Sequencing methods are evolving rapidly. The CEA's Institut de biologie François-Jacob recently participated in the nanopore sequencing of a tomato variety. This technique involves passing a strand of DNA through a biological pore in order to identify the sequence of bases (A, C, G, T) that make up this DNA fragment. This biological pore is composed of a bacterial protein anchored in a membrane, across which an electric field is passed. Intensity disturbances related to the nature of the DNA strand are then measured and translated into bases.

"Thanks to recent improvements, the MinION sequencing technology, marketed by Oxford Nanopore Technologies, makes it possible on the one hand to obtain gigabases of data and on the other hand to read large fragments of DNA", explains Jean-Marc Aury, a researcher from the Genoscope, at the Institut François-Jacob. Indeed, the available sequencing technologies in the past were capable of great sensitivity, but could only read small fragments. Today, the MinION greatly increases the world of possibilities. "We nearly gained a factor of 100", says the scientist. "Thus, the average size of sequenced fragments now averages 12,000 bases, as compared to 150 previously." The researchers were therefore able to sequence a tomato variety whose genome is composed of about one gigabase (one billion bases), equal to one-third the size of the human genome.

As part of the international consortium that conducted this work, the team from the Genoscope was involved in the genome assembly step, which aimed to reconstruct the genome sequence 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 displays great continuity, and half of the genome is now contained in genomic sequences of more than 2.5 megabases (millions of bases). Moreover, it is very complete, since it contains about 97% of the genes of this plant. This study takes a new step in adopting nanopore sequencing by demonstrating that the portable MinION sequencer can be used to sequence and assemble gigabase-sized plant genomes, with an improved cost/quality ratio in comparison to other equipment of the same sensitivity. This technology is used at the Genoscope to sequence the different genomes under study, since it makes it possible (unlike the Illumina technology) to provide a better representation of the genome and especially the repeated regions.