7/6/2023 0 Comments Dfind old genome assemblies![]() Using nanopore sequencing alone, the genome was captured in just 159 contigs. Using the PromethION 24 device and a plant-trained basecalling model, the KeyGene team generated the most contiguous lettuce genome ever assembled. The insights obtained using a high-quality reference genome enable better and faster selection of important breeding traits - allowing new plant varieties to be brought to market faster. A significant focus is crop improvement through breeding for traits such as pathogen resistance, extended shelf life, and improved taste and colour. Identifying new technologies and their applications is a key aspect of the work we do and we will continue to monitor opportunities in this area.Scientists at KeyGene in the Netherlands are at the forefront of technology innovation for crop improvement. "For all projects requiring long-range sequence information, we are now promoting this method as our Gold Standard approach. Since its development, this approach has already been successfully implemented in a number of our high profile sequencing projects such as bread wheat, durum wheat, Aegilops sharonensis and a European Ash Tree more resistant to Ash Dieback Disease, all with very impressive results. Matt Clark, last author, Plant and Microbial Genomics Group Leader at TGAC, added: "Generating high-quality genome assemblies is important as they form the base upon which we build an understanding of an organism's genetics. Providing a better understanding of traits of economic interest in crops and animals which are seen as key requirements for breeders such as disease-resistance. The scientists hope that this new library construction approach will be widely adopted within the scientific community, having a positive effect in improving genome assemblies. While most projects wouldn't require sequencing all 12 fractions we can select the best fractions for sequencing". "Previous approaches limited us to targeting a single size range at a time, whereas using this new protocol we can simultaneously target up to 12 different size fractions improving the likelihood of achieving the best long range data from a given DNA source, saving both time and money. "Improving LMP libraries has been a goal of TGAC's for some time, and we have previously published a software tool for processing this data to 'clean it up' before using it in genome assemblies," said Darren Heavens, Lead Author and Team Leader in the Platforms & Pipelines at TGAC.Įuropean Ash Tree and wheat (example organisms this method has already been applied to produce high-quality genome assemblies). The protocol would be more tolerant to DNA quality and quantity and could ensure that the best possible data was generated for any given sample. ![]() The TGAC team gained early access to a new piece of technology, the SageELF from Sage Scientific, with the aim to develop a more robust, global approach for accurately sized long-range sequence data. ![]() This new approach allows construction of 12 libraries for less than twice the cost of a single library and reduces the time by 3 to 2 days. More complex genomes, typically benefit from accurately size selected LMP data to produce the highest quality genome assemblies.Īlthough producing a single high-quality size selected LMP library can be difficult, several LMP libraries are often used for larger genome sequencing projects. Illumina's Nextera Mate Pair Sample Preparation Kit has helped improve the quality of long range (LMP) data, but they can still be challenging to generate. While generating the short range data is relatively straightforward, the long range data is more problematic as quality and quantity of DNA are major factors influencing the outcome. ![]()
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