Tissue sampling methods and standards for vertebrate genomics

GigaScience

G10KCOS³  Robert W Murphy⁵  Ya-ping Zhang^1,10  Byrappa Venkatesh²  Andrew C Bentley⁹  Gabriela Mastromonaco⁴  Polina Perelman¹  Marlys L Houck⁷  Klaus-Peter Koepfli⁶  David Haussler^1,11  Stephen J O’Brien⁸  Oliver A Ryder⁷  Warren E Johnson⁶  Edward O Wiley⁹  Pamela BY Wong⁵ 

[1] Laboratory of Animal Cytogenetics, Institute of Molecular and Cellular Biology, Lavrentiev 10, Novosibirsk, 630090, Russia;Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, 138673, Singapore;Genome 10 K Community of Scientists. http://www.genome10k.org/, Santa Cruz, California, USA;Reproductive Physiology, Toronto Zoo, 361A Old Finch Avenue, Scarborough, Ontario, M1B 5K7, Canada;Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen`s Park, Toronto, Ontario, M5S 2C6, Canada;Laboratory of Genomic Diversity, National Cancer Institute, 31 Center Drive, Frederick, Maryland, 21702-1201, USA;San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California, 92027, USA;Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 8 Viborgskaya Street, St. Petersburg, 194044, Russia;Division of Ichthyology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045, USA;Laboratory for Conservation and Utilization of Bioresources, Yunnan University, 2 North Cuihu Road, Kunming, Yunnan, 650091, China;Center for Biomolecular Science and Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA

关键词: DNA;    RNA;    Tissue culture;    Cell line;    Tissue storage;    Tissue sampling;    Genomics;    Vertebrates;    Sequencing;    Genome 10K;   

Others  :  861916
DOI  :  10.1186/2047-217X-1-8

 received in 2012-03-08, accepted in 2012-07-12,  发布年份 2012

【 摘 要 】

The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.

【 授权许可】

   
2012 Wong et al.; licensee BioMed Central Ltd.

【 图 表 】

【 参考文献 】

• [1]Schwartz MK, Luikart G, McKelvey KS, Cushman SA: Landscape genomics: a brief perspective. In Spatial complexity, informatics, and wildlife conservation. Edited by Cushman SA, Huettmann F. Springer, New York; 2009:165-174.
• [2]Gayral P, Weinert L, Chiari Y, Tsagkogeorga G, Ballenghien M, Galtier N: Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Mol Ecol Resour 2011, 11:650-661.
• [3]Glenn TC: Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011, 11:759-769.
• [4]Genome 10 K Community of Scientists: Genome 10 K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. J Hered 2009, 100:659-674.
• [5]Nadeau NK, Jiggins CD: A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. TIG 2010, 26:484-492.
• [6]Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma RK, Hedrick PW: Conservation genetics in transition to conservation genomics. TIG 2010, 26:177-187.
• [7]Renn SCP, Siemens DH: Ecological genomics––changing perspectives on Darwin’s basic concerns. Mol Ecol 2010, 19:3025-3030.
• [8]Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, Bouffard P, Nielsen SCA, Rasmussen M, Willerslev E, Gilbert MTP, Harkins T: Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 2010, 20:908-916.
• [9]Wang Z, Shen X, Liu B, Su J, Yonezawa T, Yu Y, Guo S, Ho SYW, Vilà C, Hasegawa M, Liu J: Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. J Biogeogr 2010, 37:2332-2344.
• [10]Butlin RK: Population genomics and speciation. Genetica 2008, 138:409-418.
• [11]Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H: Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol 2010, 19:266-276.
• [12]Allendorf FW, Hohenlohe PA, Luikart G: Genomics and the future of conservation genetics. Nature Rev Genet 2010, 11:697-709.
• [13]Scoble J, Lowe AJ: A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning. Diversity Distrib 2010, 16:343-353.
• [14]Primmer CR: From conservation genetics to conservation genomics. Ann NY Acad Sci 2009, 1162:367-368.
• [15]United States Department of Agriculture: Animal Welfare Act. Government Printing Office, Washington; 1966.
• [16]Canadian Council on Animal Care: Guide to the care and use of experimental animals. Canadian Council on Animal Care, Ottawa; 1993.
• [17]Australian Government: Environment Protection and Biodiversity Conservation Act. Australian Government, Canberra; 1999.
• [18]New Zealand Parliamentary Office: Animal Welfare Act 1999. Government of New Zealand, Wellington; 1999.
• [19]Government of Western Australia: Animal Welfare Act 2002. State of Western Australia, Perth; 2002.
• [20]Secretariat of the Convention on Biological Diversity: Nagoya protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their utilization to the convention on biological diversity. Secretariat of the Convention on Biological Diversity, United Nations, Montreal; 2011.
• [21]Convention on Biological Diversity: [http://www.cbd.int/abs/text/] webciteText of the Nagoya Protocol. Secretariat of the Convention on Biological Diversity, United Nations, Montreal; 2011.
• [22]Government of Canada: Canada Wildlife Act (RSC c W-9). Government of Canada, Ottawa; 1985a.
• [23]Government of Canada: Export and Import Permits Act (RSC, c E-19). Government of Canada, Ottawa; 1985b.
• [24]U.S. Fish and Wildlife Service: [http://library.fws.gov/IA_Pubs/permits_legacy02.pdf] webciteLeaving a lasting legacy, permits as a conservation tool. U.S. Fish and Wildlife Service, Arlington; 2002.
• [25]Government of Canada: Wildlife Area Regulations (CRC, c 1609). Government of Canada, Ottawa; 2010.
• [26]National Park Service: [https://science.nature.nps.gov/research/ac/ResearchIndex] webciteNational Park Service Research Permit and Reporting System. U.S. Department of Interior, Washington; April, 2012.
• [27]Parks Canada. Research and Collection Permit System: [http://www.pc.gc.ca/apps/rps/RPSSpecCond_e.asp] webciteHeritage Area Specific Information and Conditions. Parks Canada, Ottawa; April, 2012.
• [28]New Zealand Parliamentary Office: Wildlife Act 1953. Government of New Zealand, Wellington; 1953.
• [29]Waitangi Tribunal: WAI 262, The flora and fauna and cultural intellectual property claim. New Zealand Ministry of Justice, Wellington; 2006.
• [30]International Union for the Conservation of Nature: Convention on International Trade in Endangered Species of Wild Fauna and Flora. IUCN, Washington DC; 1973. 1973
• [31]Australian Government Department of Sustainability, Environment, Water, Population, and Communities (DSEWPC): [http://www.environment.gov.au/biodiversity/trade-use/permits/index.html] webciteWildlife Trade and Conservation. DSEWPC, Canberra ACT; April, 2012.
• [32]Canadian Food Inspection Agency: [http://www.inspection.gc.ca/animals/eng/1299155513713/1299155693492] webciteAnimals. Government of Canada, Ottawa; April, 2012.
• [33]Government of New Zealand Ministry of Agriculture and Forestry (MAF): [http://www.maf.govt.nz/biosecurity-animal-welfare] webciteBiosecurity and Animal Welfare. MAF, Wellington; 2011.
• [34]U.S. Fish and Wildlife Service (FWS): [http://www.fws.gov/permits/ImportExport/ImportExport.html] webciteImport and Export Permits. Department of the Interior, FWS, Arlington; 2010.
• [35]International Air Transport Association: [http:/ / www.iata.org/ whatwedo/ cargo/ dangerous_goods/ Documents/ DGR53_SignificantChanges.pdf] webciteDangerous Goods Regulations. 52nd edition. International Air Traffic Association, Montreal; 2012.
• [36]International Air Transport Association: [http://www.iata.org/whatwedo/cargo/dangerous_goods/Pages/download.aspx] webciteDangerous Goods (HAZMAT). International Air Traffic Association, Montreal; April, 2012.
• [37]Wilson MA, Makova KD: Evolution and survival of eutherian sex chromosomes. PLoS Genet 2009., 5
• [38]The Institutional Animal Care and Use Committee (IACUC): [http://www.iacuc.org] webciteAmerican Association for Laboratory Animal Science. IACUC, Memphis;
• [39]American Veterinary Medical Association: [http://www.avma.org/issues/animal_welfare/euthanasia_guidelines/default.asp] webciteAVMA Animal Welfare Policies Open for Comment. American Veterinary Medical Association, Schaumburg; April, 2012.
• [40]Nagy ZT: A hands-on overview of tissue preservation methods for molecular genetic analyses. Org Divers Evol 2010, 10:91-105.
• [41]Dessauer HC, Cole CJ, Hafner MS: Collection and storage of tissues. In Molecular Systematics. Edited by Hills DM, Moritz C. Sinauer Associates Inc, Sunderland; 1990:25-41.
• [42]Engstrom MD, Murphy RW, Haddrath O: Sampling vertebrate collections for molecular research: practice and policies. In Managing the modern herbarium. Edited by Metsger DA, Byers SC. Granville Island Publishing, Vancouver; 1990:315-330.
• [43]Seutin G, White BN, Boag P: Preservation of avian blood and tissue samples for DNA analyses. Can J Zool 1991, 69:82-90.
• [44]Schulte-Hostedde AI, Montgomerie R: Intraspecific variation in ejaculate traits of the northern watersnake (Nerodia sipedon). J Zool 2006, 270:146-152.
• [45]Blanco JM, Wildt DE, Höfle U, Voelker W, Donoghue AM: Implementing artificial insemination as an effective tool for conservation of endangered avian species. Theriogenol 2009, 71:200-213.
• [46]Lakra WS, Raja Swaminathan T, Joy KP: Development, characterization, conservation, and storage of fish cell lines: a review. Fish Physiol Biochem 2011, 37:1-20.
• [47]Houck ML, Ryder OA, Kumamoto AT, Benirschke K: Cytogenetics of the Rhinocerotidae. Verh ber Erkrg Zootiere 1995, 37:25-32.
• [48]Stanyon R, Galleni L: A rapid fibroblast culture technique for high resolution karyotypes. Boll Zool 1991, 58:81-83.
• [49]Mastromonaco GF, Perrault SD, Betts DH, King WA: Role of chromosome stability and telomere length in the production of viable cell lines for somatic cell nuclear transfer. BMC Devel Biol 2006, 6:41. BioMed Central Full Text
• [50]Houck ML, Ryder OA, Váhala J, Kock RA, Oosterhuis JE: Diploid chromosome number and chromosomal variation in the white rhinoceros (Ceratotherium simum). J Hered 1994, 85:30-34.
• [51]Mauger PE, Le Bail PY, Labbé C: Cryobanking of fish somatic cells: optimization of fish explants culture and fish cell cryopreservation. Comp Biochem Physiol Part B: Biochem Mol Biol 2006, 144:29-37.
• [52]Ezaz T, O’Meally D, Quinn AE, Sarre SD, Georges A, Marshall Graves JA: A simple non-invasive protocol to establish primary cell lines from tail and toe explants for cytogenetic studies in Australian dragon lizards (Squamata: Agamidae). Cytotechnol 2008, 58:135-139.
• [53]Arsham M, Barch M, Lawce H: Animal Cytogenetics. In The Association of Genetic Technologists (AGT) Cytogenetics Laboratory Manual. 4th edition. Edited by Arsham M, Brach M, Lawce HNY. Springer Publishing Company, New York; In press.
• [54]Fresney RI: Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications. 6th edition. Wiley-Blackwell, New York; 2010.
• [55]Masters JRW: Animal Cell Culture: A Practical Approach. 3rd edition. Oxford University Press, New York; 2000.
• [56]Böhmer HV, Wöhler W, Wendel U, Passarge E, Rüdiger HW: Studies on the optimal cooling rate for freezing diploid human fibroblasts. Exp Cell Res 1973, 79:496-498.
• [57]Corthals A, Desalle R: An application of tissue and DNA banking for genomics and conservation: the Ambrose Monell Cryo-Collection (AMCC). Syst Biol 2005, 54:819-823.
• [58]Biodiversity Information Standards (TDWG): [http://rs.tdwg.org/dwc/index.htm] webciteDarwin Core. Taxonomic Databases Working Group, Hobart; 2009.
• [59]Genome 10 K Community of Scientists (G10KCOS): [http://www.genome10k.org/sites/default/files/g10kSubmissionGuide_0.pdf] webciteGenome 10 K Data Submission Guidelines. G10KCAS, Santa Cruz; April, 2012.
• [60]Troyer D: Biorepository standards and protocols for collecting, processing, and storing human tissues. In Tissue Proteomics: Pathways, Biomarkers, and Drug Discovery. Edited by Liu BCS, Ehrlich JR. Humana Press, New Jersey; 2008:193-220.
• [61]Kilpatrick CW: Noncryogenic preservation of mammalian tissues for DNA extraction: an assessment of storage methods. Biochem Genet 2002, 40:53-62.
• [62]Mutter GL, Zahrieh D, Liu C, Neuberg D, Finkelstein D, Baker HE, Warrington JA: Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 2004., 5 BioMed Central Full Text
• [63]Edwards SV, Birks S, Brumfield RT, Hanner R: Future of avian genetic resources collections: archives of evolutionary and environmental history. Auk 2005, 122:979-984.
• [64]Biomatrica: [http://www.biomatrica.com/dnagardtissue.php] webciteDNAgard Tissues and Cells. Biomatrica, San Diego; April, 2012.
• [65]Biomatrica: [http://www.biomatrica.com/dnagardblood.php] webciteDNAgard Blood. Biomatrica, San Diego; April, 2012.
• [66]Biomatrica: [http://www.biomatrica.com/dnastable.php] webciteDNAstable®/DNAstable® LD Overview. Biomatrica, San Diego; April, 2012.
• [67]Life Technologies: [http://www.invitrogen.com/site/us/en/home/brands/Product-Brand/rnalater.html] webciteRNAlater® Solutions. Life Technologies, Grand Island; April, 2012.
• [68]Qiagen: [http:/ / www.qiagen.com/ products/ rnastabilizationpurification/ rnalaterrnaprotectsystems/ rnalatertissueprotect.aspx] webciteRNAlater TissueProtect Tubes. Qiagen, Hilden; April, 2012.
• [69]Biodiversity Institute of Ontario: [http://www.barcodinglife.org] webciteBarcode of Life Data Systems. University of Guelph, Guelph; April, 2012.
• [70]Bentley A: Shipping and handling of natural history specimens in dangerous goods. Collection Forum 2007, 22:66-73.
• [71]Bentley A: New special provision for international shipping of natural history specimens. SPNHC Newsletter 2011, 25(1–2):9.
• [72]Canadian Centre for DNA Barcoding: [http://www.dnabarcoding.ca] webciteAdvancing Species Identification and Discovery. University of Guelph, Guelph; April, 2012.
• [73]Consortium for the Barcode of Life: [http://www.barcodeoflife.org/] webciteIdentifying Species with DNA Barcoding. Smithsonian Institution, Washington; April, 2012.
• [74]International Barcode of Life[http://ibol.org] webcite
• [75]i5K Insect and other Arthropods Genome Sequencing Initiative[http://arthropodgenomes.org/wiki/i5K] webcite