About the Authors
- Jonathan A Eisen
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*To whom correspondence should be addressed. E-mail: jaeisen@ucdavis.edu
Current address: University of California Davis Genome Center, Section of Evolution and Ecology, School of Biological Sciences and Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Robert S Coyne
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Martin Wu
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Dongying Wu
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Mathangi Thiagarajan
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Jennifer R Wortman
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Jonathan H Badger
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Qinghu Ren
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Paolo Amedeo
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Kristie M Jones
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Luke J Tallon
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Arthur L Delcher
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Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Steven L Salzberg
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Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Joana C Silva
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Brian J Haas
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Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- William H Majoros
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Current address: Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Maryam Farzad
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Current address: Agilent Technologies, Inc., Santa Clara, California, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Jane M Carlton
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Current address: Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Roger K Smith Jr.
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Current address: Dupont Agriculture and Nutrition, Wilmington, Delaware, United States of America
Affiliation The Institute for Genomic Research, Rockville, Maryland, United States of America
- Jyoti Garg
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Affiliation Department of Biology, York University, Toronto, Ontario, Canada
- Ronald E Pearlman
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Affiliations Department of Biology, York University, Toronto, Ontario, Canada , Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
- Kathleen M Karrer
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Affiliation Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
- Lei Sun
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Affiliation Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
- Gerard Manning
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Affiliation Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of America
- Nels C Elde
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Current address: Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
Affiliation Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
- Aaron P Turkewitz
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Affiliation Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
- David J Asai
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Affiliation Department of Biology, Harvey Mudd College, Claremont, California, United States of America
- David E Wilkes
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Affiliation Department of Biology, Harvey Mudd College, Claremont, California, United States of America
- Yufeng Wang
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Affiliation Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America
- Hong Cai
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Affiliation Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
- Kathleen Collins
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Affiliation Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
- B. Andrew Stewart
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Affiliation Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
- Suzanne R Lee
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Affiliation Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
- Katarzyna Wilamowska
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Affiliation Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
- Zasha Weinberg
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Current address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
Affiliation Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
- Walter L Ruzzo
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Affiliation Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
- Dorota Wloga
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Affiliation Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
- Jacek Gaertig
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Affiliation Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
- Joseph Frankel
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Affiliation Department of Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America
- Che-Chia Tsao
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Affiliation Department of Biology, University of Rochester, Rochester, New York, United States of America
- Martin A Gorovsky
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Affiliation Department of Biology, University of Rochester, Rochester, New York, United States of America
- Patrick J Keeling
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Affiliation Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Ross F Waller
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Current address: School of Botany, The University of Melbourne, Melbourne, Australia
Affiliation Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Nicola J Patron
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Current address: School of Botany, The University of Melbourne, Melbourne, Australia
Affiliation Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- J. Michael Cherry
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Affiliation Department of Genetics, Stanford University, Stanford, California, United States of America
- Nicholas A Stover
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Affiliation Department of Genetics, Stanford University, Stanford, California, United States of America
- Cynthia J Krieger
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Affiliation Department of Genetics, Stanford University, Stanford, California, United States of America
- Christina del Toro
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Current address: Meharry Medical College, Nashville, Tennessee, United States of America
Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Hilary F Ryder
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Current address: Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, United States of America
Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Sondra C Williamson
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Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Rebecca A Barbeau
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Current address: Lung Biology Center, University of California San Francisco, San Francisco, California, United States of America
Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Eileen P Hamilton
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Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Eduardo Orias
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Affiliation Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
Competing Interests
The authors have declared that no competing interests exist.
Author Contributions
JAE coordinated the project. JAE, RSC, EPH, and EO wrote and edited the majority of the manuscript. JAE, RSC, MW, DW, JHB, and MT performed multiple bioinformatics analyses. MT, JRW, PA, MF, RKS, and BJH coordinated the annotation. KMJ and LJT carried out genome closure. ALD and SLS generated and analyzed genome assemblies. JCS, KMK, and LS analyzed mobile DNA elements. WHM generated gene models. QR conducted analyses of membrane transporters. JMC, JG, and REP generated and analyzed ESTs. GM analyzed protein kinases. NCE and APT analyzed membrane trafficking. DJA and DEW analyzed dyneins. YW and HC analyzed proteases. KC, BAS, SRL, WLR, KW, and ZW analyzed ncRNA. DW, JG, MAG, JF, and CCT analyzed cytoskeletal associated proteins. PJK, RFW, NJP, and JHB searched for plastid-derived genes. JMC, NAS, and CJK built TGD. CdT, HFR, SCW, and RAB performed the RAPD analyses. EPH, EO, SLS, JAE, and MW examined genome structure.