Projects

CAPTURE (2017-2018) - Long sequence DNA capture, plastomes and crops: mastering third generation sequencing for agrobiodiversity studies - Funded by Agropolis Fondation (France)

Project leader: T Couvreur

Scientists involved from our team : T Couvreur, N Scarcelli, C Mariac, M Couderc, Y Vigouroux

High throughput sequencing is revolutionizing agrobiodiversity research allowing for the generation of thousands of genomes. If the initial technology allowed to increase data quantity and number of short reads, the third generation sequencing (TGS) will revolutionize the sequencing landscape by allowing sequencing of significantly longer reads. TGS allows long DNA fragments of mean read length of 15kb to be sequenced in real time. Moreover, some TGS technologies have enabled the miniaturization and portability of the sequencing devices becoming as small as a USB key Weighting just 90 g, the MinION of Oxford Nanopore Technologies is the smallest sequencing device available.

Longer reads allow several key new advances: faster and higher quality genome assembly, study of structural variation, developing long fragment metagenomes, and ultra-barcoding. Miniaturization also allows to expand this technology closer to the field notably in tropical countries. These tropical countries harbor hotspots of diversity and utilization of these new technologies will help better describe and manage such diversity. However, our ability to capture long DNA fragments prior to TGS sequencing is a key step for higher organism genomes like the larger genome of plants. DNA capture reduces genome complexity needed to increase read depth and sequence quality. CAPTURE aims to apply TGS to the study of higher plant DNA sequencing, thus opening the doors of this technology for agrobiodiversity research. Three specific objectives will be achieved:

-      Optimize a long range DNA sequence capture protocol for plant plastomes using MinION;

-      Design a set of monocot specific nuclear probes for long range capture

-      Sequence plastomes of specific economically important African and South American plant species using TGS/MinION technology.

We shall first test a capture protocol using the well known genome of Oryza sativa in order to develop the protocol. This will be achieved by using low cost in house probes. Once the protocol is validated will shall apply TGS to plastome sequencing of six economically important African and South American monocot species using Mybaits probes.