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.
breveGroupContextAnalyses
The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the breve species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
LionephaContextAnalyses
The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the genus Lionepha (Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
obscuripenneGroupContextAnalyses
The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the obscuripenne species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
TrepanedorisContextAnalyses
The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Trepanedoris (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
NotaphusContextAnalyses
The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Notaphus (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DNA3890 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s018-indexD712-D502-AGCGATAG-GCCTCTAT-LIB0206_S18_L006_R1_001 (paired) trimmed (paired) contig list.fas
DNA3782 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane5-index05-ACAGTG-3782_ACAGTG_L005_R1_001 (paired) trimmed (paired) contig list.fas
DNA4233 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s001-indexD705-D505-ATTCAGAA-CTTCGCCT-LIB0120_S1_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0217 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane2-s096-indexD711-D504-TCTCGCGC-TCAGAGCC-LIB0217_S96_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fas
LIB0216 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane2-s095-indexD710-D505-TCCGCGAA-CTTCGCCT-LIB0216_S95_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fas
LIB0213 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane1-s009-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0213_S9_L001_R1_001 (paired) trimmed (paired) contig list.fas
LIB0179 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane1-s002-indexD707-D504-CTGAAGCT-TCAGAGCC-LIB0179_S2_L001_R1_001 (paired) trimmed (paired) contig list.fas
LIB0178 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s857-indexD706-D506-GAATTCGT-TAAGATTA-LIB0178_S857_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0182 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane1-s003-indexD711-D506-TCTCGCGC-TAAGATTA-LIB0182_S3_L001_R1_001 (paired) trimmed (paired) contig list.fas
LIB0171 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s854-indexD710-D504-TCCGCGAA-TCAGAGCC-LIB0171_S854_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0175 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s855-indexD702-D508-TCCGGAGA-GTCAGTAC-LIB0175_S855_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0154 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s851-indexD708-D502-TAATGCGC-GCCTCTAT-LIB0154_S851_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0153 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s850-indexD704-D508-GAGATTCC-GTCAGTAC-LIB0153_S850_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0184 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s859-indexD707-D505-CTGAAGCT-CTTCGCCT-LIB0184_S859_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0147 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s840-indexD705-D506-ATTCAGAA-TAAGATTA-LIB0147_S840_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0157 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s853-indexD702-D506-TCCGGAGA-TAAGATTA-LIB0157_S853_L007_R1_001 (paired) trimmed (orphans) contig list.fas
LIB0177 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s856-indexD705-D502-ATTCAGAA-GCCTCTAT-LIB0177_S856_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0181 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s858-indexD710-D503-TCCGCGAA-AGGATAGG-LIB0181_S858_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0210 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane1-s006-indexD708-D501-TAATGCGC-AGGCTATA-LIB0210_S6_L001_R1_001 (paired) trimmed (paired) contig list.fas
LIB0180 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s847-indexD708-D505-TAATGCGC-CTTCGCCT-LIB0180_S847_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0183 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s848-indexD712-D501-AGCGATAG-AGGCTATA-LIB0183_S848_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0176 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s009-indexD704-D502-GAGATTCC-GCCTCTAT-LIB0176_S9_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0155 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane7-s852-indexD705-D503-ATTCAGAA-AGGATAGG-LIB0155_S852_L007_R1_001 (paired) trimmed (paired) contig list.fas
LIB0164 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s843-indexD703-D508-CGCTCATT-GTCAGTAC-LIB0164_S843_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0168 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s845-indexD709-D502-CGGCTATG-GCCTCTAT-LIB0168_S845_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0167 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s844-indexD706-D501-GAATTCGT-AGGCTATA-LIB0167_S844_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0173 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s846-indexD707-D503-CTGAAGCT-AGGATAGG-LIB0173_S846_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0149 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s841-indexD701-D503-ATTACTCG-AGGATAGG-LIB0149_S841_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0186 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane1-s004-indexD704-D507-GAGATTCC-ACGTCCTG-LIB0186_S4_L001_R1_001 (paired) trimmed (paired) contig list.fas
LIB0185 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s849-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0185_S849_L006_R1_001 (paired) trimmed (paired) contig list.fas
LIB0150 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane6-s842-indexD702-D504-TCCGGAGA-TCAGAGCC-LIB0150_S842_L006_R1_001 (paired) trimmed (paired) contig list.fas
DNA3205 de novo assembly
List of contigs generated from the de novo assembly in CLC Genomics Workbench
lane4_NoIndex_L004_R1_001 (paired) trimmed (paired) contig list.fas