09:22pm Sunday 20 August 2017

New method to generate extended data for genome assemblies

Long range genetic data (long mate pair – LMP) is an invaluable source for plant, crop and animal genetic research. Sequencing genomes requires breaking them into small manageable pieces and then working out how they go back together – similar to a million or billion piece jigsaw puzzle. To do this, a combination of short range (a jigsaw piece) and long range (tells you about the nearby pieces) sequence data is needed.

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. More complex genomes, typically benefit from accurately size-selected LMP data to produce the highest quality genome assemblies.

The TGAC team gained early access to a new piece of technology, the SageELF from Sage Scientific to develop a more robust, global approach to achieve the most accurate long range sequence data for any given sample.

“Although producing a single high-quality size selected LMP library can be difficult, several LMP libraries are often used for larger genome sequencing projects. Our new genome analysis protocol allows concurrent construction of 12 long-range data libraries for less than twice the cost of a single library and reduces the time by 3 to 2 days,” said Darren Heavens, Lead Author and Team Leader in the Platforms & Pipelines at TGAC.

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. 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.

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. 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.

The advanced online version of the paper, titled: “A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost” is published in BioTechniques (PDF) .



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