Biology subjects

Patrick Wincker

Publications and source records attributed to Patrick Wincker.

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

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ocean microbes drive global-scale biogeochemical cycling1, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories2-5. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are known5. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions6,7. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups8,9). This roughly triples known ocean viral populations10, doubles known candidate bacterial and archaeal virus genera9, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks.

Ecology↗

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↗