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De Silva S, Cagliero C, Gostel MR, Johnson G, Anderson JL. Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility. PLANT METHODS 2024; 20:91. [PMID: 38877523 PMCID: PMC11177442 DOI: 10.1186/s13007-024-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications. RESULTS In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis. CONCLUSIONS The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5 mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.
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Affiliation(s)
- Shashini De Silva
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Turin, I-10125, Italy
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, TX, 76107-3400, USA
| | | | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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Burns JA, Becker KP, Casagrande D, Daniels J, Roberts P, Orenstein E, Vogt DM, Teoh ZE, Wood R, Yin AH, Genot B, Gruber DF, Katija K, Wood RJ, Phillips BT. An in situ digital synthesis strategy for the discovery and description of ocean life. SCIENCE ADVANCES 2024; 10:eadj4960. [PMID: 38232174 DOI: 10.1126/sciadv.adj4960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024]
Abstract
Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. We present and demonstrate an interdisciplinary approach that uses emerging quantitative imaging technologies, an innovative robotic encapsulation system with in situ RNA preservation and next-generation genomic sequencing to gain comprehensive biological, biophysical, and genomic data from deep-sea organisms. The synthesis of these data provides rich morphological and genetic information for species description, surpassing traditional passive observation methods and preserved specimens, particularly for gelatinous zooplankton. Our approach enhances our ability to study delicate mid-water animals, improving research in the world's oceans.
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Affiliation(s)
- John A Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Kaitlyn P Becker
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - David Casagrande
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - Joost Daniels
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, CA 95039, USA
| | - Paul Roberts
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, CA 95039, USA
| | - Eric Orenstein
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, CA 95039, USA
| | - Daniel M Vogt
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | | | - Ryan Wood
- PA Consulting, Concord, MA 01742, USA
| | - Alexander H Yin
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - Baptiste Genot
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - David F Gruber
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY 10010, USA
| | - Kakani Katija
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, CA 95039, USA
| | - Robert J Wood
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Brennan T Phillips
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI 02882, USA
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DeSanctis ML, Soranno EA, Messner E, Wang Z, Turner EM, Falco R, Appiah-Madson HJ, Distel DL. Greater than pH 8: The pH dependence of EDTA as a preservative of high molecular weight DNA in biological samples. PLoS One 2023; 18:e0280807. [PMID: 36689492 PMCID: PMC9870144 DOI: 10.1371/journal.pone.0280807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is a divalent cation chelator and chemical preservative that has been shown to be the active ingredient of the popular DNA preservative DESS. EDTA may act to reduce DNA degradation during tissue storage by sequestering divalent cations that are required by nucleases naturally occurring in animal tissues. Although EDTA is typically used between pH 7.5 and 8 in preservative preparations, the capacity of EDTA to chelate divalent cations is known to increase with increasing pH. Therefore, increasing the pH of EDTA-containing preservative solutions may improve their effectiveness as DNA preservatives. To test this hypothesis, we stored tissues from five aquatic species in 0.25 M EDTA adjusted to pH 8, 9, and 10 for 12 months at room temperature before DNA isolation. For comparison, tissues from the same specimens were also stored in 95% ethanol. DNA extractions performed on tissues preserved in EDTA pH 9 or 10 resulted in as great or greater percent recovery of high molecular weight DNA than did extractions from tissues stored at pH 8. In all cases examined, percent recovery of high molecular weight DNA from tissues preserved in EDTA pH 10 was significantly better than that observed from tissues preserved in 95% ethanol. Our results support the conclusion that EDTA contributes to DNA preservation in tissues by chelating divalent cations and suggest that preservative performance can be improved by increasing the pH of EDTA-containing DNA preservative solutions.
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Affiliation(s)
- Mia L. DeSanctis
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elizabeth A. Soranno
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ella Messner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ziyu Wang
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elena M. Turner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Rosalia Falco
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
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Bogdanova NV, Radmanesh H, Ramachandran D, Knoechelmann AC, Christiansen H, Derlin T, von Klot CAJ, Merten R, Henkenberens C. The Prognostic Value of Liquid Biopsies for Benefit of Salvage Radiotherapy in Relapsed Oligometastatic Prostate Cancer. Cancers (Basel) 2022; 14:cancers14174095. [PMID: 36077632 PMCID: PMC9454496 DOI: 10.3390/cancers14174095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Around 30% of patients with oligometastatic prostate cancer relapse will benefit from local PET/CT-guided ablative radiotherapy (RT) with improved progression-free and ADT (Androgene Deprivation Therapy)-free survivals. Therefore, there is an urgent need for predictive testing for therapeutic benefits prior to initiation. Various tests have already been established on tumor specimens for the prediction of prostate cancer’s behavior or therapy outcome. However, in imaging-proven relapse tumor tissue from the local recurrence or metastases is often not available. Hence, there is a need for a liquid biopsy-based testing. We aimed to assess the prognostic value of CTCs- associated mRNA and blood-derived RNA for the benefit of PSMA PET-guided salvage RT in oligometastatic prostate cancer relapses. Significant correlations were found between the relative transcript levels of several investigated genes and clinicopathological parameters. Furthermore, distinct “transcriptional signatures” were found in patients with temporary and long-term benefits from RT. Abstract To assess the prognostic value of “liquid biopsies” for the benefit of salvage RT in oligometastatic prostate cancer relapse, we enrolled 44 patients in the study between the years 2016 and 2020. All the patients were diagnosed as having an oligometastatic prostate cancer relapse on prostate-specific membrane antigen (PSMA)-targeted PET-CT and underwent irradiation at the Department of Radiotherapy at the Hannover Medical School. Tumor cells and total RNA, enriched from the liquid biopsies of patients, were processed for the subsequent quantification analysis of relative transcript levels in real-time PCR. In total, 54 gene transcripts known or suggested to be associated with prostate cancer or treatment outcome were prioritized for analysis. We found significant correlations between the relative transcript levels of several investigated genes and the Gleason score, PSA (prostate-specific antigen) value, or UICC stage (tumor node metastasis -TNM classification of malignant tumors from Union for International Cancer Control). Furthermore, a significant association of MTCO2, FOXM1, SREBF1, HOXB7, FDXR, and MTRNR transcript profiles was found with a temporary and/or long-term benefit from RT. Further studies on larger patients cohorts are necessary to prove our preliminary findings for establishing liquid biopsy tests as a predictive examination method prior to salvage RT.
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Affiliation(s)
- Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Hoda Radmanesh
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Dhanya Ramachandran
- Gynecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Thorsten Derlin
- Department of Nuclear Medicine, Hannover Medical School, 30625 Hannover, Germany
| | | | - Roland Merten
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence: ; Tel.: +49-(0)-511-532-3590
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Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan W, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience 2022; 11:giac068. [PMID: 35946988 PMCID: PMC9364683 DOI: 10.1093/gigascience/giac068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. RESULTS We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. CONCLUSION We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
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Affiliation(s)
- Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | | | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Iliana Bista
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | | | | | | | - Karen Oliver
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michelle Smith
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Anne Kraus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Stephen Mac
- Arima Genomics, Inc., San Diego, CA 92121, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Tanya Lama
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Samara Brown
- The Rockefeller University, New York, NY 10065, USA
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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6
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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7
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Blom MPK. Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing. Mol Ecol 2021; 30:5935-5948. [PMID: 33786900 DOI: 10.1111/mec.15909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
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Affiliation(s)
- Mozes P K Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
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8
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Miller AH, Davis HR, Luong AM, Do QH, Pham CT, Ziegler T, Lee JL, De Queiroz K, Reynolds RG, Nguyen TQ. Discovery of a New Species of Enigmatic Odd-Scaled Snake (Serpentes: Xenodermidae: Achalinus) from Ha Giang Province, Vietnam. COPEIA 2020. [DOI: 10.1643/ch2020060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Aryeh H. Miller
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013; (AHM) ; (JLL) ; and (KdQ) . Send reprint requests to AHM
| | - Hayden R. Davis
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085
| | - Anh Mai Luong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam; (AML) ; (QHD) ; (CTP) ; and (TQN) nqt2@yaho
| | - Quyen Hanh Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam; (AML) ; (QHD) ; (CTP) ; and (TQN) nqt2@yaho
| | - Cuong The Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam; (AML) ; (QHD) ; (CTP) ; and (TQN) nqt2@yaho
| | - Thomas Ziegler
- AG Zoologischer Garten Köln, Riehler Strasse 173, D-50735 Cologne, Germany;
| | - Justin L. Lee
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013; (AHM) ; (JLL) ; and (KdQ) . Send reprint requests to AHM
| | - Kevin De Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013; (AHM) ; (JLL) ; and (KdQ) . Send reprint requests to AHM
| | - R. Graham Reynolds
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, North Carolina 28804; (RGR)
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam; (AML) ; (QHD) ; (CTP) ; and (TQN) nqt2@yaho
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9
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DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative? PLoS One 2020; 15:e0237356. [PMID: 32817618 PMCID: PMC7440624 DOI: 10.1371/journal.pone.0237356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 01/20/2023] Open
Abstract
DESS is a formulation widely used to preserve DNA in biological tissue samples. Although it contains three ingredients, dimethyl sulfoxide (DMSO), ethylenediaminetetraacetic acid (EDTA) and sodium chloride (NaCl), it is frequently referred to as a DMSO-based preservative. The effectiveness of DESS has been confirmed for a variety of taxa and tissues, however, to our knowledge, the contributions of each component of DESS to DNA preservation have not been evaluated. To address this question, we stored tissues of three aquatic taxa, Mytilus edulis (blue mussel), Faxonius virilis (virile crayfish) and Alitta virens (clam worm) in DESS, each component of DESS individually and solutions containing all combinations of two components of DESS. After storage at room temperature for intervals ranging from one day to six months, we extracted DNA from each tissue and measured the percentage of high molecular weight (HMW) DNA recovered (%R) and normalized HMW DNA yield (nY). Here, HMW DNA is defined as fragments >10 kb. For comparison, we also measured the %R and nY of HMW DNA from extracts of fresh tissues and those stored in 95% EtOH over the same time intervals. We found that in cases where DESS performed most effectively (yielding ≥ 20%R of HMW DNA), all solutions containing EDTA were as or more effective than DESS. Conversely, in cases where DESS performed more poorly, none of the six DESS-variant storage solutions provided better protection of HMW DNA than DESS. Moreover, for all taxa and storage intervals longer than one day, tissues stored in solutions containing DMSO alone, NaCl alone or DMSO and NaCl in combination resulted in %R and nY of HMW DNA significantly lower than those of fresh tissues. These results indicate that for the taxa, solutions and time intervals examined, only EDTA contributed directly to preservation of high molecular weight DNA.
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10
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Mulcahy DG, Lee JL, Miller AH, Chand M, Thura MK, Zug GR. Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data. Zookeys 2018:85-152. [PMID: 29780268 PMCID: PMC5958176 DOI: 10.3897/zookeys.757.24453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/09/2018] [Indexed: 11/12/2022] Open
Abstract
Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave., Washington, DC, 20013 USA
| | - Justin L Lee
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park Maryland, 20742 USA
| | - Aryeh H Miller
- Department of Biology, University of North Carolina Asheville, Asheville, NC 28804 USA
| | - Mia Chand
- College of William & Mary, Williamsburg, Virginia, 23187 USA
| | - Myint Kyaw Thura
- Myanmar Environment Sustainable Conservation (MESC), Yangon, Myanmar
| | - George R Zug
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013 USA
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11
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González VL, Devine AM, Trizna M, Mulcahy DG, Barker KB, Coddington JA. Open access genomic resources for terrestrial arthropods. CURRENT OPINION IN INSECT SCIENCE 2018; 25:91-98. [PMID: 29602368 DOI: 10.1016/j.cois.2017.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 06/08/2023]
Abstract
Genome sequencing initiatives like the Arthropod i5k project and other biodiversity genomics research rely on access to high quality DNA and/or tissue. Global collection initiatives such as the Smithsonian Global Genome Initiative (GGI) and its partner network, the Global Genome Biodiversity Network (GGBN) aim to provide access to these resources at high-quality standards. Here, we review progress toward providing genomic resources (tissues, DNA, genomes) for terrestrial arthropods, a megadiverse animal group, and compare progress in genome sequencing to all other animals.
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Affiliation(s)
- Vanessa L González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
| | - Amanda M Devine
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Mike Trizna
- Smithsonian DNA Barcode Network, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Katharine B Barker
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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Hofmann EP, Townsend JH. Origins and biogeography of the Anolis crassulus subgroup (Squamata: Dactyloidae) in the highlands of Nuclear Central America. BMC Evol Biol 2017; 17:267. [PMID: 29268694 PMCID: PMC5740896 DOI: 10.1186/s12862-017-1115-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/14/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Recent studies have begun to reveal the complex evolutionary and biogeographic histories of mainland anoles in Central America, but the origins and relationships of many taxa remain poorly understood. One such group is the Anolis (Norops) crassulus species subgroup, which contains ten morphologically similar highland taxa, the majority of which have restricted distributions. The nominal taxon A. crassulus has a disjunct distribution from Chiapas, Mexico, through Guatemala, in the highlands of El Salvador, and in the Chortís Highlands of Honduras. We test the relationships of these species using multiple mitochondrial and nuclear loci in concatenated and multispecies coalescent frameworks, in an effort to both resolve long-standing taxonomic confusion and present new insights into the evolution and biogeography of these taxa. RESULTS Sequences of multiple mitochondrial and nuclear loci were generated for eight of the ten species of the Anolis crassulus species subgroup. We analyzed phylogenetic relationships and estimated divergence times and ancestral ranges of the subgroup, recovering a monophyletic subgroup within Anolis. Within the nominal taxon Anolis crassulus, we recovered multiple genetically distinct lineages corresponding to allopatric populations, and show that the Chortís Highland lineage split from the others over 13 MYA. Additionally, distinct mitochondrial lineages are present within the taxa A. heteropholidotus and A. morazani, and importantly, samples of A. crassulus and A. sminthus previously used in major anole phylogenetic analyses are not recovered as conspecific with those taxa. We infer a Chortís Highland origin for the ancestor of this subgroup, and estimate cladogenesis of this subgroup began approximately 22 MYA. CONCLUSIONS Our results provide new insights into the evolution, biogeography, and timing of diversification of the Anolis crassulus species subgroup. The disjunctly distributed Anolis crassulus sensu lato represents several morphologically conserved, molecularly distinct anoles, and several other species in the subgroup contain multiple isolated lineages.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA 15705-1081 USA
- Present Address: Department of Biological Sciences, Clemson University, Clemson, SC 29634 USA
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA 15705-1081 USA
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Connette GM, Oswald P, Thura MK, LaJeunesse Connette KJ, Grindley ME, Songer M, Zug GR, Mulcahy DG. Rapid forest clearing in a Myanmar proposed national park threatens two newly discovered species of geckos (Gekkonidae: Cyrtodactylus). PLoS One 2017; 12:e0174432. [PMID: 28403189 PMCID: PMC5389631 DOI: 10.1371/journal.pone.0174432] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/26/2017] [Indexed: 11/18/2022] Open
Abstract
Myanmar’s recent transition from military rule towards a more democratic government has largely ended decades of political and economic isolation. Although Myanmar remains heavily forested, increased development in recent years has been accompanied by exceptionally high rates of forest loss. In this study, we document the rapid progression of deforestation in and around the proposed Lenya National Park, which includes some of the largest remaining areas of lowland evergreen rainforest in mainland Southeast Asia. The globally unique forests in this area are rich in biodiversity and remain a critical stronghold for many threatened and endangered species, including large charismatic fauna such as tiger and Asian elephant. We also conducted a rapid assessment survey of the herpetofauna of the proposed national park, which resulted in the discovery of two new species of bent-toed geckos, genus Cyrtodactylus. We describe these new species, C. lenyasp. nov. and C. payarhtanensissp. nov., which were found in association with karst (i.e., limestone) rock formations within mature lowland wet evergreen forest. The two species were discovered less than 35 km apart and are each known from only a single locality. Because of the isolated nature of the karst formations in the proposed Lenya National Park, these geckos likely have geographical ranges restricted to the proposed protected area and are threatened by approaching deforestation. Although lowland evergreen rainforest has vanished from most of continental Southeast Asia, Myanmar can still take decisive action to preserve one of the most biodiverse places on Earth.
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Affiliation(s)
- Grant M. Connette
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian Institution, Front Royal, Virginia, United States of America
- * E-mail:
| | - Patrick Oswald
- Fauna & Flora International, San Chaung Township, Yangon, Myanmar
| | - Myint Kyaw Thura
- Myanmar Environment & Sustainable Conservation Co., LTD (MESC), Yangon, Myanmar
| | - Katherine J. LaJeunesse Connette
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian Institution, Front Royal, Virginia, United States of America
| | - Mark E. Grindley
- Fauna & Flora International, San Chaung Township, Yangon, Myanmar
| | - Melissa Songer
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian Institution, Front Royal, Virginia, United States of America
| | - George R. Zug
- Department of Vertebrate Zoology, National Museum of Natural History (NMNH), Smithsonian Institution, Washington D.C., United States of America
| | - Daniel G. Mulcahy
- Global Genome Initiative (GGI), National Museum of Natural History (NMNH), Smithsonian Institution, Washington D.C., United States of America
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14
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Droege G, Barker K, Seberg O, Coddington J, Benson E, Berendsohn WG, Bunk B, Butler C, Cawsey EM, Deck J, Döring M, Flemons P, Gemeinholzer B, Güntsch A, Hollowell T, Kelbert P, Kostadinov I, Kottmann R, Lawlor RT, Lyal C, Mackenzie-Dodds J, Meyer C, Mulcahy D, Nussbeck SY, O'Tuama É, Orrell T, Petersen G, Robertson T, Söhngen C, Whitacre J, Wieczorek J, Yilmaz P, Zetzsche H, Zhang Y, Zhou X. The Global Genome Biodiversity Network (GGBN) Data Standard specification. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw125. [PMID: 27694206 PMCID: PMC5045859 DOI: 10.1093/database/baw125] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/09/2016] [Indexed: 11/24/2022]
Abstract
Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL:http://terms.tdwg.org/wiki/GGBN_Data_Standard
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Affiliation(s)
- G Droege
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, Berlin 14195, Germany
| | - K Barker
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - O Seberg
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83, opg. S, Copenhagen DK-1307, Denmark
| | - J Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - E Benson
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife KY15 5RJ, UK
| | - W G Berendsohn
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, Berlin 14195, Germany
| | - B Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, Braunschweig 38124, Germany
| | - C Butler
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - E M Cawsey
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - J Deck
- Berkeley Natural History Museums, University of California at Berkeley, Berkeley, CA 94720, USA
| | - M Döring
- Global Biodiversity Information Facility Secretariat, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - P Flemons
- Australian Museum, Sydney 2010, NSW, Australia
| | - B Gemeinholzer
- Systematic Botany, Justus Liebig University, Giessen 35392, Germany
| | - A Güntsch
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, Berlin 14195, Germany
| | - T Hollowell
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - P Kelbert
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, Berlin 14195, Germany
| | - I Kostadinov
- Department of Life Sciences & Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, Bremen 28759, Germany
| | - R Kottmann
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - R T Lawlor
- ARC-Net Applied Research on Cancer Centre, Department of Pathology and Diagnostics, University of Verona, Verona 37134, Italy
| | - C Lyal
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - C Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - D Mulcahy
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - S Y Nussbeck
- Department of Medical Informatics and UMG Biobank, University Medical Center Göttingen, Robert-Koch-Str. 40, Göttingen 37075, Germany
| | - É O'Tuama
- Global Biodiversity Information Facility Secretariat, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - T Orrell
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - G Petersen
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83, opg. S, Copenhagen DK-1307, Denmark
| | - T Robertson
- Global Biodiversity Information Facility Secretariat, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - C Söhngen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, Braunschweig 38124, Germany
| | - J Whitacre
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - J Wieczorek
- Museum of Vertebrate Zoology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - P Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - H Zetzsche
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, Quedlinburg 06484, Germany
| | - Y Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - X Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
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