Vincent Ranwez

L'institut Agro | Montpellier SupAgro | SUPAGRO · Department of Biology and Ecology

Background: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic region...

To date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian...

How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits (especially life-span and reproductive mode) have been shown to be main determinants, but the underlying causes are debated. Demographic history and linked selection have been proposed as main mechanisms, but their relative im...

Leveraging knowledge graphs for post-hoc recommendation explanations has been investigated in recent years. Existing approaches rely mainly on the overlap properties (encoded by knowledge graphs) that characterize both user liked items and the recommended ones. These approaches, however, do not fully leverage the property hierarchy of knowledge gra...

Abstract Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective s...

The diversity of the item list suggested by recommender systems has been proven to impact user satisfaction significantly. Most of the existing diversity optimization approaches re-rank the list of candidate items during a post-processing step. However, the diversity level of the candidate list strongly depends on the recommender system used. Hence...

Recommender systems aim to provide users with a selection of items, based on predicting their preferences for items they have not yet rated, thus helping them filter out irrelevant ones from a large product catalogue. Collaborative filtering is a widely used mechanism to predict a particular user’s interest in a given item, based on feedback from n...

Rice plays an essential food security role for more than half of the world’s population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large Leucine‐Rich Repeat (LRR)‐containin...

Rice plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containin...

Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automa...

Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations and they allow testing whether these traits modifications are a response to selection caused by an environmental change. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes....

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the div...

Launched in 2017 and until 2024, the Convergence Institute for Digital Agriculture #DigitAg is building a Graduate School, a university research school bringing together universities, schools and research organizations.

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking....

We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of...

Genetic maps order genetic markers along chromosomes. They are, for instance, extensively used in marker-assisted selection to accelerate breeding programs. Even for the same species, people often have to deal with several alternative maps obtained using different ordering methods or different datasets, e.g. resulting from different segregating pop...

Multiple sequence alignment is a prerequisite for many evolutionary analyses. MACSE is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates dow...

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny rec...

Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum...

Gene trees and species trees can be discordant due to several processes. Standard models of reconciliations consider macro-evolutionary events at the gene level: duplications, losses and transfers of genes. However, another common source of gene tree-species tree discordance is incomplete lineage sorting (ILS), whereby gene divergences correspondin...

Key message: The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to c...

In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted “the end of incongruence”, it soon appeared that analysing large amounts of sequence data without an adequate model of sequence evolution am...

Motivation: Marker-assisted selection strongly relies on genetic maps to accelerate breeding programs. High-density maps are now available for numerous species. Dedicated tools are required to compare several high-density maps on the basis of their key characteristics, while pinpointing their differences and similarities. Results: We developed t...

Background: Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeate...

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cu...

Background: Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evol...

In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As...

The need of indexing biomedical papers with the MeSH is incessantly growing and automated approaches are constantly evolving. Since 2013, the BioASQ challenge has been promoting those evolutions by proposing datasets and evaluation metrics. In this paper, we present our system, USI, and how we adapted it to participate to this challenge this year....

Background Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus. However, this task is time-consuming and requires a high-level of exp...

Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events). While numerous methods have been proposed to infer them, little has been done to study the underlying reconciliation space. In this paper, we characterise the reconcil...

The genetic diversity in durum wheat, Triticum turgidum durum, has been strongly reduced since the domestication of the wild Triticum turgidum dicoccoides. Monitoring durum wheat composite crosses incorporating related tetraploid taxa, such as wild and domesticated emmer wheat, is a suitable evolutionary pre-breeding method. Transcriptome sequencin...

Concept-based information retrieval is known to be a powerful and reliable process. It relies on a semantically annotated corpus, i.e. resources indexed by concepts organized within a domain ontology. The conception and enlargement of such index is a tedious task, which is often a bottleneck due to the lack of (semi-)automated solutions. In this pa...

Background Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale. Results We studied available sequenced angiosperm genomes to assess the frequency...

Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian M...

Multigenic families of Plant Defensin type 1 (PDF1) have been described in several species, including the model plant Arabidopsis thaliana as well as zinc tolerant and hyperaccumulator A. halleri. In A. thaliana, PDF1 transcripts (AtPDF1) accumulate in response to pathogen attack following synergic activation of ethylene/jasmonate pathways. However...

Genes located in the same chromosome region share common evolutionary events more often than other genes (e.g. a segmental duplication of this region). Their evolution may also be related if they are involved in the same protein complex or biological process. Identifying co-evolving genes can thus shed light on ancestral genome structures and funct...

The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in...

Background Using Next Generation Sequencing, SNP discovery is relatively easy on diploid species and still hampered in polyploid species by the confusion due to homeology. We develop HomeoSplitter; a fast and effective solution to split original contigs obtained by RNAseq into two homeologous sequences. It uses the differential expression of the tw...

Plant defensins are recognized for their antifungal properties. However, a few type 1 defensins ( PDF 1s) were identified for their cellular zinc (Zn) tolerance properties after a study of the metal extremophile Arabidopsis halleri . In order to investigate whether different paralogues would display specialized functions, the A. halleri PDF 1 famil...

Despite the rapid increase of size in phylogenomic datasets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable o...

Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species f...

Background Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes. It is well-known that gene trees inferred from molecular sequences can be partly erroneous due to incorrect sequence alignments as well as phylogenetic re...

Comparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that...

The exponential growth of available electronic data is almost useless without efficient tools to retrieve the right information at the right time. It is now widely acknowledged that information retrieval systems need to take semantics into account to enhance the use of available information. However, there is still a gap between the amounts of rele...

Ontologies are successfully used as semantic guides when navigating through the huge and ever increasing quantity of digital documents. Nevertheless, the size of numerous domain ontologies tends to grow beyond the human capacity to grasp information. This growth is problematic for a lot of key applications that require user interactions such as doc...

We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dyn...

We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dyn...

It is widely assumed that our mammalian ancestors, which lived in the Cretaceous era, were tiny animals that survived massive asteroid impacts in shelters and evolved into modern forms after dinosaurs went extinct, 65 Ma. The small size of most Mesozoic mammalian fossils essentially supports this view. Paleontology, however, is not conclusive regar...

We have sequenced the genome of the emerging human pathogen Babesia microti and compared it with that of other protozoa. B. microti has the smallest nuclear genome among all Apicomplexan parasites sequenced to date with three chromosomes encoding ∼3500 polypeptides, several of which are species specific. Genome-wide phylogenetic analyses indicate t...

Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a co...

The least common ancestor on two vertices, denoted lca(x,y), is a well defined operation in a directed acyclic graph (dag) G. We introduce U lca (S), a natural extension of lca(x,y) for any set S of vertices. Given such a set S 0 , one can iterate S k+1 =U lca (S k ) in order to obtain an increasing set sequence. G being finite, this sequence has a...

Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models...

Les performances d'un système de recherche d'information (SRI) peuvent être dégradées en termes de précision du fait de la difficulté pour des utilisateurs à formuler précisément leurs besoins en information. La reformulation ou l'expansion de requêtes constitue une des réponses à ce problème dans le cadre des SRI. Dans cet article, nous proposons...

The analysis of extant sequences shows that molecular evolution has been heterogeneous through time and among lineages. However, for a given sequence alignment, it is often difficult to uncover what factors caused this heterogeneity. In fact, identifying and characterizing heterogeneous patterns of molecular evolution along a phylogenetic tree is v...

During last decade, ontologies have been successfully used as semantic guidelines while navigating through huge and ever increasing quantity of digital documents. Nevertheless, the size of most ontologies, especially those shared and accepted as standards in a given domain, tends to grow beyond the human capacity to grasp information. This growth i...

Background: Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications...

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Seco...

Gene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses...

Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene tr...

Gene trees are leaf-labeled trees inferred from molecular sequences. Because of gene duplication events arising in genomes, some species host several copies of the same gene, hence individual gene trees usually have several leaves labeled with identical species names. Dealing with such multi-labeled gene trees (MUL trees) is a substantial problem i...

Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of retrieved documents and no explanation for their adequacy to the query. Users may thus be confused by the selectio...

Motivation: Tree reconciliation is a computational approach that explains the discrepancy between two evolutionary trees by proposing a number of evolutionary events such as speciations, duplications, transfers and losses. It has important applications in ecology, biogeography and genomics in estimating the evolutionary scenarios that have shaped t...

The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconst...

Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes and taxa. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. This task is generally conducted by a two-step approach whereby a binary representation of the initial trees is first inf...

Pour exploiter efficacement des corpus documentaires toujours plus volumineux, les moteurs de recherche doivent évoluer. Leurs limites actuelles concernent principalement le fait que la mesure de la pertinence d'un document par rapport à une requête est souvent non-explicite et que l'interaction avec la liste des réponses est limitée. Nous proposon...

Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for...

Gene trees are leaf-labeled trees inferred from molecular se- quences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species. Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a well- known problem in computational biology. We propose a novel approach...

GC-biased gene conversion (gBGC) is a recently discovered, recombination-associated segregation distortion, which influences GC-content dynamics in the mammalian genome. We scanned the primate proteome for examples of exon-specific, lineage-specific accelerated amino acid evolution. Here, we show that such episodes are frequently accompanied by an...

Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, libera...