A5065610197- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Banana Cultivation and Research
- Evolution and Genetic Dynamics
- Plant Diversity and Evolution
- Plant Pathogens and Fungal Diseases
- Genome Rearrangement Algorithms
- Yeasts and Rust Fungi Studies
- Bryophyte Studies and Records
- Plant Taxonomy and Phylogenetics
- Photosynthetic Processes and Mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Genomic variations and chromosomal abnormalities
- Legume Nitrogen Fixing Symbiosis
- Plant and Fungal Species Descriptions
- Plant Disease Resistance and Genetics
- RNA and protein synthesis mechanisms
Unité Évolution, Écologie et Paléontologie
2023-2024
Université de Lille
2023-2024
Centre National de la Recherche Scientifique
2023-2024
Ghent University
2018-2023
VIB-UGent Center for Plant Systems Biology
2018-2022
Abstract Hornworts, liverworts and mosses are three early diverging clades of land plants, together comprise the bryophytes. Here, we report draft genome sequence hornwort Anthoceros angustus . Phylogenomic inferences confirm monophyly bryophytes, with hornworts sister to mosses. The simple morphology correlates low genetic redundancy in plant body plan, while basic transcriptional regulation toolkit for development has already been established this lineage. Although is small characterized...
Ancient whole-genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants such events has become standard practice most genome analyses. This is especially true plants, where ancient WGDs are abundant. Common approaches to find evidence include construction KS distributions analysis intragenomic colinearity. Despite increased interest acknowledgment their evolutionary importance, user-friendly comprehensive tools lacking....
Abstract Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics phylogeny. Indeed, microsynteny—the conservation local gene content order—is recognized as a valuable source phylogenetic information, but its use the large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, maximum likelihood inference, we provide way to reconstruct based on...
Gene tree-species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic of life. Most approaches relied on using maximum likelihood trees and parsimony thereof to count specific branches interest in a reference species tree. Such do not account uncertainty gene reconciliation, or so only heuristically. The effects these simplifications inference WGDs are unclear. In particular, variation loss rates considered. Here, we...
Abstract Motivation Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase the number of available sequences. In turn, these sequences form an invaluable source for evolutionary, ecological, comparative studies. One kind analysis that has become routine is search traces ancient polyploidy, particularly plant genomes, where whole-genome duplication (WGD) rampant. Results Here, we present major update previously developed tool wgd, namely wgd v2,...
Abstract Background Digitaria exilis, white fonio, is a minor but vital crop of West Africa that valued for its resilience in hot, dry, and low-fertility environments the exceptional quality grain human nutrition. Its success hindered, however, by low degree plant breeding improvement. Findings We sequenced fonio genome with long-read SMRT-cell technology, yielding ∼761 Mb assembly 3,329 contigs (N50, 1.73 Mb; L50, 126). The approaches high level completion, BUSCO score >99%. was...
Abstract We consider how the genetic architecture underlying locally adaptive traits determines strength of a barrier to gene flow in mainland-island model. Assuming general life cycle, we derive an expression for effective migration rate when local adaptation is due variation at many loci under directional selection on island, allowing arbitrary fitness and dominance effects across loci. show can be combined with classical single-locus diffusion theory accurately predict multilocus...
Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be driver evolution, also hexapod animals.
Summary Ferns, and particularly homosporous ferns, have long been assumed to experienced recurrent whole‐genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, degrees polyploidy among many extant members. As the number sequenced fern genomes is limited, recent studies employed transcriptome data find evidence for WGDs in ferns. However, they reached conflicting results concerning occurrence ancient polyploidy, instance,...
Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection ancient WGDs a phylogenetic context have two main drawbacks. The first is unwarranted restrictive assumptions on "background" gene duplication and loss rates make inferences unreliable face model violations. second most methods only used examine limited set priori selected...
Abstract We consider how the genetic architecture underlying locally adaptive traits determines strength of a barrier to gene flow in mainland-island model. Assuming general life cycle, we derive an expression for effective migration rate when local adaptation is due polygenic trait under directional selection on island, allowing arbitrary fitness and dominance effects across loci. show can be combined with classical single-locus diffusion theory accurately predict multilocus differentiation...
Recent times have seen an enormous growth of 'omics' data, which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for classification sequences, common similarity-based methods often fall short providing full and reliable information. Recently, combination comparative genomics with approaches has received considerable interest function analysis, leveraging both based guilt-by-association...
Abstract Despite the wealth of genomic and transcriptomic data pivotal angiosperm species, phylogenetic relationships flowering plants are still not fully resolved. Microsynteny, or conservation relative gene order, has been recognized as a valuable alternative character to sequence-based characters (nucleotides amino acids). Here, we present novel approach for tree reconstruction based on genome-wide synteny network data. We generated analyzed networks from 123 species 52 families across 31...
Abstract Plant genomes are generally very complex and dynamic structures, vary greatly in size, organization, architecture. This is mainly due to the often-excessive numbers of transposable repetitive elements, as well fact that many plants ancient or recent polyploids. Such (recurrent) whole-genome duplications usually followed by genomic rearrangements, gene transpositions loss, making local order-based phylogenetic inference particularly challenging. Nevertheless, microsynteny, i.e....
Abstract Phylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption these is the constant per-gene loss rate in any particular family. Because possibility partial functional redundancy among members, dynamics are however likely be dependent number genes a family, and different variations commonly employed BDP indeed suggest this case. We propose simple two-type branching process model better...
Abstract Gene tree - species reconciliation methods have been employed for studying ancient whole genome duplication (WGD) events across the eukaryotic of life. Most approaches relied on using maximum likelihood trees and parsimony thereof to count specific branches interest in a reference tree. Such do not account uncertainty gene reconciliation, or so only heuristically. The effects these simplifications inference WGDs are unclear. In particular variation loss rates considered. Here, we...
Abstract Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection ancient WGDs a phylogenetic context have two main drawbacks. The first is unwarranted restrictive assumptions on ‘background’ gene duplication and loss rates make inferences unreliable face model violations. second most methods only used examine limited set priori...
Abstract Ferns, and particularly homosporous ferns, have long been assumed to experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, degrees polyploidy among many extant members. Although, consequently, the number sequenced fern genomes is very limited, recent studies using transcriptome data find evidence for WGDs in ferns reached conflicting results concerning occurrence ancient polyploidy,...