Data from: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA
Data files
Feb 10, 2017 version files 2.12 GB
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breveGroupContextAnalyses.nex
238.38 KB
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lane1-s002-indexD707-D504-CTGAAGCT-TCAGAGCC-LIB0179_S2_L001_R1_001 (paired) trimmed (paired) contig list.fas
5.31 MB
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lane1-s003-indexD711-D506-TCTCGCGC-TAAGATTA-LIB0182_S3_L001_R1_001 (paired) trimmed (paired) contig list.fas
16.83 MB
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lane1-s004-indexD704-D507-GAGATTCC-ACGTCCTG-LIB0186_S4_L001_R1_001 (paired) trimmed (paired) contig list.fas
3.39 MB
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lane1-s006-indexD708-D501-TAATGCGC-AGGCTATA-LIB0210_S6_L001_R1_001 (paired) trimmed (paired) contig list.fas
9.18 MB
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lane1-s009-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0213_S9_L001_R1_001 (paired) trimmed (paired) contig list.fas
11.40 MB
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lane2-s095-indexD710-D505-TCCGCGAA-CTTCGCCT-LIB0216_S95_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fas
262.73 MB
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lane2-s096-indexD711-D504-TCTCGCGC-TCAGAGCC-LIB0217_S96_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fas
109.83 MB
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lane4_NoIndex_L004_R1_001 (paired) trimmed (paired) contig list.fas
288.32 MB
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lane5-index05-ACAGTG-3782_ACAGTG_L005_R1_001 (paired) trimmed (paired) contig list.fas
197.70 MB
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lane6-s001-indexD705-D505-ATTCAGAA-CTTCGCCT-LIB0120_S1_L006_R1_001 (paired) trimmed (paired) contig list.fas
173.83 MB
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lane6-s009-indexD704-D502-GAGATTCC-GCCTCTAT-LIB0176_S9_L006_R1_001 (paired) trimmed (paired) contig list.fas
78.66 MB
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lane6-s018-indexD712-D502-AGCGATAG-GCCTCTAT-LIB0206_S18_L006_R1_001 (paired) trimmed (paired) contig list.fas
103.34 MB
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lane6-s840-indexD705-D506-ATTCAGAA-TAAGATTA-LIB0147_S840_L006_R1_001 (paired) trimmed (paired) contig list.fas
137.49 MB
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lane6-s841-indexD701-D503-ATTACTCG-AGGATAGG-LIB0149_S841_L006_R1_001 (paired) trimmed (paired) contig list.fas
10.83 MB
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lane6-s842-indexD702-D504-TCCGGAGA-TCAGAGCC-LIB0150_S842_L006_R1_001 (paired) trimmed (paired) contig list.fas
3.06 MB
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lane6-s843-indexD703-D508-CGCTCATT-GTCAGTAC-LIB0164_S843_L006_R1_001 (paired) trimmed (paired) contig list.fas
15.13 MB
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lane6-s844-indexD706-D501-GAATTCGT-AGGCTATA-LIB0167_S844_L006_R1_001 (paired) trimmed (paired) contig list.fas
82.61 MB
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lane6-s845-indexD709-D502-CGGCTATG-GCCTCTAT-LIB0168_S845_L006_R1_001 (paired) trimmed (paired) contig list.fas
107.93 MB
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lane6-s846-indexD707-D503-CTGAAGCT-AGGATAGG-LIB0173_S846_L006_R1_001 (paired) trimmed (paired) contig list.fas
22.84 MB
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lane6-s847-indexD708-D505-TAATGCGC-CTTCGCCT-LIB0180_S847_L006_R1_001 (paired) trimmed (paired) contig list.fas
77.83 MB
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lane6-s848-indexD712-D501-AGCGATAG-AGGCTATA-LIB0183_S848_L006_R1_001 (paired) trimmed (paired) contig list.fas
32.85 MB
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lane6-s849-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0185_S849_L006_R1_001 (paired) trimmed (paired) contig list.fas
18.93 MB
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lane7-s850-indexD704-D508-GAGATTCC-GTCAGTAC-LIB0153_S850_L007_R1_001 (paired) trimmed (paired) contig list.fas
3.08 MB
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lane7-s851-indexD708-D502-TAATGCGC-GCCTCTAT-LIB0154_S851_L007_R1_001 (paired) trimmed (paired) contig list.fas
1.11 MB
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lane7-s852-indexD705-D503-ATTCAGAA-AGGATAGG-LIB0155_S852_L007_R1_001 (paired) trimmed (paired) contig list.fas
90.81 MB
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lane7-s853-indexD702-D506-TCCGGAGA-TAAGATTA-LIB0157_S853_L007_R1_001 (paired) trimmed (orphans) contig list.fas
22.09 MB
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lane7-s854-indexD710-D504-TCCGCGAA-TCAGAGCC-LIB0171_S854_L007_R1_001 (paired) trimmed (paired) contig list.fas
113.20 MB
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lane7-s855-indexD702-D508-TCCGGAGA-GTCAGTAC-LIB0175_S855_L007_R1_001 (paired) trimmed (paired) contig list.fas
71.58 MB
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lane7-s856-indexD705-D502-ATTCAGAA-GCCTCTAT-LIB0177_S856_L007_R1_001 (paired) trimmed (paired) contig list.fas
7.32 MB
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lane7-s857-indexD706-D506-GAATTCGT-TAAGATTA-LIB0178_S857_L007_R1_001 (paired) trimmed (paired) contig list.fas
8.93 MB
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lane7-s858-indexD710-D503-TCCGCGAA-AGGATAGG-LIB0181_S858_L007_R1_001 (paired) trimmed (paired) contig list.fas
14.82 MB
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lane7-s859-indexD707-D505-CTGAAGCT-CTTCGCCT-LIB0184_S859_L007_R1_001 (paired) trimmed (paired) contig list.fas
14.76 MB
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LionephaContextAnalyses.nex
387.63 KB
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NotaphusContextAnalyses.nex
138.60 KB
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obscuripenneGroupContextAnalyses.nex
286.22 KB
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TrepanedorisContextAnalyses.nex
136.74 KB
Abstract
Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3–6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58–159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1–10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers, and library amplification. We present these guidelines to facilitate more economical use of valuable DNA, and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.