Biology subjects

Jean-Marc Aury

Publications and source records attributed to Jean-Marc Aury.

3 recordsLinked to original sources

bioRxiv2016

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small and low-cost single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments. The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a matter of seconds. It has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high continuity allowed us to accurately detect large structural variations across the 21 studied genomes. Moreover, because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.

Bioinformatics↗

bioRxiv2016

Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis

Root-knot nematodes (genus Meloidogyne) show an intriguing diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most damaging species to the world agriculture are those that reproduce without meiosis and without sex. To understand this parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of 3 obligatory ameiotic asexual Meloidogyne species and have compared them to those of meiotic relatives with facultative or obligatory asexual reproduction. Our comparative genomic analysis shows that obligatory asexual root-knot nematodes have a higher abundance of transposable elements (TE) compared to the facultative sexual and contain duplicated regions with a high within-species average nucleotide divergence of 8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events. The average nucleotide divergence in the coding portions between duplicated regions is ~5-6 % and we detected diversifying selection between the corresponding gene copies. Genes under diversifying selection covered a wide spectrum of predicted functional categories which suggests a high impact of the genome structure at the functional level. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, suggesting that these putative hybrids share a recent common maternal donor lineage. The intriguing parasitic success of mitotic root-knot nematodes in the absence of sex may be partly explained by TE-rich composite genomes resulting from multiple allo-polyploidization events and promoting plasticity in the absence of sex.

Evolutionary Biology↗

bioRxiv2015

MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

BackgroundScaffolding is a crucial step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in continuity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring.\n\nResultsWe present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase continuity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency.\n\nConclusionsMaGuS is a powerful reference-free evaluator of assembly quality and a map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the continuity of large and complex genome assemblies.

Genomics↗