Biology subjects

Flot, J.-F.

Publications and source records attributed to Flot, J.-F..

36 records · Page 2Linked to original sources

bioRxiv2023

Intra- and interspecific variations in genome sizes of Agaricia corals from Curacao

Genome size is a fundamental biological trait that is known to exhibit high diversity among eukaryotic species, but its intraspecific diversity has only scarcely been studied to date. In scleractinian corals, genome size data are only available for a few species. In this study, intra- and interspecific variations in genome size of the coral genus Agaricia collected from Curacao were investigated. Morphology was congruent with genetic analyses of the nuclear markers internal transcribed spacer 2 (ITS2) and L-threonine 3-dehydrogenase (TDH) in delimiting three Agaricia species among our samples. A refined Feulgen Image Analysis Densitometry (FIAD) protocol yielded genome sizes that ranged from 0.359 pg to 0.593 pg within this genus (a 1.7-fold range). The highest intraspecific variation in genome size was recorded in the depth-generalist A. lamarcki (1.5-fold range), followed by the depth specialist A. humilis (1.4-fold range) and A. agaricites (1.3-fold range), the species with an intermediate depth distribution. The mean genome size of A. agaricites (0.495 pg) was significantly larger than that of A. lamarcki (0.448 pg) and A. humilis (0.434 pg). No correlation between average genome size and nucleotide polymorphism{pi} was detected, but we found an almost linear correlation between intraspecific variance of genome size and{pi} of ITS2 (Pearsons r = 0.984, p = 0.113). Genome size and collection depths of both A. lamarcki (Pearsons r = 0.328, p = 0.058) and A. agaricites (Pearsons r = -0.270, p = 0.221) were also not significantly associated. To our knowledge, this study provides the first account of intraspecific variation in corals; the apparent correlation detected between the nucleotide polymorphism of a species and the variance of its genome size will have to be tested using a larger taxonomic spectrum of scleractinian corals as well as in other groups of animals.

evolutionary biology↗

bioRxiv2023

Water diviners multiplied: cryptic diversity in the Niphargus aquilex species complex in Northern Europe

As for many other groups, patterns of biodiversity for subter-ranean crustaceans in Europe indicate larger morphospecies ranges at higher latitudes (the so-called Rapoport effect). However, this observed correlation may be artefactual if many of those high-latitude, widely distributed morphospecies are actually species complexes. To test this hypothesis, we looked for previously undetected species boundaries within Niphargus aquilex and Niphargus schellenbergi, two closely related morphospecies of groundwater amphipods widely distributed in northern Europe, by sequencing fragments of the mitochondrial cytochrome c oxidase subunit I gene (COI) and of the nuclear 28S ribosomal RNA gene of 198 individuals collected across their area of distribution. Distance-based and allele sharing-based species delimitation approaches were congruent in revealing the existence of at least eight species within N. aquilex and at least two species with N. schellenbergi. Our data demonstrate that these two common morphospecies with large ranges are actually complexes of species with narrower distributions, suggesting that the Rapoport effect might be the result of increased morphological stasis at high latitudes rather than actual differences in sizes of distribution ranges.

zoology↗

bioRxiv2023

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, and many aspects of their biology and evolution are still unknown, partially due to the lack of genomic resources for this phylum. As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensis Schmidt-Rhaesa & Fernandez sp. nov.). The final assembly has a total length of 288 Mb in 396 scaffolds with an N50 of 64.4 Mb, 97% of which is scaffolded into 5 pseudochromosomes. The circular mitochondrial genome was also assembled into a 15-kilobases sequence. Gene annotation predicted 10,320 protein-coding genes in the nuclear genome. In this study, we contribute a key genomic resource to not only explore the evolution of Ecdysozoa, but also to further our understanding on the genomic basis of parasitic lifestyles. In addition, we describe a species new to science from this enigmatic animal phyla.

evolutionary biology↗

bioRxiv2023

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

AimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. LocationWestern Amazonia TaxonThe uakari monkey (genus Cacajao) MethodsWe performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. ResultsOur continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River at [~]1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. The demographic analysis indicates that C. calvus, C. amuna, and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

evolutionary biology↗

bioRxiv2022

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture

The European flat oyster (Ostrea edulis L.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds. O. edulis has been the subject of numerous studies and programs in population genetics and on the presence of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response of O. edulis to M. refringens. This genome will serve as a reference for genomic studies on O. edulis to better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.

genomics↗

bioRxiv2022

Polyphyly of the Niphargus stygius species group (Crustacea, Amphipoda, Niphargidae) in the Southern Limestone Alps

AO_SCPLOWBSTRACTC_SCPLOWThe Niphargus stygius species complex is a groundwater group of large-sized, sexually dimorphic species inhabiting mainly caves and, less frequently, wells and springs. According to the taxonomists of the last century, this species complex was supposed to be present in the whole Southern Limestone Alps of Italy as well as in peninsular Italy, Slovenia, and Croatia. Considering the large, presumed distribution area, we tested the contrasting hypotheses of monophyly versus paraphyly of this subterranean species complex, taking in account the presence of putative cryptic species. For this reason, we sampled the type localities of all the described species in the complex present in the Italian Southern Limestone Alps and neighbouring areas, and used nuclear rDNA (28S, ITS region) and mtDNA (COI) markers to assess the phylogenetic relationships and species richness. Phylogenetic analysis confirmed that the Niphargus stygius complex in the Southern Limestone Alps is polyphyletic comprising an eastern clade (the N. julius clade, present in NW Italy, northern Slovenia, and southern Austria) and two western clades (the N. brixianus and N. montellianus clades). These two clades are not closely related to the eastern one but rather form a monophyletic group together with a widely distributed Apennine clade (N. speziae clade). None of these clades is closely related to typical N. stygius. Three different molecular species delimitation methods applied to COI and rDNA sequences recognized slighlty different numbers of putative species, suggesting that each clade is a species complex. Bayesian time-calibrated phylogeny revealed that most clades began to split up during Miocene and Pliocene, ruling out the effect of Pleistocene glaciations, evidenced only by the COI marker, in explaining their speciation process and justifying the presence of several putative cryptic or pseudocryptic species.

evolutionary biology↗

bioRxiv2022

Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: steppingstones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

AO_SCPLOWBSTRACTC_SCPLOWCataglyphis are thermophilic ants that forage during the day when temperatures are highest and sometimes close to their critical thermal limit. Several Cataglyphis species have evolved unusual reproductive systems such as facultative queen parthenogenesis or social hybridogenesis, which have not yet been investigated in detail at the molecular level. We generated high-quality genome assemblies for two hybridogenetic lineages of the Iberian ant Cataglyphis hispanica using long-read Nanopore sequencing and exploited chromosome conformation capture (3C) sequencing to assemble contigs into 26 and 27 chromosomes, respectively. Further karyotype analyses confirm this difference in chromosome numbers between lineages; however, they also suggest it may not be fixed among lineages. We obtained transcriptomic data to assist gene annotation and built custom repeat libraries for each of the two assemblies. Comparative analyses with 19 other published ant genomes were also conducted. These new genomic resources pave the way for exploring the genetic mechanisms underlying the remarkable thermal adaptation and the molecular mechanisms associated with transitions between different genetic systems characteristic of the ant genus Cataglyphis.

genomics↗

bioRxiv2021

KoT: an automatic implementation of the K/θ method for species delimitation

AO_SCPLOWBSTRACTC_SCPLOWK/{theta} is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity{theta} of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/{theta} method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/{theta} threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/{theta} threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/

evolutionary biology↗

bioRxiv2021

GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes. As haploid chromosome-level assemblies are now commonly achieved for all types of organisms, phasing assemblies has become the new frontier for genome reconstruction. Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity. We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

bioinformatics↗

bioRxiv2020

Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

Life in Movile Cave (Romania) relies entirely on carbon fixation by bacteria. The microbial community in the surface water of Movile Caves hypoxic air bells is dominated by large spherical-ovoid bacteria we identified as Thiovulum sp. (Campylobacterota). These form a separate phylogenetic cluster within the Thiovulaceae, consisting mostly of freshwater cave bacteria. We compared the closed genome of this Thiovulum to that of the marine strain Thiovulum ES, and to a genome we assembled from public data from the sulfidic Frasassi caves. The Movile and Frasassi Thiovulum were very similar, differing greatly from the marine strain. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, respectively. NO3-, is likely reduced to NH3 via dissimilatory nitrate reduction to ammonia using periplasmic nitrate reductase (Nap) and hydroxylamine oxidoreductase. Thus, Thiovulum, is likely important to both S and N cycles in sulfidic subterranean aquatic ecosystems. Additionally, we suggest that the short peritrichous flagella-like structures typical of Thiovulum are type IV pili, for which genes were found in all Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells and the exceptionally fast swimming of these bacteria.

microbiology↗

bioRxiv2020

The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer to Pseudoniphargidae

Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

zoology↗

bioRxiv2020

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

The several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloid A. vaga validated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescent in situ hybridization (FISH), we demonstrate that the A. vaga genome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure of A. vaga and the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonal A. vaga suggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.

evolutionary biology↗

bioRxiv2020

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

BackgroundThird-generation sequencing, also called long-read sequencing, is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are also error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Although failure to properly collapse haplotypes results in fragmented and/or structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking. ResultsTo fill this gap, we tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering out shorter reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups. ConclusionsTesting these strategies separately and in combination revealed several approaches able to generate haploid assemblies with genome sizes, coverage distributions, and completeness close to expectations.

genomics↗

bioRxiv2019

Distinct biogeographic origins of androgenetic Corbicula lineages followed by genetic captures

AO_SCPLOWBSTRACTC_SCPLOW"Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

evolutionary biology↗

bioRxiv2019

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

MotivationsShort-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information. ResultsWe propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. Availability and ImplementationThe implementation is open source and available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package. ContactAntoine Limasset antoine.limasset@gmail.com & Jean-Francois Flot jflot@ulb.ac.be & Pierre Peterlongo pierre.peterlongo@inria.fr

bioinformatics↗

bioRxiv2018

mtDNA recombination indicative of hybridization suggest a role of the mitogenome in the adaptation of reef building corals to extreme environments

mtDNA recombination following hybridization is rarely found in animals and was never until now reported in reef-building corals. Here we report unexpected topological incongruence among mitochondrial markers as evidence of mitochondrial introgression in the phylogenetic history of Stylophora species distributed along broad geographic ranges. Our analyses include specimens from the Indo-Pacific, the Indian Ocean and the full latitudinal (2000 km) and environmental gradient (21{degrees}C-33{degrees}C) of the Red Sea (N=827). The analysis of Stylophora lineages in the framework of the mitogenome phylogenies of the family Pocilloporidae, coupled with analyses of recombination, shows the first evidence of asymmetric patterns of introgressive hybridization associated to mitochondrial recombination in this genus. Hybridization likely occurred between an ancestral lineage restricted to the Red Sea/Gulf of Aden basins and migrants from the Indo-Pacific/Indian Ocean that reached the Gulf of Aden. The resulting hybrid lives in sympatry with the descendants of the parental Red Sea lineage, from which it inherited most of its mtDNA (except a highly variable recombinant region that includes the nd6, atp6, and mtORF genes) and expanded its range into the hottest region of the Arabian Gulf, where it is scarcely found. Noticeably, across the Red Sea both lineages exhibit striking differences in terms of phylogeographic patterns, clades-morphospecies association, and zooxanthellae composition. Our data suggest that the early colonization of the Red Sea by the ancestral lineage, which involved overcoming multiple habitat changes and extreme temperatures, resulted in changes in mitochondrial proteins, which led to its successful adaptation to the novel environmental conditions.

evolutionary biology↗

bioRxiv2018

Reply to Cross-Contamination Explains \"Inter and Intraspecific Horizontal Genetic Transfers\" between Asexual Bdelloid Rotifers (Wilson, Nowell & Barraclough 2018)

We thank Wilson et al. (2018) for their thorough re-analysis of our data and for their constructive criticisms that led our groups to exchange many stimulating emails over the last two years. Although we agree that inter-individual contamination can yield patterns suggestive of inter-individual recombination, we are not fully convinced by their criticisms of our 2016 dataset and would like to point here briefly to some inaccuracies and likely errors in their interpretation of our chromatograms.

evolutionary biology↗

bioRxiv2017

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates corals into a robust and complex clade dating back to at least 245 mya. However, the genomic consequences and clade-specific evolution remain unexplored. In this study we have produced the genome of a robust coral, Stylophora pistillata, and compared it to the available genome of a complex coral, Acropora digitifera. We conducted a fine-scale gene-based analysis focusing on ortholog groups. Among the core set of conserved proteins, we found an emphasis on processes related to the cnidarian-dinoflagellate symbiosis. Similarly, genes associated with the algal symbiosis were also independently expanded in both species, but both corals diverged on the identity of ortholog groups expanded, and we found uneven expansions in genes associated with innate immunity and stress response. Our analyses demonstrate that coral genomes can be surprisingly disparate. Importantly, if the patterns elucidated here are representative of differences between corals from the robust and complex clade, the ability of a coral to respond to climate change may be dependent on its clade association.

genomics↗