Lessons from genome skimming of arthropod-preserving ethanol
File(s)
Accepted version
Author(s)
Linard, B
Arribas, P
Andujar, C
Crampton-Platt, A
Vogler, AP
Type
Journal Article
Abstract
Field-collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects (from a freshwater habitat and terrestrial habitat) to evaluate the efficiency of DNA transfer from the specimens to the ethanol. In parallel, the specimens themselves were subjected to bulk DNA extraction and shotgun sequencing, followed by assembly of mitochondrial genomes for 39 of 40 species in the two pools. Shotgun sequencing from the ethanol fraction and read-matching to the mitogenomes detected ~40% of the arthropod species in the ethanol, confirming the transfer of DNA whose quantity was correlated to the biomass of specimens. The comparison of diversity profiles of microbiota in specimen and ethanol samples showed that ‘closed association’ (internal tissue) bacterial species tend to be more abundant in DNA extracted from the specimens, while ‘open association’ symbionts were enriched in the preservative fluid. The vomiting reflex of many insects also ensures that gut content is released into the ethanol, which provides easy access to DNA from prey items. Shotgun sequencing of DNA from preservative ethanol provides novel opportunities for characterizing the functional or ecological components of an ecosystem and their trophic interactions.
Date Issued
2016-06-23
Date Acceptance
2016-05-06
Citation
Molecular Ecology Resources, 2016, 16 (6), pp.1365-1377
ISSN
1755-098X
Publisher
Wiley
Start Page
1365
End Page
1377
Journal / Book Title
Molecular Ecology Resources
Volume
16
Issue
6
Copyright Statement
© 2016 John Wiley & Sons Ltd. This is the accepted version of the following article: Linard, B., Arribas, P., Andújar, C., Crampton-Platt, A. and Vogler, A. P. (2016), Lessons from genome skimming of arthropod-preserving ethanol. Mol Ecol Resour, 16: 1365–1377. doi:10.1111/1755-0998.12539, which has been published in final form at https://dx.doi.org/10.1111/1755-0998.12539
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000385941500008&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Ecology
Evolutionary Biology
Environmental Sciences & Ecology
bacterial symbionts
Coleoptera
genome skimming
mitochondrial metagenomics
preservative ethanol
ENVIRONMENTAL DNA
MITOCHONDRIAL METAGENOMICS
PRESERVATIVE ETHANOL
BIODIVERSITY
DROSOPHILA
INSECTS
SPIROPLASMA
DIVERSITY
WOLBACHIA
PHYLOGENY
Animals
DNA
Ethanol
Insects
Preservation, Biological
Sequence Analysis, DNA
Solvents
06 Biological Sciences
Publication Status
Published