:00 +0000

Déborah Tellatin, Luc Cornet, Valdes Snauwaert, Philippe Compère, Marc Ongena, Loïc Quinton, Nudzejma Stulanovic, Silvia Ribeiro Monteiro, Augustin Rigolet, Pierre Burguet, Petra Van Damme, Lorena Carro and Sébastien Rigali
Most micro-organisms remain unculturable under standard laboratory conditions, limiting our understanding of microbial diversity and ecological interactions. One major cause of this uncultivability is the loss of access to essential cross-fed metabolites when bacteria are removed from their natural communities. During a bioprospecting campaign targeting actinomycetes of an Apis mellifera beehive, we identified five isolates (DT32, DT45T, DT55, DT59 and DT194) that required co-cultivation for growth recovery, suggesting a dependence on microbial interactions in their native habitat. Whole-genome sequencing and phylogenetic analysis positioned these isolates within a distinct lineage of Micromonosporaceae, separate from the five officially recognized clades of the Micromonospora genus. A combination of microscopic, chemotaxonomic and physiological characterizations further supported their uniqueness. Notably, they exhibited high auxotrophy, being unable to use all carbon sources tested, likely due to genome reduction (4.6 Mbp) compared to other Micromonosporaceae. Pangenomic comparisons with their closest Micromonospora relatives revealed gene losses in key metabolic pathways, including the glyoxylate bypass and the Entner–Doudoroff pathway, which may explain their metabolic reliance. These findings reveal a highly specialized, ecologically adapted lineage with deep evolutionary divergence and further support microbial interdependence isolation strategies to explore the microbial dark matter. We propose Melissospora conviva as a novel genus and species within the Actinomycetota phylum, with isolate DT45T as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.
https://doi.org/10.1099/ijsem.0.006868

Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Valérian Lupo, Stéphane Declerck and Denis Baurain
Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms.
https://doi.org/10.3390/applmicrobiol4010009

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Mon, 01 Jan 0001 00:00:00 +0000

Carlos J Pardo-De la Hoz , Nicolas Magain , Bryan Piatkowski , Luc Cornet , Manuela Dal Forno , Ignazio Carbone , Jolanta Miadlikowska , François Lutzoni
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.
https://doi.org/10.1093/sysbio/syad008

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

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet , Benoit Durieu , Frederik Baert , Elizabet D’hooge , David Colignon , Loic Meunier , Valérian Lupo , Ilse Cleenwerck , Heide-Marie Daniel , Leen Rigouts , Damien Sirjacobs , Stéphane Declerck , Peter Vandamme , Annick Wilmotte , Denis Baurain and Pierre Becker
Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material 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 were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts).
https://doi.org/10.1093/gigascience/giad022

Contamination detection in genomic data: more is not enough

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet and Denis Baurain
The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection.
https://link.springer.com/article/10.1186/s13059-022-02619-9

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Ilse Cleenwerck, Jessy Praet, Raphaël R. Leonard, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, Denis Baurain, Peter Vandamme
Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a 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 honeybees 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 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.
https://doi.org/10.1128/msystems.01500-21

Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Nicolas Magain, Denis Baurain, François Lutzoni
Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.
https://doi.org/10.1016/j.ympev.2021.107100

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Anne-Catherine Ahn, Annick Wilmotte, and Denis Baurain
he continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination 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.

AMAW: automated gene annotation for non-model eukaryotic genomes

Mon, 01 Jan 0001 00:00:00 +0000

Loïc Meunier, Denis Baurain, Luc Cornet
Background: The annotation of genomes is a crucial step regarding the analysis of new genomic data and resulting insights, and this especially for emerging organisms which allow researchers to access unexplored lineages, so as to expand our knowledge of poorly represented taxonomic groups. Complete pipelines for eukaryotic genome annotation have been proposed for more than a decade, but the issue is still challenging. One of the most widely used tools in the field is MAKER2, an annotation pipeline using experimental evidence (mRNA-seq and proteins) and combining different gene prediction tools. MAKER2 enables individual laboratories and small-scale projects to annotate non-model organisms for which pre-existing gene models are not available. The optimal use of MAKER2 requires gathering evidence data (by searching and assembling transcripts, and/or collecting homologous proteins from related organisms), elaborating the best annotation strategy (training of gene models) and efficiently orchestrating the different steps of the software in a grid computing environment, which is tedious, time-consuming and requires a great deal of bioinformatic skills. Methods: To address these issues, we present AMAW (Automated MAKER2 Annotation Wrapper), a wrapper pipeline for MAKER2 that automates the above-mentioned tasks. Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2. Use case: The performance of AMAW is illustrated through the annotation of a selection of 32 protist genomes, for which we compared its annotations with those produced with gene models directly available in AUGUSTUS. Conclusions: Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2.
https://f1000research.com/articles/12-186

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Elizabet D’hooge, Nicolas Magain, Dirk Stubbe, Ann Packeu, Denis Baurain, and Pierre Becker
The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.
https://doi.org/10.1099/mgen.0.000707

Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics

Mon, 01 Jan 0001 00:00:00 +0000

Valérian Lupo, Mick Van Vlierberghe, Hervé Vanderschuren, Frédéric Kerff, Denis Baurain and Luc Cornet
Contaminating sequences in public genome databases is a pervasive issue with potentially far-reaching consequences. This problem has attracted much attention in the recent literature and many different tools are now available to detect contaminants. Although these methods are based on diverse algorithms that can sometimes produce widely different estimates of the contamination level, the majority of genomic studies rely on a single method of detection, which represents a risk of systematic error. In this work, we used two orthogonal methods to assess the level of contamination among National Center for Biotechnological Information Reference Sequence Database (RefSeq) bacterial genomes. First, we applied the most popular solution, CheckM, which is based on gene markers. We then complemented this approach by a genome-wide method, termed Physeter, which now implements a k-folds algorithm to avoid inaccurate detection due to potential contamination of the reference database. We demonstrate that CheckM cannot currently be applied to all available genomes and bacterial groups. While it performed well on the majority of RefSeq genomes, it produced dubious results for 12,326 organisms. Among those, Physeter identified 239 contaminated genomes that had been missed by CheckM. In conclusion, we emphasize the importance of using multiple methods of detection while providing an upgrade of our own detection tool, Physeter, which minimizes incorrect contamination estimates in the context of unavoidably contaminated reference databases.
https://doi.org/10.3389/fmicb.2021.755101

ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Mon, 01 Jan 0001 00:00:00 +0000

Raphaël R. Léonard, Marie Leleu, Mick Van Vlierberghe, Luc Cornet, Frédéric Kerff, Denis Baurain
TQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ].
https://peerj.com/articles/11348/

Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq

Mon, 01 Jan 0001 00:00:00 +0000

Devang Mehta, Luc Cornet, Matthias Hirsch-Hoffmann, Syed Shan-e-Ali Zaidi and Hervé Vanderschuren
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.
https://www.nature.com/articles/s41596-020-0301-0

Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects

Mon, 01 Jan 0001 00:00:00 +0000

Loïc Meunier , Pierre Tocquin , Luc Cornet , Damien Sirjacobs , Valérie Leclère , Maude Pupin , Philippe Jacque sand Denis Baurain
To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), 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 and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database.
https://doi.org/10.1093/bioinformatics/btaa517

Cyanobacteria evolution: Insight from the fossil record

Mon, 01 Jan 0001 00:00:00 +0000

Catherine F. Demoulin, Yannick J. Lara, Luc Cornet, Camille François, Denis Baurain, Annick Wilmotte, Emmanuelle J. Javaux
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.
https://doi.org/10.1016/j.freeradbiomed.2019.05.007

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

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Annick Wilmotte, Emmanuelle J. Javaux and Denis Baurain
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.
https://link.springer.com/article/10.1186/s13104-018-3543-y

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Loïc Meunier, Mick Van Vlierberghe, Raphaël R. Léonard, Benoit Durieu, Yannick Lara, Agnieszka Misztak, Damien Sirjacobs, Emmanuelle J. Javaux, Hervé Philippe, Annick Wilmotte, Denis Baurain
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.
https://doi.org/10.1371/journal.pone.0200323

Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

Mon, 01 Jan 0001 00:00:00 +0000

Yannick Lara, Benoit Durieu, Luc Cornet, Olivier Verlaine, Rosmarie Rippka, Igor S. Pessi, Agnieszka Misztak, Bernard Joris, Emmanuelle J. Javaux, Denis Baurain, Annick Wilmotte
Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. 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.
https://doi.org/10.1128/genomea.01546-16

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Mon, 01 Jan 0001 00:00:00 +0000

*Marta Maciejewska, Magdalena Całusińska, Luc Cornet,Delphine Adam, Igor S. Pessi 1, Sandrine Malchair, Philippe Delfosse,Denis Baurain, Hazel A. Barton,Monique Carnol, and Sébastien Rigali
Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave “Grotte des Collemboles” via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable Streptomyces strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three studied collection points, while 34% were exclusive to one deposit, indicating that distinct speleothems host their own population, despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.
https://doi.org/10.3390/antibiotics7020027

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

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Amandine R. Bertrand, Marc Hanikenne, Emmanuelle J. Javaux, Annick Wilmotte and Denis Baurain
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.
https://doi.org/10.1099/mgen.0.000212

The unusual Gasteromycetes Lycogalopsis solmsii belongs to the gomphoid-phalloid group.

Mon, 01 Jan 0001 00:00:00 +0000

VINCENT DEMOULIN, LUC CORNET, EMILIE DELBRUYÈRE and DENIS BAURAIN
The rare tropical Gasteromycetes Lycogalopsis solmsii has been found twice at thirty years interval in the Singapore Botanic Gardens. From the most recent find a culture could be isolated, which allowed DNA extraction and sequencing of about 2000 bp from the nuclear ribosomal DNA. Comparison to a large sample of Basidiomycetes was only possible for a part of the large ribosomal subunit, but clearly indicated affiliation to the gomphoid-phalloid group, without any relationship to Lycoperdales or Agaricales, as stated in the Dictionary of the Fungi.
https://orbi.uliege.be/bitstream/2268/151465/1/Demoulin_et_al_2013_Acta_Mycologica_postprint_editor.pdf

A Middle Devonian Callixylon (Archaeopteridales) from Ronquières, Belgium

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Philippe Gerrienne, Brigitte Meyer-Berthaud and Cyrille Prestianni
A permineralized Callixylon trunk is reported from Ronquières, a mid to late Givetian (Middle Devonian) locality from Belgium. The specimen consists of an 80 cm long trunk adpression whose central area is preserved as a pyrite permineralization. The pyritized area is composed of a eustele surrounded by secondary xylem. Tracheids show radially aligned groups of pits separated by unpitted regions on the radial walls of tracheids. The specimen belongs to a group of species characterized by a predominance of uniseriate rays and the lack of ray tracheids. This Callixylon specimen is one of the earliest representatives of the genus. It coexists at the locality with large cladoxylopsids and provides direct evidence that the tree habit had evolved in the archaeopteridalean progymnosperms by the Givetian.