Jean-Marc Aury
De novo sequencing and assembly of plant genomes using nanopore long reads
About Jean-Marc Aury
Jean-Marc Aury is a researcher at Genoscope since 2003. He was focused on eukaryotic genome analysis and was a main actor of several genome projects, like paramecium, grape, banana, cocoa and oak. He is now the team leader of a bioinformatic group which is focused on sequencing data production, genome assembly and gene prediction in eukaryotic genomes, with a broad interest in methodological development. Genoscope acts as the French National Sequencing Centre since 1998 and has an extensive experience in large sequencing projects (for example the Tara Oceans metagenomic project). Genoscope has participated in the MinION and PromethION Early Access Program.
Recent publications
Istace, B. et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience 6, (2017).
Schmidt, M. H. et al. de novo assembly of a new Solanum pennellii accession using nanopore sequencing. The Plant Cell tpc.00521.2017 (2017). doi:10.1105/tpc.17.00521
Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nature Communications 9,(2018).
Madoui, M. A. et al. Genome assembly using nanopore-guided long and error-free DNA reads. BMC Genomics 16, (2015).
Abstract
Plant genomes are often characterized by their high level of repetitiveness and polyploid nature. As a direct consequence, genome assemblies of plant genomes are challenging. The introduction of short-reads technologies ten years ago, significantly increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few of them are at the chromosome-scale. Recently, Oxford Nanopore sequencing technology was commercialized with the promise to sequence long DNA fragments (kilobases to megabases order) and then, by using efficient algorithms, provide assembly of high quality in terms of contiguity and completeness of the repetitive regions. Here we describe the de novo sequencing and assembly of several plant genomes (banana, citrus and brassicaceae) and the impact of read length on the contiguity and completion of genome assemblies.
Jean-Marc Aury