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Symposium on Sunflower and Climate Change

The International Symposium on Sunflower and Climate Change was organized in the frame of the SUNRISE project, by INRA Toulouse (Institut National de Recherche en Agronomie) and the French technical c...

In brief

In an unprecedented effort - 8 years project, investment of €21m, 16 partners including 9 public laboratories with a specific investment of INRA, 6 companies involved in sunflower breeding and the ...

The Project

In a context of climate changes and of world increasing demand for oilseed production, it is crucial to improve resistance to drought and yields of sunflower crops in such conditions. To improve ge...

Publication on the Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

The method for extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules has been published in the BioTechniques journal:

2016 Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños BioTechniques, Vol. 61, No. 4, October 2016, pp. 203–205 (link)

 
Abstract

De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

Next-generation sequencing (NGS) is commonly used in genomics and, until recently, only produced sequences hundreds of nucleotides long. The genomes of higher eukaryotes, especially plants, contain a large number of repeated sequences that can reach several tens of kilobases in length. De novo assemblies of large complex genomes based on short reads result in fragmented genome sequences containing thousands to millions of contigs or scaffolds. Third-generation sequencers based on the sequencing of a single DNA molecule produce sequences of several tens of kilobases, which can improve genome assemblies because the longer reads can often span repeated regions