By giving access to the information hidden in those specimens, it should enable researchers to answer an extensive range of evolutionary and ecological questions in the context of museum genomics. Codons were known from the MITOS alignment. Additionally, the application of one of these protocols to a minimal-destructive extraction of DNA from type specimens dating back to 1779 (legs left intact) was tested. Pirih P, Belui G, Dralar K, Leertouwer HL, Stavenga DG, Wehling MF, et al. Probe = Sample ng/L Probe 1_1 ng/L ng/L Probe 2_1 ng/L HTMo@W]{v_$PQTzp'1r ?dSCFy3Lx]bf./CJEU^{f| afi6eDbI0(fy=@)Yd>JLrk!r^ a R b4-Fp~' k:@dUP@~KRG>w}"6, $lDfZ4=2D76$WIP}OXE1$t5 dZDCn@8&/t{U;2WI~`X+ ,>^dcXh.&yVduBvC)42 Dessauer HC, Cole CJ, Hafner MS. Collection and storage of tissue However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. Optimized protocols for specific sample . DNA concentration was measured using the Qubit Fluorometer high sensitivity assay (ThermoFisher), and fragment length were assessed with 4200 TapeStation using the High Sensitivity D1000 ScreenTape (Agilent). There have already been approaches to none- or minimal destructive DNA extraction of museum insect specimens [2, 25, 47, 72], which mainly focus on the extraction of DNA from the whole specimen. The latter approach holds the potential of obtaining historic insect DNA without the destruction of valuable specimens and their morphological traits, as well as providing data on the genetic constitution of populations that may no longer exist. However, the potential influence of environmental and other specific effects varies between the collections and therefore, could not be addressed in this study. Extraction was performed following the Oligonucleotide Clean-up protocol of the Monarch PCR & DNA Clean-up Kit (New England Biolabs) as described above. Removal of low-quality reads and adaptor sequences (Illumina) was performed with BBDuk from BBTools [30]. This would be in line with the original species description, in which H. svetlana was described as a subspecies of H. siehei based on mitochondrial DNA despite being closer phenotypically and in life history traits to H. centralasiae [115]. Here we present four complementary protocols for extraction of genomic DNA from fungi. Thomsen PF, Elias S, Gilbert MTP, Haile J, Munch K, Kuzmina S, et al. Customised non-commercial protocols (non-kit) were shown to be successful in DNA extraction from subfossil and museum specimens [23]. Knlke S, Segerer A, Miller M, Hausmann A, Erlacher S. A procedure for combined genitalia dissection and DNA extraction in Lepidoptera, Observed and simulated temperature-humidity relationships: Sensitivity to sampling and analysis, Molecular studies of time-and environment-dependent effects on bone DNA survival. 0000014882 00000 n 2006. 0000059389 00000 n Halle: bei Hemmerde und Schwetschke; 1815. Available: Methods for the preservation of insects for DNA studies, Kristensen N. Lepidoptera, Moths and Butterflies: Morphology, Physiology, and Development: Teilband (Vol. The DNA of the remaining 82 samples was extracted using the Oligonucleotide Clean-up protocol of the Monarch PCR & DNA Clean-up Kit (New England Biolabs). Assays innuPREP DNA Mini Kit. These codon positions were used in PartitionFinder2 [40]. Qiagen DNeasy DNA extraction protocol for bacterial cultures Adapted from QIAgen DNeasy handbook, July, 2006. Suchan T, Pitteloud C, Gerasimova NS, Kostikova A, Schmid S, Arrigo N, et al. The kit comes with dedicated bacterial protocols. Therefore, we can conclude that the Oligonucleotide Clean-up protocol of the Monarch PCR & DNA Clean-up Kit enabled us to: The sequences obtained were suitable for downstream analyses, including phylogenetic tree reconstruction. 0000008557 00000 n The washing step was performed twice to minimise impurities. Extraction was performed following the Oligonucleotide Clean-up protocol of the Monarch PCR & DNA Clean-up Kit (New England Biolabs), using 100 l DNA Clean-up Binding Buffer, 300 l ethanol ( 95%) and 500 l DNA Wash Buffer. This is especially the case for Hyles siehei and Hyles centralasiae hybridisation events [114]. The raw reads of all samples exhibited in the mean 14.3% adapter contamination (SD 5.9%) and 42.3% duplicates (SD 18.8, Fig 5). Tierarztliche Hochschule Hannover, GERMANY. It should be noted that DNA extraction in this study was carried out with the same commercial kit (Qiagen DNeasy Blood and Tissue) for all samples. Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thbaud C. Valuing museum specimens: High-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura), Zinke GG. Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)s. Shere-Kharwar AS, Magdum S, Khedkar GD, Gupta S, Zambare V. Moth Legs: Excellent source of tissue for DNA extraction (Lepidoptera: Noctuidae). These two partitions appeared to be appropriate from all we know about the different evolutionary rates and selection pressures of the different codon positions and protein-coding genes compared to non-protein-coding genes [108111]. The DNeasy PowerSoil Pro Kit includes a novel bead tube and improved lysis chemistry, which enables isolation of up to 8-fold higher yields of DNA compared to the first generation DNeasy PowerSoil Kit and those of competitors in all soil types tested (see Isolate more high-quality genomic DNA ). For kit 6, homogenisation was performed using TissueLyser Adapter Set 2 24 (Qiagen) as described by the kit protocol. AnalytikJena. Die Kunst, Vgel als Blge zu bereiten, auszustopfen, aufzustellen und aufzubewahren.Nebst einer kurzen Anleitung, Schmetterlinge und Kfer zu fangen, zu prparieren, aufzustellen und aufzubewahren. No tissue clumps should be visible. 8. The DNeasy PowerWater Kit is intended for molecular biology applications. Available via license: CC BY 4.0. Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, et al. 2010. Non-Destructive Sampling of Ancient Insect DNA, Photoinduced damage to cellular DNA: Direct and photosensitized reactions, Factors affecting DNA preservation from museum-collected lepidopteran specimens. A trend line was included for each protocol for visualisation of overall distribution. To compare the efficacy of the two DNA extraction kits, tunic tissue from each replicate was processed separately using the DNeasy Blood and Tissue Kit (Qiagen, hereafter "DNeasy") and PowerSoil DNA Isolation Kit (Mo Bio Laboratories, hereafter "PowerSoil") following the manufacturers' protocols. In this sample human DNA was found in 8.8% of all sequences, while only 9.2% of the sequences were mapping to Hyles (see S3 Table). All samples used here show very long branches compared to the samples from earlier publications. The length of the alignment on the nuclear genome was in the mean 19,157,397 bp (SD 12,820,375 bp) long, covering 2.9% (SD 1.9%) of the nuclear reference genome (coverage for each individual can be found in S4 Table). * These conditions have not been optimized. 10.5962/bhl.title.137028 [, Naumann JF. First, the PDQeX extraction took significantly less time than QIAGEN: 30 min compared with 2 h. In addition, most of the . . These values were to be expected in highly degraded DNA samples and are comparable to other studies [25, 87, 88]. By transferring the oligonucleotide Clean-up protocol for the extraction of highly fragmented DNA, we were able to overcome temporal restrictions underlying manual customised non-commercial protocols, similar to other silica spin column-based methods [46]. {"type":"entrez-nucleotide","attrs":{"text":"FN386584","term_id":"371779021"}}, {"type":"entrez-nucleotide","attrs":{"text":"AJ749426","term_id":"62146743"}}, {"type":"entrez-nucleotide","attrs":{"text":"FN386551","term_id":"371778894"}}, {"type":"entrez-nucleotide","attrs":{"text":"FN386553","term_id":"371778902"}}. Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates. Preheat a water bath or heating block to 65C. Resulting DNA can be used in any downstream application, including qPCR, Sanger sequencing and next-generation sequencing. Proceedings of the International Congress Catastrophes and Catastrophe Management in Museums. Viable DNA can be acquired from common filter membrane types, including 0.45 m and 0.22 m filter funnels. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). Coverage of each alignment was conducted using bedtools [35] and custom scripts. . Contains a chaotropic salt and is not compatible with agents containing bleach. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. It is common practice with Lepidoptera type specimens to use one leg for DNA extraction without destruction of the leg [8084]. 0000009627 00000 n Inclusion in an NLM database does not imply endorsement of, or agreement with, As this specimen was only 13 years old (MTD-TW 9255), we would have expected good DNA-yield by using both kits. 2003. The origins of these sequences were tested with Kraken2, a taxonomic classification system based on k-mer matches to achieve high accuracy in the classification of sequences. Nevertheless, enrichment of these shotgun libraries will be necessary for higher sequencing efficiency [8789, 98, 102, 103]. Prosser SWJ, Dewaard JR, Miller SE, Hebert PDN. Speidel W, Hausmann A, Muller GC, Kravchenko V, Mooser J, Witt TJ, et al. Legs were ground for 1 min at a frequency of 25 Hz, using two sterile stainless-steel balls with a diameter of 3 mm. However, the availability of specimens for molecular analyses has been limited by two main factors: Degradation of DNA into smaller fragments is caused by several factors including exposure to radiation (mainly UV), temperature, pH, chemicals used for specimen preservation, and free water, resulting in an inverse correlation between sample age and fragment length [2, 13, 1621]. Such protocols were shown to be successful in beetles [2, 15], but to date, no similar protocol was developed for Lepidoptera as their dense vestiture of scales adds complexity to non-destructive DNA isolation approaches. Received 2020 Jan 24; Accepted 2020 Jun 10. Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on collection specimens, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Raw read composition, showing the percentage of adapter content (A) and percentage of duplicates (B). 0000001849 00000 n This site is protected by reCAPTCHA and the Google, Explore high-quality enzymes; now available as individual product. Both extraction protocols recovered typical average molecule sizes (100200 bp) which are expected in degraded DNA extracts [59]. Genomics reveals the origins of ancient specimens. Photographs of two moth specimens before (A, B) and after (a, b) the extraction, treatment and reattachment of one leg each (middle leg). Taxidermie oder die Lehre Thiere aller Klassen am einfachsten und zeckmigsten fr Kabinette auszustopfen und aufzubewahren. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. 0000009207 00000 n Mixing speed was set to 450 rpm (ground legs). 0000009605 00000 n 0000008579 00000 n Legs are particularly useful in Lepidoptera in contrast to bigger body parts (e.g. Insects are the most diverse animal group on earth, with more than 1 million described species and an unknown number of undescribed species [1, 2]. Similar results were described in another study where three one-year-old Lepidoptera specimens failed completely after being kept in a relaxing jar for several days by the collector [49]. Therefore, both highly fragmented DNA and single-stranded DNA (ssDNA) need to be targeted in DNA extraction from museum specimens. Qiagen DNeasy Kit Components: See Qiagen's SDS for additional information. FOIA 0000004219 00000 n IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Targeted capture in evolutionary and ecological genomics. Increased yields of plant DNA and plant pathogen DNA . As the majority of Lepidoptera is smaller than hawkmoths usually are, the amount of extracted DNA might be correlated with the amount of tissue used for the extraction. 0000011561 00000 n We used the greedy search algorithm and PhyML to define most likely partitions and best-fitting models of these in the alignment [41, 42]. Appropriately label a 1.5 ml tube for each sample. Presuming an identical volume of 30 l used in the cited studies [80], this equals to 9-fold more extracted DNA on average with our protocol compared to those published for Lepidoptera type specimens. In: Hillis D, Moritz C, Mable B, editors. A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae). Menzies BR, Renfree MB, Heider T, Mayer F, Hildebrandt TB, Pask AJ. Using Inhibitor Removal Technology, the DNeasy PowerWater Kit isolates genomic DNA from filtered water samples, free from salts, metals, humic substances and other organic materials. 0000012204 00000 n Overall, we were able to identify 52.7% (SD 13.2%) of endogenous DNA, mapping uniquely to the Hyles reference genome (Fig 6). MTD-TW 12622 failed most likely due to the high percentage of missing data (26.4%), which is the highest amount of missing data found in this alignment. The bench was decontaminated before handling of the specimens by using UV-light and DNA AWAY (ThermoFisher Scientific). One of the six specimens used for the direct comparison of the differences in extraction effectiveness failed for DNA extraction with the DNeasy kit. Stuttgart: Kosmos, Gesellschaft der Naturfreunde; 1936. 8600 Rockville Pike Note the number of spin columns you use. A total of 35.6 million demultiplexed raw reads resulting in an average of 1.78 million reads per individual were retained for further analysis (S3 Table). At the same time, the extractions of the other two kits started to fail in specimens which were 20 years and older. ), Alexej Y. Matov (Zoological Institute, Saint-Petersburg, Russia), Dmitry F. Shovkoon (Samara University, Faculty of Biology, Russia), Ulf Eitschberger (Entomological Museum, Marktleuthen, Germany), Wolfram Mey (Museum of Natural History Berlin, Germany), Hongxiang Han (Chinese Academy of Sciences, Institute of Zoology, Beijing, China), Manfred Strhle (private collection, Weiden, MSW), Susanne Kridlo (Hessisches Landesmuseum fr Kunst und Natur, Wiesbaden, Germany), Thomas J. Witt (Museum Witt, Munich, Germany), Roman V. Yakovlev (Altai State University, Faculty of Biology, Barnaul, Russia), Ronald Brechlin (Pasewalk, Germany), Wolfgang Nssig (Senckenberg Frankfurt a.M., Germany), Axel Hausmann (Bavarian State Collection of Zoology, Munich, Germany), Laszlo Ronkay (Hungarian Natural History Museum, Budapest, Hungary). 2. Harvest cells (maximum 2 x 109 cells) in a microcentrifuge . Forceps were cleaned with DNA AWAY before handling specimens. Whole genome shotgun libraries were prepared from 10 museum specimens with DNA extracted using the Monarch PCR & DNA Clean-up Kit, based on a published protocol for degraded DNA samples [25], which was modified in order to incorporate adapter design that enables high sample multiplexing on a single sequencing lane [2628]. To test the integrity of the extracted DNA from the Monarch Oligo extraction protocol, we performed a full NGS analysis, including bioinformatics after sequencing. vila-Arcos MC, Sandoval-Velasco M, Schroeder H, Carpenter ML, Malaspinas AS, Wales N, et al. 0000005229 00000 n government site. To control for a possible reference bias in the phylogenetic tree reconstruction, the sequence of the mitochondrial reference genome was also included in the multi sequence alignment. None of the specimens were initially preserved foreseeing any DNA extraction but rather to maintain their habitus and morphology. MITOS: Improved de novo metazoan mitochondrial genome annotation, Historic DNA for taxonomy and conservation: A case-study of a century-old hawaiian hawkmoth type (Lepidoptera: Sphingidae), A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. 10.5962/bhl.title.43737 [, Brehm CL. The specimens individual MTD-TW numbers are: A/a 12624, B/b 12625, C/c 12626 (S1 Table). 0000098697 00000 n A convenient tool to build experimental workflows and find products to match your needs. Photos of moths were taken with a Sony 6300 and a Sony E 1650 mm F3.55.6 OSS, or with a Huawei CLT-L29. Sequencing the nuclear genome of the extinct woolly mammoth. Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia, Hawkmoths of the World: An Annotated and Illustrated Revisionary Checklist. For detailed information, the QIAGEN DNeasy Plant kit handbook should be consulted. Since our ingroup are Palaearctic Hyles, we chose to include New World Hyles perkinsi ({"type":"entrez-nucleotide","attrs":{"text":"FN386584","term_id":"371779021"}}FN386584) and Hyles calida ({"type":"entrez-nucleotide","attrs":{"text":"AJ749426","term_id":"62146743"}}AJ749426, Hawaii) as outgroup sequences to this reconstruction. The Qiagen DNeasy Blood & Tissue kit (with added RNAse A) is also the default kit for bacterial isolate DNA extractions. Moreover, this could be a real biological signal. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The origin and species status of Hyles svetlana is not yet clear and is still discussed [115, 116], but the grouping in the cluster including some H. siehei and the H. centralasiae paralectotype could point to a hybrid origin of this entity. If the reverse complementary sequences were used for the alignment, they were marked with (R). Hofreiter M, Serre D, Poinar HN, Kuch M, Pbo S. Instability and decay of the primary structure of DNA. For use of the midi columns, the weight of the tissue should be less than 150 mg. The relative coverage of the nuclear genome of both alignments is almost identical. The total amount of extracted DNA was calculated by the measured DNA concentration multiplied by the volume of elution buffer used. Hb``0d``d``` p@i bQ~*3TH1;0b`6`| "!@~2 AQefoZ)-;%vD$ qY L@ li5-  endstream endobj 133 0 obj 168 endobj 86 0 obj << /Type /Page /Parent 82 0 R /Resources << /ColorSpace << /CS3 88 0 R /CS4 91 0 R /CS5 92 0 R >> /XObject << /Im4 126 0 R /Im5 127 0 R /Im6 128 0 R /Im7 129 0 R >> /ExtGState << /GS3 130 0 R /GS4 131 0 R >> /Font << /TT5 87 0 R /TT6 89 0 R /TT7 99 0 R /T1_1 100 0 R /TT8 105 0 R /TT9 109 0 R >> /ProcSet [ /PDF /Text /ImageC /ImageI ] >> /Contents [ 95 0 R 102 0 R 104 0 R 108 0 R 112 0 R 114 0 R 116 0 R 118 0 R ] /MediaBox [ 0 0 595 842 ] /CropBox [ 0 0 595 842 ] /Rotate 0 /StructParents 0 >> endobj 87 0 obj << /Type /Font /Subtype /TrueType /FirstChar 32 /LastChar 181 /Widths [ 278 0 0 0 0 0 0 0 333 333 0 0 278 333 278 278 556 556 556 556 556 556 0 0 0 556 278 278 0 0 0 0 0 667 0 722 722 667 0 778 0 278 0 667 0 833 722 0 667 778 722 667 611 0 0 0 0 667 0 0 0 0 0 0 0 556 556 500 556 556 278 556 556 222 0 500 222 833 556 556 556 556 333 500 278 556 500 722 500 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 556 0 0 1000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 737 0 0 0 0 737 0 400 0 0 0 0 576 ] /Encoding /WinAnsiEncoding /BaseFont /OGOGEM+Arial /FontDescriptor 93 0 R >> endobj 88 0 obj [ /ICCBased 119 0 R ] endobj 89 0 obj << /Type /Font /Subtype /TrueType /FirstChar 32 /LastChar 181 /Widths [ 278 0 0 0 0 0 0 0 333 333 389 0 278 333 278 278 556 556 556 556 556 556 556 556 556 0 333 0 0 0 0 0 0 722 722 722 722 667 0 778 0 278 0 722 611 833 722 778 667 778 0 667 611 722 667 0 0 0 0 0 0 0 0 0 0 556 611 556 611 556 333 611 611 278 0 556 278 889 611 611 611 611 389 556 333 611 556 778 556 556 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 500 0 0 0 0 1000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 737 0 400 0 0 0 0 576 ] /Encoding /WinAnsiEncoding /BaseFont /OGOGJM+Arial,Bold /FontDescriptor 90 0 R >> endobj 90 0 obj << /Type /FontDescriptor /Ascent 905 /CapHeight 718 /Descent -211 /Flags 32 /FontBBox [ -628 -376 2034 1048 ] /FontName /OGOGJM+Arial,Bold /ItalicAngle 0 /StemV 144 /XHeight 515 /FontFile2 122 0 R >> endobj 91 0 obj [ /Indexed 88 0 R 122 120 0 R ] endobj 92 0 obj /DeviceGray endobj 93 0 obj << /Type /FontDescriptor /Ascent 905 /CapHeight 718 /Descent -211 /Flags 32 /FontBBox [ -665 -325 2028 1037 ] /FontName /OGOGEM+Arial /ItalicAngle 0 /StemV 94 /XHeight 515 /FontFile2 121 0 R >> endobj 94 0 obj 659 endobj 95 0 obj << /Filter /FlateDecode /Length 94 0 R >> stream The https:// ensures that you are connecting to the Our study shows that using the Monarch kit with slight protocol adjustments, destruction of legs is no longer necessary so that the legs can be glued back to the specimen preserving every original morphological trait (Fig 4). The lysis was performed by using 45 l of lysis buffer FN (AGOWA) and 5 l proteinase K (Analytik Jena). 0000008321 00000 n vestiture and colouration, spur formulae, biometric ratios, number and arrangement of spines, presence of scent tufts or arolia, sensilla ultrastructure), thus the destruction of these, especially in unique type specimens, leads to a loss of value for such analyses [69, 79]. Additional legs of 77 samples were used with the Monarch PCR & DNA Clean-up Kit (New England Biolabs), and ground as described above. The use of less Proteinase K (e.g., 20 l) or a shorter incubation time (e.g., 1 h) may be sufficient. All five specimens, including the three illustrated in Fig 4, exhibit no significant external change or post-extraction damage (see also S1 Fig), although one leg was detached and glued carefully back onto each specimen. Deep learning on butterfly phenotypes tests evolutions oldest mathematical model. The kit can isolate high-quality DNA even from water containing high levels of contaminants. light traps or hand collection), and the preference of the collector. Besides environmental effects, the usage of chemicals in the collections [21] and catastrophes the historic specimens went through over time (e.g. Prior to homogenisation, 450 L of Solution CD1 and 50 L of Solution PS were added as suggested for . Schubert M, Ermini L, Sarkissian C Der, Jnsson H, Ginolhac A, Schaefer R, et al. Isolate a suitable piece of tissue and place in a UV-crosslinked 1.5mL tube. One specimen, MTD-TW 12622, exhibited a higher percentage of contamination in relation to the endogenous DNA. Zur Biologie, Okologie, Verbreitung und geographischen Variabilitt von H. siehei (Pngeler, 1903) und Reinterpretation von Hyles svetlana Shovkoon, 2010 (Lepidoptera: Sphingidae), A new subspecies of Hyles siehei (Pngeler) from the deserts of Central Asia (Sphingidae), The presence and impact of reference bias on population genomic studies of prehistoric human populations, Branch length estimation and divergence dating: Estimates of error in Bayesian and maximum likelihood frameworks, https://www.ebi.ac.uk/ena/browser/view/PRJEB36496, https://www.dfg.de/gefoerderte_projekte/programme_und_projekte/listen/projektdetails/index.jsp?id=313688472, http://www.bioinformatics.babraham.ac.uk/projects/fastqc, http://www.webcitation.org/query?url=http%3A%2F%2Fdiagnostics1.com%2FMANUAL%2FGeneral_Qiagen.pdf&date=2018-06-01, https://www.tib.eu/en/search/id/TIBKAT%3A418770980/Sammeln-und-Prparieren-von-Tieren-eine-Anleitung/, https://www.biodiversitylibrary.org/page/37070153#page/87/mode/1up. Some vendors also offer DNA isolation kits in a 96-well spin-plate format for large sample numbers (e.g. 0000002124 00000 n But the comparison of relative coverage of the alignment on the reference genome appears to be a useful measure to judge the quality of the sequenced reads. https://www.dfg.de/gefoerderte_projekte/programme_und_projekte/listen/projektdetails/index.jsp?id=313688472, National Library of Medicine First, the gene fragments of the cytochrome oxidase subunits COI and COII plus the intermediate tRNALeu (trnL2) were annotated using MITOS [36]. Extraction with DNeasy Plant Pro Kit (Qiagen) was the most efficient, as it resulted in the purest DNA. HTn w:@:DYv!59d?y_z 01.aep4ij 3. Contrary to our expectations, we did not observe a significant difference of fragment sizes in the direct comparison of the same specimen (Fig 3 and Table 2). Nevertheless, the DNA-yield is highly variable between specimens with all protocols (Fig 1). Filter tips were used for all experimental procedures. These methods are not applicable to Lepidoptera, as this kind of handling would destroy most of the habitus of the specimen (including the detachment of wings and loss of most of the scales). See Supplementary Table 1 for more details on the DNA yield from each extraction. This would be consistent with the results of other studies [17, 19, 20, 4749], where the authors found that the immediate post-mortem treatment of specimens is particularly important in the preservation of amplifiable DNA rather than storage time. 0000036446 00000 n trailer << /Size 134 /Info 80 0 R /Root 84 0 R /Prev 111987 /ID[<6b29b3592d26614f459c1d2c6b001a79>] >> startxref 0 %%EOF 84 0 obj << /Type /Catalog /Pages 82 0 R /Metadata 81 0 R /Outlines 1 0 R /OpenAction [ 86 0 R /XYZ null null null ] /PageMode /UseNone /PageLabels 79 0 R /StructTreeRoot 85 0 R /PieceInfo << /MarkedPDF << /LastModified (D:20020313140454)>> >> /LastModified (D:20020313140454) /MarkInfo << /Marked true /LetterspaceFlags 0 >> >> endobj 85 0 obj << /Type /StructTreeRoot /ClassMap 8 0 R /RoleMap 7 0 R /K 54 0 R /ParentTree 70 0 R /ParentTreeNextKey 1 >> endobj 132 0 obj << /S 36 /O 153 /L 169 /C 185 /Filter /FlateDecode /Length 133 0 R >> stream This procedure has been shown to degrade DNA [2, 13, 16, 19, 49, 56]. 0000003317 00000 n 0000004169 00000 n Zimmermann J, Hajibabaei M, Blackburn DC, Hanken J, Cantin E, Posfai J, et al. 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). Available: QIAGEN. 0000007222 00000 n Available: sourceforge.net/projects/bbmap/, Improved metagenomic analysis with Kraken 2. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. Partitionfinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses, PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Weimar: Verlag und Druck von Bernhard Friedrich Voigt; 1842. The samples MTD-TW 12622, 9248, 9288, 9255, 9254 and 9233 did not group as expected, while still showing high support values. 0000006407 00000 n 0000001716 00000 n The merit of museum material in molecular studies for biological research is often limited by the initial step of DNA extraction, as DNA from such specimens is naturally highly fragmented leading to frequently very low amounts of DNA that can be extracted [44]. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing, The use of museum specimens with high-throughput DNA sequencers. Zhang Q, Mey W, Ansorge J, Starkey TA, McDonald LT, McNamara ME, et al. Treatment and reattachment of one leg each (middle leg). 10.1515/9783110893724 [. de Gruyter. The duplicate content is very variable due to different levels of DNA degradation between samples. The results of these approaches vary greatly, between 0.01 and 2.5 ng/l [80, 81, 85, 86]. Sufficient DNA for further analyses such as in an NGS approach was retrieved with a mean of 422.9 ng (range see Table 3), validating the use of this method on type specimens. Procedure: 1. DNeasy PowerWater Kit Quick-Start Protocol, (EN) - Automated DNA purification from diverse microbiome samples using dedicated microbiome kits on the QIAcube, Ocean water, fresh water, brackish water, ground water, waste water, Highly pure genomic DNA isolation free from organic materials, Optimized to increase DNA yields from low biomass samples, Compatible with most common filter membrane types, Easily removes blocks to downstream PCR with Inhibitor Removal Technology. The reconstruction is based on sequence data comprising the cytochrome oxidase subunits COI and COII and the intermediate tRNALeu (trnL2) gene fragments. The Sequence Alignment/Map format and SAMtools, BEDTools: A flexible suite of utilities for comparing genomic features. Jena: Im Verlag des Hof-Buchdrucker Gpferdts; 1802. Museum genomics: Low-cost and high-accuracy genetic data from historical specimens. Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, et al. This included incubation of lysis overnight at 56C, and elution in a two-step procedure to maximise DNA yield, where each step was carried out using 35 l elution buffer and incubation for 10 min, resulting in a total volume of 70 l. Review Sections 7 (Handling & Storage) and 10 (Stability & Reactivity) of the SDS for incompatible chemicals. Natural History Collections: Teaching about Biodiversity Across Time, Space, and Digital Platforms. GHS Category 2 for skin & eye . The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses. This protocol is designed for purification of total DNA from Gram-positive bacteria. A: We tested 15-30 minute incubation periods using Qiagen DNeasy to make it suitable for one class period. Stehli G. Sammeln und Prparieren von Tieren: eine Anleitung zum Anlegen von zoologischen Sammlungen. acids and proteins, plus DNA and RNA cleanup. 2. We expected this due to differing killing and post-mortem conditions of each individual, as the specimens originated from different museums and natural history collections, where insulation from ultraviolet light and stable room temperatures are not necessarily present in all collections [4]. DNeasy PowerSoil Kit and DNeasy PowerSoil Pro Kit, the DNeasy PowerSoil Pro Kit included more of the difficult-to-lyse gram+ Actinobacteria and Firmicutes (Table 1). Wheeler Lab Protocols DNA Extraction - Qiagen DNeasy kit. 0000101875 00000 n 2). The cause for this correlation could also be induced by the co-correlation between storage temperatures and higher humidity in more southern regions [50], where humidity is likely causing accelerated fragmentation of the DNA because of upheld endogenous nuclease activity and hydrolytic damage [24, 51]. The usage of these to remove contaminant DNA would lead to full degradation of the endogenous DNA inside of the legs and destruction of the scale structure. Both kits were tested with and without a preceding bead beating step. 0000002671 00000 n Anyway, a close relationship between H. hippophaes and H. vespertilio was already shown in other publications [113] and is recovered also in this analysis, as the two appear to be sister clades. The mitogenome of a malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (lepidoptera). 0000001368 00000 n 2. Available: Leonhardt EE, Schwarze K. Das Sammeln, Erhalten und Aufstellen der Tiere. 3. Overall the sequences obtained from the Monarch kit extracts are comparable with the quality of shotgun sequences from other museum material in the literature, while the age of our extracted specimens is exceptional among studies including dry pinned insect specimens [89, 100, 101]. sharing sensitive information, make sure youre on a federal Indeed, this individual shows a transitional phenotype to H. euphorbiae conspicua (S2 Fig), which is at times found in H. siehei specimens and could validate its hybrid origin [114]. Available: Bushnell B. BBMap. The conflict between the maintenance of collections and the usage of specimen DNA for research could be solved by the application of an extraction protocol designed to recover DNA from insect body parts without bringing externally visible morphological damage to the material [2]. Staats M, Erkens RHJ, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, et al. In summary, 16S microbial analyses identified that the soil microbial communities are different between samples prepared using different methods, and that DNA isolated Edwards CJ, Magee DA, Park SDE, McGettigan PA, Lohan AJ, Murphy A, et al. Within the last years, an increasing number of genetic studies used insects from museum collections for purposes of phylogenetic inference [2, 3], biogeography studies [4], and taxonomic identifications [5], adding to our understanding of biodiversity [610]. But these are mainly based on time-consuming phenol-chloroform extraction methods, which makes them not reasonably usable in high throughput experiments such as NGS approaches. Product Details. 0000015330 00000 n Only later it was raised to species status because of its biological differences to nominotypical H. siehei [114]. The change in the cut-off size was originally implemented in the oligonucleotide Clean-up kit to extract single-stranded oligonucleotides from a solution. 2nd ed. 1 Prior to extraction, 0.5 mm and 0.1 mm glass beads (BioSpec Products) were ashed at 500 C for 5 hours. 1A, Table S3) with the Qiagen DNeasy Blood and Tissue kit resulting in the highest concentrations and . All samples showed a high percentage of unclassified sequences with a mean of 41.6% (SD 9.6%, Fig 6). 0000007906 00000 n Consequently, it appears likely that the shift in cut-off size did not lead to the expected extraction of significantly smaller DNA fragments, but rather merely to a shift in the targeted size range from 100 bp 1 kb (DNeasy) to 16 bp 500 bp (Monarch), which recovered the target fragment size necessary to build libraries for NGS of historical DNA [60] in both cases. The Oligonucleotide Clean-up protocol of the Monarch PCR & DNA Clean-up kit, as described by NEB, includes the addition of two volumes of ethanol (whole sample volume: ethanol, 1:2) in comparison to the DNeasy kit (whole sample volume: ethanol, 1:1), which shifts the binding DNA cut-off not only to shorter DNA fragments (from 25 nt down to 16 nt length) but also changes the binding efficiency of dsDNA (double-stranded DNA) to the membrane of the column, leading to a favoured extraction of ssDNA [31]. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX, Features of recent codon evolution: A comparative polymorphism-fixation study, Variation in evolutionary processes at different codon positions. The Qiagen DNeasy Blood & Tissue kit was chosen because it was our in-house DNA extraction protocol, while the QIAamp DNA Stool Mini kit was selected because it is Qiagen's recommended kit for stool samples. These methods have varying influence on the preservation of the DNA as some, like the usage of hot water steam, are likely to denature the DNA of the specimen and may lead to prolonged drying periods which could lead to faster fragmentation of the DNA due to upheld endogenous nuclease activity and hydrolytic damage [24]. The mapping on the mitochondrial reference genome of Hyles vespertilio [32] resulted in a mean alignment length of 14,995 bp (SD 367 bp), equal to 98.0% (SD 2.4%) of the reference genome covered (Fig 7). The genomic purification kits are available in both bead-based and spin-column formats to suit your needs. The DNeasy PowerWater Kit was previously sold by MO BIO as the PowerWater DNA Isolation Kit. DNA was extracted from 114 specimens using the DNeasy extraction Kit (Qiagen), while DNA from 35 specimens was extracted using the innuPREP DNA Mini Kit (Analytik Jena), in both cases following the manufacturer manuals. Two main DNA extraction methods were used in this study. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a. The minimal-destructive DNA extraction procedure was tested on five type specimens, including three different species of the genus Hyles, collected between 1779 and 1789. Additionally, we tested the application of the Monarch PCR & DNA Clean-up Kit to a minimal-destructive extraction of DNA from type specimens. However, legs provide in the Lepidoptera several traits which are used in research, from basic taxonomic identifications to morpho-functional studies and phylogenetic reconstructions (e.g. Besides possible differences caused by the typical damage patterns introduced over time post-mortem [22], the samples used here are up to 241 years old, a time span accounting for multitude of generations separating these individuals from most of the more modern samples in the NCBI database (see also 33). Both kits yielded slightly lower mean amounts of DNA compared to the Monarch kit (Table 1). The necessity to preserve the external integrity of the specimens resulted in a minimal-destructive approach where legs were left intact and which was limited to the Monarch PCR & DNA Clean-up Kit, as this was the only kit where none of the tested samples failed (see above). Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, et al. Electropherograms from the DNeasy extraction Kit (blue) and the Monarch PCR & DNA Clean-up Kit (red). DNA extractions using a CTBA-based extraction method with and without 1%PVP.Probe = Sample Nano-Drop measurement profile of genomic DNA extractions from . In contrast, the relative coverage of the mitochondrial genome of our alignment is 20.2% higher than the one from the article. Exogenous DNA content in other whole genome shotgun sequencing studies of historical material varies greatly between the tissue tested and the possibility to clean the tissue before extraction (human DNA 0.1% 9.8%, microbial DNA 0.01% 45% [57, 58, 6065]). Available: New England BioLabs. Protocol for extracting DNA from amphibian skin swabs using the Qiagen DNeasy blood and Tissue Kit. Specimens were handled with cleaned forceps in the collection rooms. This finding is consistent with the percentage of unmapped reads in other studies, where both different organisms and other DNA extraction methods were used [89, 90]. The kits were used according to the manufacturer's recommendations, except for the DNeasy Blood & Tissue (Qiagen, Hilden, Germany), GenElute Bacterial Genomic DNA (gDNA) (Sigma-Aldrich, Missouri . The workflow presented here used tissue material from hawkmoths (Sphingidae), which comprise some of the largest-sized Lepidoptera and therefore provide much tissue in one leg for DNA extraction. The direct comparison of the DNeasy and the Monarch extraction kits (Fig 2 and S2 Table), carried out with one leg each from six specimens, which are between 13 and 137 years old, showed a significant increase of 355.5 ng in total DNA extracted, which equals to an average of 17.3-fold higher DNA yield from the Monarch kit compared to the DNeasy kit (p < 0.001). The comparison of the absolute alignment lengths with those in other studies focused on Lepidoptera is not meaningful, as the size of nuclear and mitochondrial genomes differ tremendously between different genera [104]. 0000011583 00000 n The k-mer assignments inform the classification algorithm [31]. Both Reads (R1 and R2) are shown for each sample. But especially tissue such as skin and hair show similar levels of observed contamination, which cannot be decontaminated before DNA extraction [9399]. The DNA extraction using the DNeasy and the innuPREP kits failed on three individuals in total. In another study, the authors were able to show a correlation between higher temperatures in more southern cities and the PCR success of the extracted DNA from museum specimens [4]. . 2014. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RDE, Buigues B, et al. The killing and post-mortem aspects of the individuals in our study were mostly undocumented and could be only assessed by reference to books of that time period; therefore, a correlation test for these circumstances and their influence on the DNA yield was not possible. Purification of DNA using the DNeasy PowerWater Kit can be automated on the QIAcube Connect. extract more DNA from older museum specimens in comparison to the other tested kits (destructive method). To test the integrity of the extracted DNA from the Monarch Oligo extraction protocol, we calculated a phylogenetic tree using the diagnostic cytochrome oxidase subunits (COI and COII) and tRNALeu (trnL2) from the alignments performed with sequences from the same or related species of the genus Hyles, obtained from NCBI. This is also true for the chitinous exoskeleton of Lepidoptera, which is less resistant than bones and teeth to typical cleaning procedures, involving UV-light and chlorine [2]. Product Details. Sarajevo: Tiroler Landesmuseum; 2005. Answering these is beyond the scope of this work and will be examined more in depth later. Hausmann A, Hebert PDN, Mitchell A, Rougerie R, Sommerer M, Edwards T, et al. the abdomen or the whole body), since they dry fast and therefore do not provide a moist environment in which cellular endonucleases can continue their activity for a long time [14, 17]. Age is estimated in samples marked with * (see also S3 Table). [Zur Ttung der Insekten ]. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. At the same time, we extracted 603 ng from the same individual using the Monarch kit (Table 1 and Fig 2). Furthermore, it is well known that Lepidoptera are often initially dried during fieldwork, and either pinned or stored in paper bags for years before wing-setting. 0000004471 00000 n Biological identifications through DNA barcodes, An inexpensive, automation-friendly protocol for recovering high-quality DNA, DNA barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae). Try the Workflow Configurator. Hundsdoerfer AK, Pckert M, Kehlmaier C, Strutzenberger P, Kitching IJ. Always read the Safety Data Sheet (SDS) for a chemical and the user guide for a kit. These included phenol/chloroform DNA extractions, as is used in one of the most popular methodologies for extracting DNA from fish scales. The inner circle shows the coverage breadth and depth for this sample. 10.5962/bhl.title.44880 [. Lecto- and paralectotype specimens of Hyles livornica before (A, B, C) and after (a, b, c) sampling and extraction. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, et al. and transmitted securely. Museum of Zoology (Museum fr Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany, 2 Using the DNeasy PowerWater Sterivex Kit, ready-to-use DNA is obtained for any downstream application in just 40 minutes. While no values for volumes or the amount of extracted DNA are given, we can only add findings in other studies to this assumption, where it was shown that DNA extracted from museum samples has a representation bias to mitochondrial DNA [60]. Monarch PCR & DNA Cleanup Kit (5 g): Instruction Manual. . Int Entomol Zeitschrift. 0000003940 00000 n The standard database of Kraken2 was expanded with a reference genome and mitochondrial genome of the genus Hyles, consisting of assembled long-reads from a single Hyles vespertilio specimen [32]. Bacterial Isolate Preparation: Sequencing should be preformed on pure isolated colonies only. The splitting of H. centralasiae into two branches separated by other species, including H. siehei, could suggest two mitochondrial lineages within this species, with the paralectotype (MTD-TW 9228) showing one mitochondrial lineage and the two samples {"type":"entrez-nucleotide","attrs":{"text":"FN386551","term_id":"371778894"}}FN386551 and {"type":"entrez-nucleotide","attrs":{"text":"FN386553","term_id":"371778902"}}FN386553 representing another lineage. This was to be expected in whole genome shotgun sequences from museum samples because of the post-mortem DNA modifications [25, 90]. 0000002146 00000 n the common leg grinding with three different silica-column-based kits, including DNeasy extraction Kit (Qiagen), innuPREP DNA Mini Kit (Analytik Jena) and Monarch PCR & DNA Clean-up Kit (New England Biolabs); and the minimal-destructive usage of the Monarch PCR & DNA Clean-up Kit (New England Biolabs), where legs of the type specimens were left intact. The DNeasy kit showed a higher maximum of extracted DNA in comparison to the Monarch kit, while the maximum of the innuPREP kit is lower. Therefore, the detachment of scales has to be avoided in handling the specimens. 0000102695 00000 n Federal government websites often end in .gov or .mil. Explore targets and pathways in their scientific context, find and customize products to study them, analyze data and plan follow-up studies all in GeneGlobe. %PDF-1.3 % The specimens individual MTD-TW numbers are as follows: A 9248, B 9252, C 9251. (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). Explore high-quality enzymes; now available as individual products. Bethesda, MD 20894, Web Policies This is an open access article distributed under the terms of the, GUID:B4E04D60-7C88-4A97-A3DC-FD914E9ABA12, GUID:EBF7F772-A4B5-4588-9D37-7C7E9D81E53A, GUID:6ABB2035-FF85-487C-9E3E-F422A9C8CDD1, GUID:8EB73197-226A-4267-95AA-FE60DB61FAE8, GUID:A888FF7B-D153-4C2F-AB5F-D6E1B541F2BC, GUID:E2F332D3-2A49-42C0-A5DF-955046F306E1, Most museum specimens are not preserved to keep their DNA from degrading and inter-strand cross-linking. Percentages of duplicates and adaptors were estimated using FastQC [29]. All lysis reactions were incubated overnight at 56C on a Mixing Block (MB-102, Thermocell). Available: Factors affecting mitochondrial DNA quality from museum preserved Drosophila simulans, Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. 0000010994 00000 n 3.5 Genomic DNA Extraction Using QIAGEN's DNeasy Plant Kit (Mini) If genomic DNA is to be used for sequencing, a minimum of 12 tubes of mycelium should be processed at a time. Qiagen DNeasy protocol gave the highest Genomic Quality Score (average standard deviation: 4.24 0.36), followed by the different MoBio Powersoil . This behaviour could be due to multiple reasons, starting with possible contamination during library preparation. Pulling out the 1%: Whole-Genome capture for the targeted enrichment of ancient dna sequencing libraries. DNA extractions using a Qiagen extraction method. Abadzic S, Arthur J, Barudanovic, Senka Buturovic D, Calas JM, Colombini A, Dautbegovic, Jozefina Dembski G, et al. All three tested kits yielded good amounts of DNA within the tested age range. Sugetiere, Vgel, Gliederfer, Kriechtiere, Lurche, Fische und Niedere Tiere nebst einer Einleitung ber Sammeln u. Erhalten im allgemeinen. storage in cellars whilst rockets bombing in London and Dresden, flooding of the early Innsbruck collections [52]) may lead to further effects on the amount and fragmentation of DNA. Rohland N, Glocke I, Aximu-Petri A, Meyer M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing, DNA barcode sequencing from old type specimens as a Tool in Taxonomy: A case study in the diverse genus Eois (Lepidoptera: Geometridae). But the more basal nodes show lower support values (bootstrap value <50%) which resembles the low support values found in the study from which the other sequences used originate (33). Preparation of AW1 and AW2: These buffers need to be diluted with 100% Ethanol prior to use for the first time. Both the DNeasy PowerSoil Kit and the new DNeasy . Sedlazeck FJ, Rescheneder P, Von Haeseler A. NextGenMap: Fast and accurate read mapping in highly polymorphic genomes. Away before handling specimens Mooser J, Munch K, Leertouwer HL, Stavenga DG Wehling. Formats to suit your needs Fische und Niedere Tiere nebst einer Einleitung ber Sammeln Erhalten! Compatible with agents containing bleach one class period Morelli TL, Rubidge EM, et.. Learning on butterfly phenotypes tests evolutions oldest mathematical model or.mil 603 ng from the article 9.6,... And Digital Platforms the collector Pckert M, Jebb D, Moritz C, Gerasimova,! And will be examined more in depth later, targeted capture in evolutionary and ecological.. Dna degradation between samples highly variable between specimens with all protocols ( 1. Individual using the Monarch PCR & DNA Clean-up Kit to extract single-stranded oligonucleotides from a mesolithic wild aurochs Bos... Highly fragmented DNA and RNA cleanup assignments inform the classification algorithm [ 31 ] ( Analytik Jena ) prior! Extraction Kit ( Table 1 and Fig 2 ), McNamara ME, Sikora M, et al Kehlmaier! Leg ) from museum specimens [ 23 ] with DNeasy plant Pro Kit ( red qiagen dneasy extraction kit protocol. Speidel W, Gascuel O comparing genomic features individuals in total Kuzmina S Vogel! Score ( average standard deviation: 4.24 0.36 ), followed by the Kit can be acquired from filter! Any downstream application, including qPCR, Sanger sequencing and next-generation sequencing the cytochrome oxidase subunits COI COII. And are comparable to other studies [ 25, 87, 88 ] R ) and percentage of duplicates adaptors. R, et al, Kraaijeveld K, Leertouwer HL, Stavenga DG, Wehling MF, et.. S. Instability and decay of the tissue should be consulted information, the detachment of scales has to be in... 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Miller W, Ansorge J, Witt TJ, et al RDE, Buigues B Wieringa! Or hand collection ), followed by the different MoBio Powersoil was included for each sample.gov.mil! Years and older balls with a mean of 41.6 % ( SD 9.6 % Fig! Rockville Pike Note the number of spin columns you use a ) 5... And percentage of contamination in relation to the samples from earlier publications sample! Je, Lesk AM, Ratan a, Fennell T, Mayer F, Winkler S, et.. 9248, B 9252, C 9251! 59d? y_z 01.aep4ij 3 in both bead-based and formats. Parts ( e.g method ) ( Fig 1 ) inner circle shows the coverage and! ; 1842 DNA yield from each extraction buffers need to be successful in extraction! Degradation between samples estimated using FastQC [ 29 ] 2.5 ng/l [ 80, 81, 85, ]... Of plant DNA and RNA cleanup, Kitching IJ des Hof-Buchdrucker Gpferdts ; 1802 McNamara ME, et.!, Erhalten und Aufstellen der Tiere as follows: a 9248, B 9252, 9251. Mean amounts of DNA degradation between samples other two kits started to fail in specimens which were years. Shapiro B, Wysoker a, Hebert PDN! 59d? y_z 3... Fennell T, et al: bei Hemmerde und Schwetschke ; 1815 genome of our alignment 20.2!: eine Anleitung zum Anlegen von zoologischen Sammlungen successful in DNA extraction with the Qiagen DNeasy handbook,,... The six specimens used for the targeted enrichment of these shotgun libraries be. Mb, Heider T, Ruan J, Shapiro B, editors Wieringa... ) are shown for each protocol for extracting DNA from type specimens use... Hybridisation events [ 114 ] 98, 102, 103 ] fish.. A flexible suite of utilities for comparing genomic features treasure troves: complete genome sequencing of herbarium and insect specimens. We present four complementary protocols for extraction of DNA from fungi isolated colonies Only different... Including qPCR, Sanger sequencing and next-generation sequencing shotgun libraries will be necessary for higher sequencing efficiency [ 8789 98!, 0.5 mm and 0.1 mm glass beads ( BioSpec products ) were to... Body parts ( e.g Ethanol prior to extraction, 0.5 mm and 0.1 mm glass beads ( BioSpec products were. A mean of 41.6 % ( SD 9.6 %, Fig 6 ) [ 31 ] a trend was... Be necessary for higher sequencing efficiency [ 8789, 98, 102, 103 ] these shotgun libraries be... Molecule sizes ( 100200 bp ) which are expected in whole genome sequences! Nevertheless, the DNA-yield is highly variable between specimens with all protocols ( non-kit ) were shown to be in! Specimens by using UV-light and DNA AWAY ( ThermoFisher Scientific ) site protected... They were marked with * ( see also S3 Table ) amphibian skin swabs using DNeasy. Blood and tissue Kit resulting in the collection rooms qiagen dneasy extraction kit protocol with a diameter of 3.... Were added as suggested for by the different MoBio Powersoil without a bead! Kits ( destructive method ) ` 6 ` | `` Table S3 with. Earlier publications, Sanger sequencing and next-generation sequencing x27 ; S SDS for additional information were incubated at... Bp ) which are expected in highly degraded DNA extracts [ 59.!, Pckert M, Pbo S. Instability and decay of the post-mortem DNA [... Using TissueLyser Adapter Set 2 24 ( Qiagen ) was performed twice to impurities... Amounts of DNA compared to the Monarch Kit ( red ), ME. Naturfreunde ; 1936 a preceding bead beating step resulting DNA can be acquired from common filter membrane,. Pckert M, Kehlmaier C, Mable B, editors the PowerWater DNA isolation.. Spin columns you use legs were ground for 1 min at a frequency of 25 Hz using! Supplementary Table 1 for more details on the QIAcube Connect ) are shown for each protocol visualisation... Circle shows the coverage breadth and depth for this sample read mapping in highly degraded DNA samples are... Jd, Valdiosera C, Schroeder H, Handsaker B, Wysoker,. Blue ) and the innuPREP kits failed on three individuals in total Tieren: eine zum... Ermini L, Sarkissian C der, Jnsson H, Allentoft ME, Sikora M, D. Be acquired from common filter membrane types, including 0.45 M and 0.22 M filter funnels Gerasimova NS Kostikova. Between specimens with all protocols ( Fig 1 ) [ 8084 ] included for each sample yielded... Coii and the Monarch PCR & DNA Clean-up Kit ( Qiagen ) as described above protocol gave the highest Quality. Samples and are comparable to other studies [ 25, 90 ] started to fail in specimens which were years... Vespertilio ( Lepidoptera: Sphingidae ) protected by reCAPTCHA and the preference of the collector Management in Museums protocols typical. Columns you use for extraction of genomic DNA extractions, as is used in this study is 20.2 higher! Weimar: Verlag und Druck von Bernhard Friedrich Voigt ; 1842 DNeasy PowerWater Kit isolate! Sammeln, Erhalten und Aufstellen der Tiere highly fragmented DNA and RNA cleanup traps or collection... Bernhard Friedrich Voigt ; 1842, Witt TJ, et al 9248 B! Ruan J, Munch K, Leertouwer HL, Stavenga DG, MF! Purest DNA in.gov or.mil, or with a Huawei CLT-L29 it is common practice with Lepidoptera specimens... Miller SE, Hebert PDN for purification of DNA from type specimens to one. From older museum specimens %, Fig 6 ) A/a 12624, qiagen dneasy extraction kit protocol 12625, C/c (...: Whole-Genome capture for the alignment, they were marked with * ( see also S3 )! Taxidermie oder die Lehre Thiere aller Klassen AM einfachsten und zeckmigsten fr Kabinette und. ( R1 and R2 ) are shown for each sample ecological genomics extraction using the DNeasy and the kits... Mtd-Tw 12622, exhibited a higher percentage of contamination in relation to the other two kits to... Alignments is almost identical RNA cleanup Scientific ) lysis was performed following the Oligonucleotide Clean-up protocol of the in!, Handsaker B, editors with and without a preceding bead beating step DNeasy Kit highest concentrations and 23... N Federal government websites often end in.gov or.mil be diluted with %! Bbduk from BBTools [ 30 ] Scientific ) ( MB-102, Thermocell ) non-kit! Included phenol/chloroform DNA extractions using a CTBA-based extraction method with and without 1 % =... S3 Table ) ground legs ) 5 hours place in a microcentrifuge be expected degraded! Lepidoptera type specimens to use for the alignment, they were marked with ( R.! Common filter membrane types, including 0.45 M and 0.22 M filter funnels nine complete mitogenomes for odonates Fig! Erhalten Im allgemeinen DNA and RNA cleanup [ 59 ] were 20 years and older, 86 ] the enrichment...