Biology subjects

Engelen, S.

Publications and source records attributed to Engelen, S..

11 recordsLinked to original sources

bioRxiv2023

Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis melo L.)

BackgroundNanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept. ResultsWe showed that each of the 15 regions we identified in two newly assembled melon genomes (subspecies melo) were successfully and accurately reconstructed as well as in a third cultivar from the agrestis subspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In the agrestis cultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS. ConclusionsAltogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.

genomics↗

bioRxiv2023

Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam

The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean zebu in the founder ancestry. Comparative analysis of whole genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. However, we did not observe any significant purge of highly deleterious variants. Interestingly, the populations success in the harsh environment can be attributed to pre-adaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. This unprecedented case study provides valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It highlights the importance of preserving the unique genetic legacies of feral populations and raises ethical questions in the eyes of conservation efforts.

evolutionary biology↗

bioRxiv2021

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

evolutionary biology↗

bioRxiv2021

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding

The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years due to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Here, we report on an optimized procedure based on long-reads produced on the ONT (Oxford Nanopore Technology) PromethION device to assemble the genome of the French bread wheat cultivar Renan. We provide the most contiguous and complete chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-Seq data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

genomics↗

bioRxiv2020

Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

BackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The Brassica genus is not exempt and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus. FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. ConclusionUsing these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

genomics↗

bioRxiv2020

BoardION: real-time monitoring of Oxford Nanopore Technologies devices

SummaryOne of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of sequencing in real time. However, the ONT sequencing interface is not sufficient to explore the quality of sequencing data in depth and existing tools do not take full advantage of real-time data streaming. We present BoardION, an interactive web application, dedicated to sequencing platforms, for real-time monitoring of all ONT sequencing devices (MinION, Mk1C, GridION and PromethION). BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the generated data during the experiment. It also enables the comparison of several flowcells to evaluate the library preparation protocols or the quality of input samples. AvailabilitySource code and a Docker image are available at http://www.genoscope.cns.fr/boardion/ Contactstefan.engelen@genoscope.cns.fr

bioinformatics↗

bioRxiv2020

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

genomics↗

bioRxiv2020

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200 nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4,964 and 4,485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.

genomics↗

bioRxiv2018

Transposon accumulation lines uncover histone H2A.Z-driven integration bias towards environmentally responsive genes

Inherited transposition events are important drivers of genome evolution but because transposable element (TE) mobilization is usually rare, its impact on the creation of genetic variation remains poorly characterized. Here, we used a population of A. thaliana epigenetic recombinant inbred lines (epiRILs) to characterize >8000 de novo insertions produced by several TEs families also active in nature. Integration was strongly biased towards genes, with evident deleterious effects. Biases were TE family-specific and associated with distinct chromatin features. Notably, we demonstrate that the histone variant H2A.Z guides the preferential integration of Ty1/Copia LTR-retrotransposons within environmentally responsive genes and that this guiding function is evolutionary conserved. Finally, we uncover an important role for epigenetic silencing in exacerbating or alleviating the effects of TE insertions on target genes. These findings establish chromatin as a major determinant of the spectrum and functional impact of TE-generated mutations, with important implications for adaptation and evolution.

genomics↗

bioRxiv2018

Mapping DNA replication with nanopore sequencing

We have harnessed nanopore sequencing to study DNA replication genome-wide at the single-molecule level. Using in vitro prepared DNA substrates, we characterized the effect of bromodeoxyuridine (BrdU) substitution for thymidine on the MinION nanopore electrical signal. Using a neural-network basecaller trained on yeast DNA containing either BrdU or thymidine, we identified BrdU-labelled tracts in yeast cells synchronously entering S phase in the presence of hydroxyurea and BrdU. As expected, the BrdU-labelled tracts coincided with previously identified early-firing, but not late-firing, replication origins. These results open the way to high-throughput, high-resolution, single-molecule analysis of DNA replication in many experimental systems.

genomics↗

bioRxiv2018

Comparison of two African rice species through a new pan-genomic approach on massive data

Pangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii, and mapped them on the external reference from Asian rice O. sativa. We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.

genomics↗