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Cummings MP, Temple GG. Broader incorporation of bioinformatics in education: opportunities and challenges. Brief Bioinform 2010; 11:537-43. [PMID: 20798182 DOI: 10.1093/bib/bbq058] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula; inherent fit of bioinformatics for promoting student learning in most biology programs; and the general experience and associated comfort students have with computers and technology. Conversely, the major challenges for broader incorporation of bioinformatics in education can be placed into three general categories: required infrastructure and logistics; instructor knowledge of bioinformatics and continuing education; and the breadth of bioinformatics, and the diversity of students and educational objectives. Broader incorporation of bioinformatics at all education levels requires overcoming the challenges to using transformative computer-requiring learning activities, assisting faculty in collecting assessment data on mastery of student learning outcomes, as well as creating more faculty development opportunities that span diverse skill levels, with an emphasis placed on providing resource materials that are kept up-to-date as the field and tools change.
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Affiliation(s)
- Michael P Cummings
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, University of Maryland, College Park, MD 20742, USA.
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153
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Abstract
Humans possess unique physical and cognitive characteristics relative to other primates. Comparative analyses of the human and chimpanzee genomes are beginning to reveal sequence changes on the human lineage that may have contributed to the evolution of human traits. However, these studies cannot identify the genetic differences that distinguish modern humans from archaic human species. Here, I will discuss efforts to obtain genomic sequence from Neanderthal, the closest known relative of modern humans. Recent studies in this nascent field have focused on developing methods to recover nuclear DNA from Neanderthal remains. The success of these early studies has inspired a Neanderthal genome project, which promises to produce a reference Neanderthal genome sequence in the near future. Technical issues, such as the level of Neanderthal sequence coverage that can realistically be obtained from a single specimen and the presence of modern human contaminating sequences, reduce the detection of authentic human-Neanderthal sequence differences but may be remedied by methodological improvements. More critical for the utility of a Neanderthal genome sequence is the evolutionary relationship of humans and Neanderthals. Current evidence suggests that the modern human and Neanderthal lineages diverged before the emergence of contemporary humans. A fraction of biologically relevant human-chimpanzee sequence differences are thus likely to have arisen and become fixed exclusively on the modern human lineage. A reconstructed Neanderthal genome sequence could be integrated into human-primate genome comparisons to help reveal the evolutionary genetic events that produced modern humans.
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Affiliation(s)
- James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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154
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Knapp M, Hofreiter M. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives. Genes (Basel) 2010; 1:227-43. [PMID: 24710043 PMCID: PMC3954087 DOI: 10.3390/genes1020227] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/24/2022] Open
Abstract
The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.
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Affiliation(s)
- Michael Knapp
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy and Structural Biology, University of Otago, 270 Great King Street, 9016 Dunedin, New Zealand.
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, YO10 5DD, York, UK.
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155
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Shapiro B, Hofreiter M. Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained. Bioessays 2010; 32:388-91. [PMID: 20414896 DOI: 10.1002/bies.201000026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000-year-old human from the Saqqaq culture of Greenland was determined to 20-fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large-scale genome-wide analysis of ancient human diversity a reality, providing a fresh look at human population history.
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Affiliation(s)
- Beth Shapiro
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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156
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Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res 2010; 38:e161. [PMID: 20587499 PMCID: PMC2938203 DOI: 10.1093/nar/gkq572] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought.
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Affiliation(s)
- Patricia Heyn
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.
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157
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Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 2010; 328:723-5. [PMID: 20448179 DOI: 10.1126/science.1188046] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.
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Affiliation(s)
- Hernán A Burbano
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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158
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Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science 2010; 328:710-722. [PMID: 20448178 PMCID: PMC5100745 DOI: 10.1126/science.1188021] [Citation(s) in RCA: 2151] [Impact Index Per Article: 153.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
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Affiliation(s)
- Richard E. Green
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Johannes Krause
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Adrian W. Briggs
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Udo Stenzel
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Martin Kircher
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Weiwei Zhai
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nancy F. Hansen
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Y. Durand
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tomas Marques-Bonet
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Can Alkan
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hernán A. Burbano
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jeffrey M. Good
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rigo Schultz
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höber
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höffner
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Madlen Siegemund
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathaniel Novod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Christine Verna
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Pavao Rudan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Dejana Brajkovic
- Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, Ante Kovacica 5, HR-10000 Zagreb, Croatia
| | - Željko Kucan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Ivan Gušic
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Javier Fortea
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Ralf W. Schmitz
- Der Landschaftverband Rheinlund–Landesmuseum Bonn, Bachstrasse 5-9, D-53115 Bonn, Germany
- Abteilung für Vor- und Frühgeschichtliche Archäologie, Universität Bonn, Germany
| | | | - Evan E. Eichler
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Falush
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Ewan Birney
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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159
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Computational challenges in the analysis of ancient DNA. Genome Biol 2010; 11:R47. [PMID: 20441577 PMCID: PMC2898072 DOI: 10.1186/gb-2010-11-5-r47] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/05/2010] [Accepted: 05/06/2010] [Indexed: 11/28/2022] Open
Abstract
A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples. High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
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160
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Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nat Genet 2010; 42:536-40. [DOI: 10.1038/ng.574] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 03/31/2010] [Indexed: 11/08/2022]
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161
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Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens). Genetica 2010; 138:745-56. [PMID: 20386959 DOI: 10.1007/s10709-010-9455-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 03/30/2010] [Indexed: 10/19/2022]
Abstract
Modern pyrosequencing has the potential to uncover many interesting aspects of genome evolution, even in lineages where genomic resources are scarce. In particular, 454 pyrosequencing of nonmodel species has been used to characterize expressed sequence tags, xenobiotics, gene ontologies, and relative levels of gene expression. Herein, we use pyrosequencing to study the evolution of genes expressed in the gonads of a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454 pyrosequencing of transcribed genes, we produced more than 125 MB of sequence data from 473,577 high-quality sequencing reads. Sequences that passed stringent quality control thresholds were assembled into 12,791 male contigs and 32,629 female contigs. Average depth of coverage was 4.2 x for the male assembly and 5.5x for the female assembly. Analytical rarefaction indicates that our assemblies include most of the genes expressed in lake sturgeon gonads. Over 86,700 sequencing reads were assigned gene ontologies, many to general housekeeping genes like protein, RNA, and ion binding genes. We searched specifically for sex determining genes and documented significant sex differences in the expression of two genes involved in animal sex determination, DMRT1 and TRA-1. DMRT1 is the master sex determining gene in birds and in medaka (Oryzias latipes) whereas TRA-1 helps direct sexual differentiation in nematodes. We also searched the lake sturgeon assembly for evidence of xenobiotic organisms that may exist as endosymbionts. Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome.
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162
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163
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Brown TA. Human evolution: Stranger from Siberia. Nature 2010:nature09006. [PMID: 20336067 DOI: 10.1038/nature09006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Terence A Brown
- Terence A. Brown is in the Faculty of Life Sciences and the Manchester Interdisciplinary Biocentre, University of Manchester,Manchester M17DN, UK.
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164
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Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TVO, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010; 463:757-62. [PMID: 20148029 DOI: 10.1038/nature08835] [Citation(s) in RCA: 461] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 01/18/2010] [Indexed: 12/29/2022]
Abstract
We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
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Affiliation(s)
- Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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165
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Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, Olsen ME, Bengtsson C, Miller GH, Schwenninger JL, Jacomb C, Walter R, Baynes A, Dortch J, Parker-Pearson M, Gilbert MTP, Holdaway RN, Willerslev E, Bunce M. Fossil avian eggshell preserves ancient DNA. Proc Biol Sci 2010; 277:1991-2000. [PMID: 20219731 DOI: 10.1098/rspb.2009.2019] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.
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Affiliation(s)
- Charlotte L Oskam
- Ancient DNA Laboratory, School of Biological Sciences, Murdoch University, Perth, Western Australia, Australia
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166
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RENAUT SÉBASTIEN, NOLTE ARNEW, BERNATCHEZ LOUIS. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae). Mol Ecol 2010; 19 Suppl 1:115-31. [DOI: 10.1111/j.1365-294x.2009.04477.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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167
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Edwards CJ, Magee DA, Park SDE, McGettigan PA, Lohan AJ, Murphy A, Finlay EK, Shapiro B, Chamberlain AT, Richards MB, Bradley DG, Loftus BJ, MacHugh DE. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). PLoS One 2010; 5:e9255. [PMID: 20174668 PMCID: PMC2822870 DOI: 10.1371/journal.pone.0009255] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 01/29/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
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Affiliation(s)
| | - David A. Magee
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Stephen D. E. Park
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Paul A. McGettigan
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Amanda J. Lohan
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Murphy
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Emma K. Finlay
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Beth Shapiro
- Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom
| | | | - Martin B. Richards
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Brendan J. Loftus
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- * E-mail:
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Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 2009; 10:677-83. [PMID: 21565072 DOI: 10.1111/j.1755-0998.2009.02824.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.
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Affiliation(s)
- Nadin Rohland
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA Department of Biology, University of York, YO10 5YW, York, UK
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170
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McKnight DA, Fisher LW. Molecular evolution of dentin phosphoprotein among toothed and toothless animals. BMC Evol Biol 2009; 9:299. [PMID: 20030824 PMCID: PMC2803795 DOI: 10.1186/1471-2148-9-299] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 12/23/2009] [Indexed: 12/22/2022] Open
Abstract
Background Dentin sialophosphoprotein (DSPP) is the largest member of the SIBLING family and is the most abundant noncollagenous protein in dentin. DSPP is also expressed in non-mineralized tissues including metabolically active ductal epithelia and some cancers. Its function, however, is poorly defined. The carboxy-terminal fragment, dentin phosphoprotein (DPP) is encoded predominantly by a large repetitive domain that requires separate cloning/sequencing reactions and is, therefore, often incomplete in genomic databases. Comparison of DPP sequences from at least one member of each major branch in the mammalian evolutionary tree (including some "toothless" mammals) as well as one reptile and bird may help delineate its possible functions in both dentin and ductal epithelia. Results The BMP1-cleavage and translation-termination domains were sufficiently conserved to permit amplification/cloning/sequencing of most species' DPP. While the integrin-binding domain, RGD, was present in about half of species, only vestigial remnants of this tripeptide were identified in the others. The number of tandem repeats of the nominal SerSerAsp phosphorylation motif in toothed mammals (including baleen whale and platypus which lack teeth as adults), ranged from ~75 (elephant) to >230 (human). These repeats were not perfect, however, and patterns of intervening sequences highlight the rapidity of changes among even closely related species. Two toothless anteater species have evolved different sets of nonsense mutations shortly after their BMP1 motifs suggesting that while cleavage may be important for DSPP processing in other tissues, the DPP domain itself may be required only in dentin. The lizard DSPP had an intact BMP1 site, a remnant RGD motif, as well as a distinctly different Ser/Asp-rich domain compared to mammals. Conclusions The DPP domain of DSPP was found to change dramatically within mammals and was lost in two truly toothless animals. The defining aspect of DPP, the long repeating phosphorylation domain, apparently undergoes frequent slip replication and recombination events that rapidly change specific patterns but not its overall biochemical character in toothed animals. Species may have to co-evolve protein processing mechanisms, however, to handle increased lengths of DSP repeats. While the RGD domain is lost in many species, some evolutionary pressure to maintain integrin binding can be observed.
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Affiliation(s)
- Dianalee A McKnight
- Craniofacial and Skeletal Diseases Branch, NIDCR, NIH, DHHS, Bethesda MD 20892, USA. -
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171
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Buckley M, Collins M, Thomas-Oates J, Wilson JC. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3843-54. [PMID: 19899187 DOI: 10.1002/rcm.4316] [Citation(s) in RCA: 213] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Species identification of fragmentary bone, such as in rendered meat and bone meal or from archaeological sites, is often difficult in the absence of clear morphological markers. Here we present a robust method of analysing genus-specific collagen peptides by mass spectrometry simply by using solid-phase extraction (a C18 ZipTip) for peptide purification, rather than liquid chromatography/mass spectrometry (LC/MS). Analysis of the collagen from 32 different mammal species identified a total of 92 peptide markers that could be used for species identification, for example, in processed food and animal feed. A set of ancient (>100 ka@10 degrees C) bone samples was also analysed to show that the proposed method has applications to archaeological bone identification.
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Affiliation(s)
- Michael Buckley
- Department of Biology, University of York, Heslington, York YO10 5YW, UK.
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172
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Brenig B, Beck J, Schütz E. Shotgun metagenomics of biological stains using ultra-deep DNA sequencing. Forensic Sci Int Genet 2009; 4:228-31. [PMID: 20457050 DOI: 10.1016/j.fsigen.2009.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 09/30/2009] [Accepted: 10/02/2009] [Indexed: 01/06/2023]
Abstract
A detailed molecular analysis of blood or other biological stains at a crime scene is often hampered by the low quantity and quality of the extractable DNA. However, the determination of the origin and composition of a stain is in most cases a prerequisite for the final elucidation of a criminal case. Standard methodologies, e.g. amplification of DNA followed by microsatellite typing or mitochondrial DNA sequencing, are often not sensitive enough to result in sufficient and conclusive data. We have applied ultra-deep DNA sequencing using the 454 pyrosequencing technology on a whole genome amplified (WGA) environmental biological stain, which was analysed unsuccessfully with standard methodologies following WGA. With the combination of WGA and 454 pyrosequencing, however, we were able to generate 7242 single sequences with an average length of 195bp. A total of 1,441,971bp DNA sequences were generated and compared with public DNA sequence databases. Using RepeatMasker and basic logical alignment search tool (BLAST) searches against known microbial and mammalian genomes it was possible to determine the metagenomic composition of the stain, i.e. 4.2% bacterial DNA, 0.3% viral DNA, 2.7% fungal DNA, 10.3% mammalian repetitive DNA, 0.9% porcine DNA, 0.13% human DNA and 81.5% DNA of unknown origin. Our data demonstrate that 454 pyrosequencing has the potential to become a powerful tool not only in basic research but also in the metagenomic analysis of biological trace materials for forensic genetics.
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Affiliation(s)
- B Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
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173
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Ray DA, Platt RN, Batzer MA. Reading between the LINEs to see into the past. Trends Genet 2009; 25:475-9. [PMID: 19837475 DOI: 10.1016/j.tig.2009.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are an important source of genome diversity and play a crucial role in genome evolution. A recent study by Zhao et al. describes novel patterns of TE diversification in the genome of the extinct mammoth Mammuthus primigenius. Analysis of Mammuthus has provided a unique genome landscape, a pivotal species for understanding TEs and genome evolution and hints at the diversity we verge on discovering by expanding our taxonomic sampling among genomes. Strategies based on this work might also revolutionize investigations of the interface between TE dynamics and genome diversity.
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Affiliation(s)
- David A Ray
- Department of Biochemistry and Molecular Biology, Box 9650, Mississippi State University, Mississippi State, MS 39762, USA
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174
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Podlaha O, Zhang J. Processed pseudogenes: the 'fossilized footprints' of past gene expression. Trends Genet 2009; 25:429-34. [PMID: 19796837 DOI: 10.1016/j.tig.2009.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/01/2009] [Accepted: 09/04/2009] [Indexed: 11/30/2022]
Abstract
Although our knowledge of the genes and genomes of extinct organisms is improving as a result of progress in sequencing ancient DNA, the transcriptomes of extinct organisms remain inaccessible, owing to the rapid degradation of messenger RNA after death. We provide empirical evidence that gene expression levels in the reproductive tissues of mice and during early mouse development correlate highly with the rate of inherited retroposition: the source of processed pseudogenes in the genome. Thus, processed pseudogenes might serve as fossilized footprints of the expression of their parent genes, shedding light on ancient transcriptomes that could provide significant insights into the evolution of gene expression.
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Affiliation(s)
- Ondrej Podlaha
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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175
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Ho SYW, Gilbert MTP. Ancient mitogenomics. Mitochondrion 2009; 10:1-11. [PMID: 19788938 DOI: 10.1016/j.mito.2009.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.
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Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT 0200, Australia.
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176
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Abstract
Developmental biology, regenerative medicine and cancer biology are increasingly occupied with the molecular characterization of stem cells. Yet recent work adds to a growing body of literature suggesting that 'stemness' cannot be reduced to the molecular features of cell types, and is instead an emergent property of cell lineages under feedback control.
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Affiliation(s)
- Arthur D Lander
- Center for Complex Biological Systems, Department of Developmental and Cell Biology, and Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92697-2300, USA.
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177
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Jakobsson M. COMPASS: a program for generating serial samples under an infinite sites model. Bioinformatics 2009; 25:2845-7. [PMID: 19762347 DOI: 10.1093/bioinformatics/btp534] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The program COMPASS can generate samples that have been collected at various points in time from a population that is evolving according to a Wright-Fisher model. The samples are generated using coalescence simulations permitting various demographic scenarios and the program uses an infinite sites model to generate polymorphism data for the samples. By generating serially sampled population-genetic data, COMPASS allows investigating properties of polymorphism data that has been collected at different time points, and aid in making inference from ancient polymorphism data. AVAILABILITY The program and the manual are available at: http://www.egs.uu.se/evbiol/Research/JakobssonLab/compass.html CONTACT mattias.jakobsson@ebc.uu.se.
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Affiliation(s)
- Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
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178
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Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD. Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. BMC Evol Biol 2009; 9:232. [PMID: 19747392 PMCID: PMC2754481 DOI: 10.1186/1471-2148-9-232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 09/11/2009] [Indexed: 11/17/2022] Open
Abstract
Background Like humans, the living elephants are unusual among mammals in being sparsely covered with hair. Relative to extant elephants, the extinct woolly mammoth, Mammuthus primigenius, had a dense hair cover and extremely long hair, which likely were adaptations to its subarctic habitat. The fibroblast growth factor 5 (FGF5) gene affects hair length in a diverse set of mammalian species. Mutations in FGF5 lead to recessive long hair phenotypes in mice, dogs, and cats; and the gene has been implicated in hair length variation in rabbits. Thus, FGF5 represents a leading candidate gene for the phenotypic differences in hair length notable between extant elephants and the woolly mammoth. We therefore sequenced the three exons (except for the 3' UTR) and a portion of the promoter of FGF5 from the living elephantid species (Asian, African savanna and African forest elephants) and, using protocols for ancient DNA, from a woolly mammoth. Results Between the extant elephants and the mammoth, two single base substitutions were observed in FGF5, neither of which alters the amino acid sequence. Modeling of the protein structure suggests that the elephantid proteins fold similarly to the human FGF5 protein. Bioinformatics analyses and DNA sequencing of another locus that has been implicated in hair cover in humans, type I hair keratin pseudogene (KRTHAP1), also yielded negative results. Interestingly, KRTHAP1 is a pseudogene in elephantids as in humans (although fully functional in non-human primates). Conclusion The data suggest that the coding sequence of the FGF5 gene is not the critical determinant of hair length differences among elephantids. The results are discussed in the context of hairlessness among mammals and in terms of the potential impact of large body size, subarctic conditions, and an aquatic ancestor on hair cover in the Proboscidea.
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Affiliation(s)
- Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Piña-Aguilar RE, Lopez-Saucedo J, Sheffield R, Ruiz-Galaz LI, de J. Barroso-Padilla J, Gutiérrez-Gutiérrez A. Revival of Extinct Species Using Nuclear Transfer: Hope for the Mammoth, True for the Pyrenean Ibex, But Is It Time for “Conservation Cloning”? CLONING AND STEM CELLS 2009; 11:341-6. [DOI: 10.1089/clo.2009.0026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Raul E. Piña-Aguilar
- Instituto de Ciencias en Reproducción Humana, León, México
- Facultad de Medicina, Universidad Autónoma de Yucatán, Mérida, México
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Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S. The Neandertal genome and ancient DNA authenticity. EMBO J 2009; 28:2494-502. [PMID: 19661919 PMCID: PMC2725275 DOI: 10.1038/emboj.2009.222] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 07/10/2009] [Indexed: 01/08/2023] Open
Abstract
Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar ‘boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.
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Affiliation(s)
- Richard E Green
- Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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181
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Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res 2009; 19:1843-8. [PMID: 19635845 DOI: 10.1101/gr.095760.109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although the emergence of high-throughput sequencing technologies has enabled whole-genome sequencing from extinct organisms, little progress has been made in accelerating targeted sequencing from highly degraded DNA. Here, we present a novel and highly sensitive method for targeted sequencing of ancient and degraded DNA, which couples multiplex PCR directly with sample barcoding and high-throughput sequencing. Using this approach, we obtained a 96% complete mitochondrial genome data set from 31 cave bear (Ursus spelaeus) samples using only two 454 Life Sciences (Roche) GS FLX runs. In contrast to previous studies relying only on short sequence fragments, the overlapping portion of our data comprises almost 10 kb of replicated mitochondrial genome sequence, allowing for the unambiguous differentiation of three major cave bear clades. Our method opens up the opportunity to simultaneously generate many kilobases of overlapping sequence data from large sets of difficult samples, such as museum specimens, medical collections, or forensic samples. Embedded in our approach, we present a new protocol for the construction of barcoded sequencing libraries, which is compatible with all current high-throughput technologies and can be performed entirely in plate setup.
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Affiliation(s)
- Mathias Stiller
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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183
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Zhao F, Qi J, Schuster SC. Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. Genome Res 2009; 19:1384-92. [PMID: 19508981 DOI: 10.1101/gr.091363.109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial and nuclear genomes of this extinct species. Mammoths belong to Afrotheria, a group of mammals exhibiting extreme morphological diversity and large genome sizes. In this study, we found that the mammoth genome contains a larger proportion of interspersed repeats than any other mammalian genome reported so far, in which the proliferation of the RTE family of retrotransposons (covering 12% of the genome) may be the main reason for an increased genome size. Phylogenetic analysis showed that RTEs in mammoth are closely related to the family BovB/RTE. The incongruence of the reconstructed RTE phylogeny indicates that RTEs in mammoth may be acquired through an ancient lateral gene transfer event. A recent proliferation of SINEs was also found in the probocidean lineage, whereas the Afrotherian-wide SINEs in mammoth have undergone a rather flat and stepwise expansion. Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages.
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Affiliation(s)
- Fangqing Zhao
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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184
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Ramírez O, Gigli E, Bover P, Alcover JA, Bertranpetit J, Castresana J, Lalueza-Fox C. Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. PLoS One 2009; 4:e5670. [PMID: 19461892 PMCID: PMC2680946 DOI: 10.1371/journal.pone.0005670] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 04/24/2009] [Indexed: 11/19/2022] Open
Abstract
Background Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. Methodology/Principals Findings A DNA extraction of a ∼6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous. Conclusions A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.
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Affiliation(s)
- Oscar Ramírez
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Elena Gigli
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Pere Bover
- Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Esporles, Mallorca, Spain
| | | | | | - Jose Castresana
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
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185
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Turner DJ, Keane TM, Sudbery I, Adams DJ. Next-generation sequencing of vertebrate experimental organisms. Mamm Genome 2009; 20:327-38. [PMID: 19452216 PMCID: PMC2714443 DOI: 10.1007/s00335-009-9187-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 04/21/2009] [Indexed: 12/22/2022]
Abstract
Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. While it is currently not possible to generate complete de novo assemblies of higher-vertebrate genomes using next-generation sequencing, improvements in sequence read lengths and throughput, coupled with new assembly algorithms for large data sets, will soon make this a reality. These developments will in turn spawn a revolution in how genomic data are used to understand genetics and how model organisms are used for disease gene discovery. This review provides an overview of the current next-generation sequencing platforms and the newest computational tools for the analysis of next-generation sequencing data. We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics.
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Affiliation(s)
- Daniel J Turner
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
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Willerslev E, Gilbert MTP, Binladen J, Ho SYW, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol 2009; 9:95. [PMID: 19432984 PMCID: PMC2694787 DOI: 10.1186/1471-2148-9-95] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 05/11/2009] [Indexed: 12/03/2022] Open
Abstract
Background The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. Results In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. Conclusion Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies. "The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945)
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Affiliation(s)
- Eske Willerslev
- Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100, Denmark.
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Morrison McKay BJ, Sansom C. Webb Miller and Trey Ideker to receive top international bioinformatics awards for 2009 from the International Society for Computational Biology. PLoS Comput Biol 2009; 5:e1000375. [PMID: 19390599 PMCID: PMC2666155 DOI: 10.1371/journal.pcbi.1000375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- B J Morrison McKay
- International Society for Computational Biology, University of California San Diego, La Jolla, California, USA.
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Ramakrishnan U, Hadly EA. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol Ecol 2009; 18:1310-30. [PMID: 19281471 DOI: 10.1111/j.1365-294x.2009.04092.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
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Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MTP, Dalén L, Arsuaga JL, Ericson PGP, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res 2009; 19:213-20. [PMID: 19139089 DOI: 10.1101/gr.082628.108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.
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Affiliation(s)
- Webb Miller
- Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA.
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Hoshino Y, Hayashi N, Taniguchi S, Kobayashi N, Sakai K, Otani T, Iritani A, Saeki K. Resurrection of a bull by cloning from organs frozen without cryoprotectant in a -80 degrees c freezer for a decade. PLoS One 2009; 4:e4142. [PMID: 19129919 PMCID: PMC2613553 DOI: 10.1371/journal.pone.0004142] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 12/01/2008] [Indexed: 11/26/2022] Open
Abstract
Frozen animal tissues without cryoprotectant have been thought to be inappropriate for use as a nuclear donor for somatic cell nuclear transfer (SCNT). We report the cloning of a bull using cells retrieved from testicles that had been taken from a dead animal and frozen without cryoprotectant in a −80°C freezer for 10 years. We obtained live cells from defrosted pieces of the spermatic cords of frozen testicles. The cells proliferated actively in culture and were apparently normal. We transferred 16 SCNT embryos from these cells into 16 synchronized recipient animals. We obtained five pregnancies and four cloned calves developed to term. Our results indicate that complete genome sets are maintained in mammalian organs even after long-term frozen-storage without cryoprotectant, and that live clones can be produced from the recovered cells.
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Affiliation(s)
- Yoichiro Hoshino
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
| | - Noboru Hayashi
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
| | - Shunji Taniguchi
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
| | - Naohiko Kobayashi
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
| | - Kenji Sakai
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
| | - Tsuyoshi Otani
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
| | - Akira Iritani
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
| | - Kazuhiro Saeki
- Department of Genetic Engineering, Kinki University, Kinokawa Wakayama, Japan
- Wakayama Industry Promotion Foundation, Wakayama, Japan
- * E-mail:
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