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Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 2010; 42:833-9. [DOI: 10.1038/ng.654] [Citation(s) in RCA: 1538] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
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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: 2097] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Kim PM, Lam HYK, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 2008; 18:1865-74. [PMID: 18842824 DOI: 10.1101/gr.081422.108] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Segmental duplications (SDs) are operationally defined as >1 kb stretches of duplicated DNA with high sequence identity. They arise from copy number variants (CNVs) fixed in the population. To investigate the formation of SDs and CNVs, we examine their large-scale patterns of co-occurrence with different repeats. Alu elements, a major class of genomic repeats, had previously been identified as prime drivers of SD formation. We also observe this association; however, we find that it sharply decreases for younger SDs. Continuing this trend, we find only weak associations of CNVs with Alus. Similarly, we find an association of SDs with processed pseudogenes, which is decreasing for younger SDs and absent entirely for CNVs. Next, we find that SDs are significantly co-localized with each other, resulting in a highly skewed "power-law" distribution and chromosomal hotspots. We also observe a significant association of CNVs with SDs, but find that an SD-mediated mechanism only accounts for some CNVs (<28%). Overall, our results imply that a shift in predominant formation mechanism occurred in recent history: approximately 40 million years ago, during the "Alu burst" in retrotransposition activity, non-allelic homologous recombination, first mediated by Alus and then the by newly formed CNVs themselves, was the main driver of genome rearrangements; however, its relative importance has decreased markedly since then, with proportionally more events now stemming from other repeats and from non-homologous end-joining. In addition to a coarse-grained analysis, we performed targeted sequencing of 67 CNVs and then analyzed a combined set of 270 CNVs (540 breakpoints) to verify our conclusions.
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Affiliation(s)
- Philip M Kim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Su YQ, Sugiura K, Woo Y, Wigglesworth K, Kamdar S, Affourtit J, Eppig JJ. Selective degradation of transcripts during meiotic maturation of mouse oocytes. Dev Biol 2006; 302:104-17. [PMID: 17022963 PMCID: PMC1847322 DOI: 10.1016/j.ydbio.2006.09.008] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 11/28/2022]
Abstract
There is massive destruction of transcripts during the maturation of mouse oocytes. The objective of this project was to identify and characterize the transcripts that are degraded versus those that are stable during the transcriptionally silent germinal vesicle (GV)-stage to metaphase II (MII)-stage transition using a microarray approach. A system for oocyte transcript amplification using both internal and 3'-poly(A) priming was utilized to minimize the impact of complex variations in transcript polyadenylation prevalent during this transition. Transcripts were identified and quantified using the Affymetrix Mouse Genome 430 v2.0 GeneChip. The significantly changed and stable transcripts were analyzed using Ingenuity Pathways Analysis and GenMAPP/MAPPFinder to characterize the biological themes underlying global changes in oocyte transcripts during maturation. It was concluded that the destruction of transcripts during the GV to MII transition is a selective rather than promiscuous process in mouse oocytes. In general, transcripts involved in processes that are associated with meiotic arrest at the GV-stage and the progression of oocyte maturation, such as oxidative phosphorylation, energy production, and protein synthesis and metabolism, were dramatically degraded. In contrast, transcripts encoding participants in signaling pathways essential for maintaining the unique characteristics of the MII-arrested oocyte, such as those involved in protein kinase pathways, were the most prominent among the stable transcripts.
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Affiliation(s)
- You-Qiang Su
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
| | - Koji Sugiura
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
| | - Yong Woo
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
- Functional Genomics Program, The University of Maine, Orono, ME 04469, United States
| | - Karen Wigglesworth
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
| | - Sonya Kamdar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
| | - Jason Affourtit
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
| | - John J. Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 United States
- *Corresponding author: Fax: 1 207 288 6073, E-mail address:
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Affourtit J, Zehr J, Paerl H. Distribution of Nitrogen-Fixing Microorganisms along the Neuse River Estuary, North Carolina. Microb Ecol 2001; 41:114-123. [PMID: 12032616 DOI: 10.1007/s002480000090] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2000] [Accepted: 10/06/2000] [Indexed: 05/23/2023]
Abstract
Nitrogen fixation genes (nifH) were amplified and sequenced from DNA extracted from surface water samples collected from six stations along the length of the Neuse River Estuary, North Carolina, in order to determine the distribution of nitrogen-fixing organisms in the transition from fresh- to saltwater. Nitrogenase genes were detected in all samples by a nested polymerase chain reaction method, and the amplification products from the upriver, midriver, and downriver stations were cloned, sequenced, and used for phylogenetic analysis. The composition of nifH clone libraries from upriver, midriver, and downriver stations (each composed of 14 randomly selected clones) were very diverse (samples from upriver and midriver stations were composed of 14 unique sequences, downriver station composed of 7 unique sequences) and differed among the stations. Some phylotypes were found at more than one station, but were usually found in the upriver and midriver stations or in the midriver and downriver stations, indicating that the phylotypes were probably transported along the river. Cyanobacterial nifH were not found at the most upriver site, but were a large fraction of sequences (50%) recovered from the downriver station, where nitrate concentration was an order of magnitude lower and salinity was higher. In contrast, g proteobacteria nifH sequences were much more common at the midriver and upriver sites (58% and 64%, respectively), compared to the downriver site (14%). Results indicate that substantially different nitrogen-fixing assemblages are present along the river, reflecting differential watershed hydrological inputs, sedimentation, and environmental selection pressures, along the salinity gradient.
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Affiliation(s)
- J. Affourtit
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA
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