We aimed to sequence and compare all the DNA (eg., the genome) of a bunch of different deer mice (genus Peromyscus) species to understand how some deer mice survive in hot deserts with little to no water. A number of deer mice tissue samples were available through natural history museums, which house the raw materials for genetic and biodiversity investigations, but the samples had been collected many years earlier. Older samples produce lower quality DNA that has been broken into many pieces over time. Our normal sequencing procedure selectively removes small fragments of DNA, which would essentially throw away all the DNA we wanted to sequence for these older samples! To circumvent this, we were able to use a different DNA library preparation method called linked-read sequencing (LRS). LRS uses standard short-read sequencing technology, but adds additional information about the location of DNA fragments within the genome by bundling and barcoding DNA fragments that are located near each other prior to sequencing (eg., ‘links’ DNA fragments together in ‘genome-space’). We found that this method improves the overall quality and completeness of genome assemblies from historical tissue samples, in less time and with less effort than traditional shot-gun sequencing methods. This alternative method may be particularly valuable for building high-quality genome assemblies for extinct species for which there are no new samples being collected for or endangered species that are difficult to sample or collect. LRS adds to the suite of genomic methods that continue to unlock the secrets of natural history collections and enable fine-scale genetic measurement of change through time.
This summary was written by the study’s first author, Jocelyn Colella.
Read the full text here.
Video credit: Jocelyn Colella. Peromyscus in the field.
Full Text: Colella JP, Tigano A, MacManes MD. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. Mol Ecol Resour. 2020;20:871–881.