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Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens

Patzold, Franziska, Zilli, Alberto, Hundsdoerfer, Anna K.·2020·PLOS ONE
DOI 10.1371/journal.pone.0235222PMC PMC7343169
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Fig 1 Distribution of the total extracted DNA from the three kits. (A) samples extracted with the DNeasy extraction Kit (Qiagen); dots in green are the samples extracted using the innuPREP DNA Mini Kit (Analytik Jena), and the dots in magenta are samples extracted with the Monarch® PCR & DNA Clean-up Kit (New England Biolabs). A trend line was included for each protocol for visualisation of overall distribution.
Fig 1 Distribution of the total extracted DNA from the three kits. (A) samples extracted with the DNeasy extraction Kit (Qiagen); dots in green are the samples extracted using the innuPREP DNA Mini Kit (Analytik Jena), and the dots in magenta are samples extracted with the Monarch® PCR & DNA Clean-up Kit (New England Biolabs). A trend line was included for each protocol for visualisation of overall distribution.CC BY · PubMed Central
Fig 2 Comparison of total amounts of DNA extracted using the two protocols for the same individuals. The T-test was used to compare the means of the two protocols (*** p < 0.001).
Fig 2 Comparison of total amounts of DNA extracted using the two protocols for the same individuals. The T-test was used to compare the means of the two protocols (*** p < 0.001).CC BY · PubMed Central
Fig 3 Comparison of fragment sizes between two protocols from three specimens. Electropherograms from the DNeasy extraction Kit (blue) and the Monarch PCR & DNA Clean-up Kit (red). The specimens individual MTD-TW numbers are as follows: A 9248, B 9252, C 9251. See Supplementary Table 1 for more details on the DNA yield from each extraction.
Fig 3 Comparison of fragment sizes between two protocols from three specimens. Electropherograms from the DNeasy extraction Kit (blue) and the Monarch PCR & DNA Clean-up Kit (red). The specimens individual MTD-TW numbers are as follows: A 9248, B 9252, C 9251. See Supplementary Table 1 for more details on the DNA yield from each extraction.CC BY · PubMed Central
Fig 4 Lecto- and paralectotype specimens of Hyles livornica before (A, B, C) and after (a, b, c) sampling and extraction. Specimens were handled with cleaned forceps in the collection rooms. Treatment and reattachment of one leg each (middle leg). The specimens’ individual MTD-TW numbers are: A/a 12624, B/b 12625, C/c 12626 (S1 Table).
Fig 4 Lecto- and paralectotype specimens of Hyles livornica before (A, B, C) and after (a, b, c) sampling and extraction. Specimens were handled with cleaned forceps in the collection rooms. Treatment and reattachment of one leg each (middle leg). The specimens’ individual MTD-TW numbers are: A/a 12624, B/b 12625, C/c 12626 (S1 Table).CC BY · PubMed Central
Fig 5 Raw read composition, showing the percentage of adapter content (A) and percentage of duplicates (B). Both Reads (R1 and R2) are shown for each sample.
Fig 5 Raw read composition, showing the percentage of adapter content (A) and percentage of duplicates (B). Both Reads (R1 and R2) are shown for each sample.CC BY · PubMed Central
Fig 6 Percentage of endogenous DNA content of sequenced whole genome shotgun libraries. Sample age and species are added to the specimens MTD-TW number. Age is estimated in samples marked with * (see also S3 Table).
Fig 6 Percentage of endogenous DNA content of sequenced whole genome shotgun libraries. Sample age and species are added to the specimens MTD-TW number. Age is estimated in samples marked with * (see also S3 Table).CC BY · PubMed Central
Fig 7 Coverage breadth and depth of the Hyles vespertilio lectotype (MTD-TW 12623) sequences along the mitochondrial reference genome of the same species (ZITAT). Coverage depth is scaled to a max depth of 100 to enable visibility of coverage depth <100X. The inner circle shows the coverage breadth and depth for this sample. The outer circle shows the mitochondrial reference genome with the annotated diagnostic subunits of the cytochrome oxidase subunits (COI and COII, green) and tRNALeu (trnL2, blue).
Fig 7 Coverage breadth and depth of the Hyles vespertilio lectotype (MTD-TW 12623) sequences along the mitochondrial reference genome of the same species (ZITAT). Coverage depth is scaled to a max depth of 100 to enable visibility of coverage depth <100X. The inner circle shows the coverage breadth and depth for this sample. The outer circle shows the mitochondrial reference genome with the annotated diagnostic subunits of the cytochrome oxidase subunits (COI and COII, green) and tRNALeu (trnL2, blue).CC BY · PubMed Central
Fig 8 Phylogenetic tree based on the 2,306 bp multi sequence alignment of 43 sequences. The reconstruction is based on sequence data comprising the cytochrome oxidase subunits COI and COII and the intermediate tRNALeu (trnL2) gene fragments. If the reverse complementary sequences were used for the alignment, they were marked with (R).
Fig 8 Phylogenetic tree based on the 2,306 bp multi sequence alignment of 43 sequences. The reconstruction is based on sequence data comprising the cytochrome oxidase subunits COI and COII and the intermediate tRNALeu (trnL2) gene fragments. If the reverse complementary sequences were used for the alignment, they were marked with (R).CC BY · PubMed Central

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Metadata

Authors
Patzold, F., Zilli, A., & Hundsdoerfer, A. K.
ORCID
Patzold, Franziska
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2020-07-08
Volume
15
Issue
7
Pages
e0235222
ISSN
1932-6203
DOI
10.1371/journal.pone.0235222
PMC
PMC7343169
Cited by
36
References
4
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
Deutsche Forschungsgemeinschaft (HU 1561/5-1)

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