10.5061/DRYAD.0179T
Heintzman, Peter D.
Royal Holloway University of London
Elias, Scott A.
Royal Holloway University of London
Moore, Karen
University of Exeter
Paszkiewicz, Konrad
University of Exeter
Barnes, Ian
Royal Holloway University of London
Data from: Characterizing DNA preservation in degraded specimens of Amara
alpina (Carabidae: Coleoptera)
Dryad
dataset
2013
Metagenomics
Late Pleistocene
Quaternary
Shotgun sequencing
Carabidae
Recent
DNA preservation
Wolbachia
museum DNA
Spiroplasma
Holocene
Amara alpina
2013-11-27T16:33:28Z
2013-11-27T16:33:28Z
en
https://doi.org/10.1111/1755-0998.12205
https://www.ncbi.nlm.nih.gov/nuccore/KF695187
https://www.ncbi.nlm.nih.gov/nuccore/KF695188
https://www.ncbi.nlm.nih.gov/nuccore/KF695189
886158276 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
DNA preserved in degraded beetle (Coleoptera) specimens, including those
derived from dry-stored museum and ancient permafrost-preserved
environments, could provide a valuable resource for researchers interested
in species and population histories over timescales from decades to
millenia. However, the potential of these samples as genetic resources is
currently unassessed. Here, using Sanger and Illumina shotgun sequence
data, we explored DNA preservation in specimens of the ground beetle Amara
alpina, from both museum and ancient environments. Nearly all museum
specimens had amplifiable DNA, with the maximum amplifiable fragment
length decreasing with age. Amplification of DNA was only possible in 45%
of ancient specimens. Preserved mitochondrial DNA fragments were
significantly longer than those of nuclear DNA in both museum and ancient
specimens. Metagenomic characterisation of extracted DNA demonstrated that
parasite-derived sequences, including Wolbachia and Spiroplasma, are
recoverable from museum beetle specimens. Ancient DNA extracts contained
beetle DNA in amounts comparable to museum specimens. Overall, our data
demonstrate that there is great potential for both museum and ancient
beetle specimens in future genetic studies.
Reference sequences for museum-1Reference sequences for sample museum-1.
Use with file 'Alignment of merged reads for
museum-1'.Amara_alpina.reference_list.museum1.fastaReference
sequences for museum-2Reference sequences for sample museum-2. Use with
file 'Alignment of merged reads for
museum-2'.Amara_alpina.reference_list.museum2.fastaReference
sequences for modern-1Reference sequences for sample modern-1. Use with
file 'Alignment of merged reads for
modern-1'.Amara_alpina.reference_list.modern1.fastaReference
sequences for modern-2Reference sequences for sample modern-2. Use with
file 'Alignment of merged reads for
modern-2'.Amara_alpina.reference_list.modern2.fastaReference
sequences for ancient-1Reference sequences for sample ancient-1. Use with
file 'Alignment of merged reads for
ancient-1'.Amara_alpina.reference_list.ancient1.fastaReference
sequences for ancient-2Reference sequences for sample ancient-2. Use with
file 'Alignment of merged reads for
ancient-2'.Amara_alpina.reference_list.ancient2.fastaPartial COI
sequence for Amara alpinaExample partial sequence of the cytochrome
oxidase subunit 1 (COI) gene for Amara alpinaPartial 28S sequence for
Amara alpinaExample partial sequence of the 28S ribosomal RNA (28S) gene
for Amara alpinaPartial ITS1 sequence for Amara alpinaExample partial
sequence of the internal transcribed spacer 1 (ITS1) for Amara
alpinaAlignment of merged reads for museum-1Merged reads that aligned to
the reference sequences for sample museum-1. Use with file 'Reference
sequences for
museum-1'.Amara_alpina.merged_alignment.museum1.samAlignment of
merged reads for museum-2Merged reads that aligned to the reference
sequences for sample museum-2. Use with file 'Reference sequences for
museum-2'.Amara_alpina.merged_alignment.museum2.samAlignment of
merged reads for modern-2Merged reads that aligned to the reference
sequences for sample modern-2. Use with file 'Reference sequences for
modern-2'.Amara_alpina.merged_alignment.modern2.samAlignment of
merged reads for modern-1Merged reads that aligned to the reference
sequences for sample modern-1. Use with file 'Reference sequences for
modern-1'.Amara_alpina.merged_alignment.modern1.samAlignment of
merged reads for ancient-1Merged reads that aligned to the reference
sequences for sample ancient-1. Use with file 'Reference sequences
for ancient-1'.Amara_alpina.merged_alignment.ancient1.samAlignment of
merged reads for ancient-2Merged reads that aligned to the reference
sequences for sample ancient-2. Use with file 'Reference sequences
for ancient-2'.Amara_alpina.merged_alignment.ancient2.samContig data
for modern-1FASTA file of all contigs considered during the metagenomic
analysis of sample modern-1. Use with 'BLAST assignment data for
modern-1' in MEGAN v4.70.Amara_alpina.contigs.modern-1.fastaContig
data for modern-2FASTA file of all contigs considered during the
metagenomic analysis of sample modern-2. Use with 'BLAST assignment
data for modern-2' in MEGAN
v4.70.Amara_alpina.contigs.modern-2.fastaContig data for museum-1FASTA
file of all contigs considered during the metagenomic analysis of sample
museum-1. Use with 'BLAST assignment data for museum-1' in MEGAN
v4.70.Amara_alpina.contigs.museum-1.fastaContig data for museum-2FASTA
file of all contigs considered during the metagenomic analysis of sample
museum-2. Use with 'BLAST assignment data for museum-2' in MEGAN
v4.70.Amara_alpina.contigs.museum-2.fastaContig data for ancient-1FASTA
file of all contigs considered during the metagenomic analysis of sample
ancient-1. Use with 'BLAST assignment data for ancient-1' in
MEGAN v4.70.Amara_alpina.contigs.ancient-1.fastaContig data for
ancient-2FASTA file of all contigs considered during the metagenomic
analysis of sample ancient-2. Use with 'BLAST assignment data for
ancient-2' in MEGAN v4.70.Amara_alpina.contigs.ancient-2.fastaBLAST
assignment data for modern-1Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample modern-1. Use with
'Contig data for modern-1' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.modern-1.BLASTBLAST
assignment data for modern-2Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample modern-2. Use with
'Contig data for modern-2' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.modern-2.BLASTBLAST
assignment data for museum-1Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample museum-1. Use with
'Contig data for museum-1' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.museum-1.BLASTBLAST
assignment data for museum-2Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample museum-2. Use with
'Contig data for museum-2' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.museum-2.BLASTBLAST
assignment data for ancient-1Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample ancient-1. Use with
'Contig data for ancient-1' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.ancient-1.BLASTBLAST
assignment data for ancient-2Unfiltered BLAST assignment file of contigs
identified during the metagenomic analysis of sample ancient-2. Use with
'Contig data for ancient-2' in MEGAN v4.70. See attached readme
file for column headers.Amara_alpina.assignments.ancient-2.BLAST
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