2022
DOI: 10.1111/1755-0998.13631
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Recovering the genomes hidden in museum wet collections

Abstract: Museum samples are challenging to work with due to the heterogeneity of sample types and the wide variety of conditions under which they are stored. Samples also often lack detailed preservation information, such as initial storage conditions (temperature and light conditions), fixatives used and post-mortem intervals. DNA preservation is highly variable among specimen types, preservation methods and storage conditions (Pääbo, 1989). In recent decades, DNA has been successfully retrieved from dried soft tissue… Show more

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Cited by 7 publications
(2 citation statements)
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“…Specimens stored in liquid preservation media are prone to various levels of DNA contamination from non-target organisms (Raxworthy and Smith 2021), caused by different handling and storage conditions that are often hard to retrace (Ruiz-Gartzia et al 2022). To detect levels of contamination from exogenous DNA in our assemblies, we used NCBI’s Foreign Contamination Screen (FCS 0.5.0) (Astashyn et al 2023), which flags both putative adapter sequences (FCS-adaptor) and contigs assigned to non-target species (FCS-GX).…”
Section: Methodsmentioning
confidence: 99%
“…Specimens stored in liquid preservation media are prone to various levels of DNA contamination from non-target organisms (Raxworthy and Smith 2021), caused by different handling and storage conditions that are often hard to retrace (Ruiz-Gartzia et al 2022). To detect levels of contamination from exogenous DNA in our assemblies, we used NCBI’s Foreign Contamination Screen (FCS 0.5.0) (Astashyn et al 2023), which flags both putative adapter sequences (FCS-adaptor) and contigs assigned to non-target species (FCS-GX).…”
Section: Methodsmentioning
confidence: 99%
“…Over the last decade, there has been a constantly expanding set of literature outlining new developments which contribute to making the recovery of sequence data from museum specimens more cost-effective and routine ( Knyshov et al 2019 ). These include breakthroughs in sample and tissue types that were previously considered intractable, including significant improvements in prospects for recovery of genomic data from formalin-fixed tissues ( Ruiz-Gartzia et al 2022 ). For instance, Straube et al (2021) used aDNA extraction protocols and single-stranded DNA library preparation to achieve high rates of success in recovering endogenous DNA from wet museum collections of a range of vertebrate taxa including formalin-fixed samples, followed by a target-capture approach to recover almost complete mitogenomes from a subset of these samples.…”
Section: Maximising the Recovery Of Endogenous Dna Sequencesmentioning
confidence: 99%