Nanopore sequencing consists of passing a strand of DNA through a biological pore to identify the sequence of bases (A, C, G, T) that make up this DNA fragment. Thanks to recent improvements, this sequencing technology (brought to the market by Oxford Nanopore Technologies) now allows obtaining gigabases of data, while also enabling the reading of large fragments of DNA (several tens of kilobases). Previously, due to its reduced throughput, this sequencing technology was principally used to analyze microbial samples with genome sizes on the order of a few million bases.
An international consortium, including a team from the CEA/Genoscope, carried out the complete sequencing of the genome of a tomato variety using MinION, a portable sequencer developed by Oxford Nanopore.
The MinION sequencer made it possible to read DNA fragments with a median size of about 12 kb. The CEA/Genoscope team has been involved in the genome assembly step, which aims to reconstruct this genome sequence by using these large fragments. The size of the readings provided by the sequencer made it possible to highlight the numerous repeated regions of the genome, which are inaccessible by conventional sequencing using short readings (Illumina sequencers). The resulting assembly has a high degree of continuity: half of the genome is now present in genomic sequences of more than 2.5 megabases. Moreover, the sequence is very complete, since it contains about 97% of the genes of this plant. This study takes a new step forward in the adoption of nanopore sequencing, by demonstrating that the portable MinION sequencer can be used to sequence and assemble plant genomes on a gigabase scale, and with an improved cost/quality ratio in comparison to other equipment. This technology is implemented at the Genoscope to sequence the different genomes studied. In contrast to the Illumina technology, the MinION sequencer makes it possible to provide a better representation of the genome, especially the repeated regions.