Originally published as Genetics Published Articles Ahead of Print on July 13, 2008.

Genetics, Vol. 179, 1601-1655, July 2008, Copyright © 2008
doi:10.1534/genetics.107.086074

Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

Stephen W. Schaeffer^*,1, Arjun Bhutkar^,, Bryant F. McAllister, Muneo Matsuda^¶, Luciano M. Matzkin^&, Patrick M. O'Grady^**, Claudia Rohde, Vera L. S. Valente, Montserrat Aguadé, Wyatt W. Anderson^¶¶, Kevin Edwards^**, Ana C. L. Garcia, Josh Goodman^&&, James Hartigan^***, Eiko Kataoka^¶, Richard T. Lapoint, Elena R. Lozovsky, Carlos A. Machado^&, Mohamed A. F. Noor, Montserrat Papaceit, Laura K. Reed^&,2, Stephen Richards^¶¶¶, Tania T. Rieger^&&&, Susan M. Russo^,****, Hajime Sato^¶, Carmen Segarra, Douglas R. Smith^***, Temple F. Smith, Victor Strelets^&&, Yoshiko N. Tobari, Yoshihiko Tomimura, Marvin Wasserman, Thomas Watts^&, Robert Wilson^&&, Kiyohito Yoshida^¶¶¶¶, Therese A. Markow^&, William M. Gelbart^,**** and Thomas C. Kaufman^&&

^* Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania 16802, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, Department of Biological Sciences, University of Iowa, Iowa City, Iowa 52242, ^¶ School of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan, ^& Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, ^** Department of Environmental Sciences, Policy and Management, University of California, Berkeley, California 94720, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, CEP 55608-680, Vitória de Santo Antão/PE, Brazil, Departamento de Genética, Universidade Federal do Rio Grande do Sul, CEP 91501-970, Porto Alegre/RS, Brazil, Departament de Genètica, Universitat de Barcelona, 08028 Barcelona, Spain, ^¶¶ Department of Genetics, University of Georgia, Athens, Georgia 30602, ^&& Department of Biology, Indiana University, Bloomington, Indiana 47405, ^*** Agencourt Bioscience, Beverly, Massachusetts 01915, Department of Biological Sciences, Illinois State University, Normal, Illinois 61790, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Biology, Duke University, Durham, North Carolina 27708, ^¶¶¶ Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, ^&&& Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, CEP 50670-900, Recife/PE, Brazil ^**** FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, Institute of Evolutionary Biology, Setagaya-ku, Tokyo 158-0098, Japan, Shiba Gakuen, Minato-ku, Tokyo 105-0011, Japan, Department of Biology, CUNY-Queens, Flushing, New York 11367 and ^¶¶¶¶ Hokkaido University, EESBIO, Sapporo, Hokkaido 060-0810, Japan

¹ Corresponding author: Department of Biology, Pennsylvania State University, 208 Erwin W. Mueller Laboratories, University Park, PA 16802-5301.
E-mail: sws4{at}psu.edu

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.

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