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Genome of Drosophila suzukii, the Spotted Wing Drosophila

Joanna C. Chiu, Xuanting Jiang, Li Zhao, Christopher A. Hamm, Julie M. Cridland, Perot Saelao, Kelly A. Hamby, Ernest K. Lee, Rosanna S. Kwok, Guojie Zhang, Frank G. Zalom, Vaughn M. Walton and David J. Begun
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2257-2271; https://doi.org/10.1534/g3.113.008185
Joanna C. Chiu
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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  • For correspondence: jcchiu@ucdavis.edu
Xuanting Jiang
China National Genebank, BGI-Shenzhen, 518083, China
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Li Zhao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Christopher A. Hamm
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Julie M. Cridland
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Perot Saelao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Kelly A. Hamby
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Ernest K. Lee
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024
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Rosanna S. Kwok
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Guojie Zhang
China National Genebank, BGI-Shenzhen, 518083, China
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Frank G. Zalom
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Vaughn M. Walton
Department of Horticulture, Oregon State University, Corvallis, Oregon 97331
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David J. Begun
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Data supplements

  • Supporting Information for Chiu et al., 2013

    Files in this Data Supplement:

    • Supporting Information - Figures S1-S4 and Tables S1-S14 (PDF, 1 MB)
    • Figure S1 - 17-kmer estimation of genome size. (PDF, 412 KB)
    • Figure S2 - Synteny map between D. suzukii and D. melanogaster genomes. (PDF, 510 KB)
    • Figure S3 - Best-scoring maximum likelihood (ML) tree of 15 Drosophila species with outgroup A. gambiae (not shown) using 5,322 gene partitions with 5,199,249 sites. (PDF, 476 KB)
    • Figure S4 - (A) GC3 content for D. suzukii X and autosomal positions. (B) GC3 content for Drosophila suzukii male biased genes (left) and the overall D. suzukii GC3 content. (PDF, 447 KB)
    • Table S1 - Data production for Drosophila suzukii genome sequencing. (PDF, 516 KB)
    • Table S2 - Drosophila suzukii 17-k-mer statistics. (PDF, 516 KB)
    • Table S3 - Statistics of the assembled genome. (PDF, 408 KB)
    • Table S4 - A list of 25 genes in Drosophila suzukii with the highest non-synonymous (dN) substitution rates. (PDF, 522 KB)
    • Table S5 - A list of Drosophila suzukii genes with sex-biased expression pattern. (PDF, 756 KB)
    • Table S6 - A list of genes showing sex-biased shift in expression between Drosophila suzukii and Drosophila melanogaster. (PDF, 527 KB)
    • Table S7 - GO term and functional classification enrichment analysis using DAVID for gene families that are expanded in the Drosophila suzukii genome as compared to 14 Drosophila species analyzed in this study. (PDF, 536 KB)
    • Table S8 - GO term and functional classification enrichment analysis using DAVID for gene families that are expanded in the Drosophila suzukii genome as compared to the basal paraphyletic group of Drosophilidae including D. ananassae, D. persimilis, D. pseudoobscura, D. willistoni, D. grimshawi, D. mojavensis, and D. virulis. (PDF, 542 KB)
    • Table S9 - GO term and functional classification enrichment analysis using DAVID for gene families that are expanded in the Drosophila suzukii genome as compared to species in the melanogaster subgroup, including D. simulans, D. sechellia, D. yakuba, D. erecta, and D. melanogaster. (PDF, 532 KB)
    • Table S10 - GO term and functional classification enrichment analysis using DAVID for gene families that are contracted in the Drosophila suzukii genome as compared to 14 Drosophila species analyzed in this study. (PDF, 542 KB)
    • Table S11 - GO term and functional classification enrichment analysis using DAVID for gene families that are contracted in the Drosophila suzukii genome as compared to the basal paraphyletic group of Drosophilidae including D. ananassae, D. persimilis, D. pseudoobscura, D. willistoni, D. grimshawi, D. mojavensis, and D. virulis. (PDF, 538 KB)
    • Table S12 - GO term and functional classification enrichment analysis using DAVID for gene families that are contracted in the Drosophila suzukii genome as compared to species in the melanogaster subgroup, including D. simulans, D. sechellia, D. yakuba, D. erecta, and D. melanogaster. (PDF, 544 KB)
    • Table S13 - Gene families of enzymes involved in metabolism and transport of xenobiotics. (PDF, 411 KB)
    • Table S14 - Total base pairs of transposable element families. (PDF, 439 KB)
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Volume 3 Issue 12, December 2013

G3: Genes|Genomes|Genetics: 3 (12)

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Genome of Drosophila suzukii, the Spotted Wing Drosophila

Joanna C. Chiu, Xuanting Jiang, Li Zhao, Christopher A. Hamm, Julie M. Cridland, Perot Saelao, Kelly A. Hamby, Ernest K. Lee, Rosanna S. Kwok, Guojie Zhang, Frank G. Zalom, Vaughn M. Walton and David J. Begun
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2257-2271; https://doi.org/10.1534/g3.113.008185
Joanna C. Chiu
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: jcchiu@ucdavis.edu
Xuanting Jiang
China National Genebank, BGI-Shenzhen, 518083, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Li Zhao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher A. Hamm
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Julie M. Cridland
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Perot Saelao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Kelly A. Hamby
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Ernest K. Lee
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024
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Rosanna S. Kwok
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Guojie Zhang
China National Genebank, BGI-Shenzhen, 518083, China
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Frank G. Zalom
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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Vaughn M. Walton
Department of Horticulture, Oregon State University, Corvallis, Oregon 97331
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David J. Begun
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Citation

Genome of Drosophila suzukii, the Spotted Wing Drosophila

Joanna C. Chiu, Xuanting Jiang, Li Zhao, Christopher A. Hamm, Julie M. Cridland, Perot Saelao, Kelly A. Hamby, Ernest K. Lee, Rosanna S. Kwok, Guojie Zhang, Frank G. Zalom, Vaughn M. Walton and David J. Begun
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2257-2271; https://doi.org/10.1534/g3.113.008185
Joanna C. Chiu
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: jcchiu@ucdavis.edu
Xuanting Jiang
China National Genebank, BGI-Shenzhen, 518083, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Li Zhao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher A. Hamm
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Julie M. Cridland
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Perot Saelao
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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Kelly A. Hamby
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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  • Search for this author on this site
Ernest K. Lee
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024
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Rosanna S. Kwok
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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  • Find this author on PubMed
  • Search for this author on this site
Guojie Zhang
China National Genebank, BGI-Shenzhen, 518083, China
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Frank G. Zalom
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California 95616
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  • Search for this author on this site
Vaughn M. Walton
Department of Horticulture, Oregon State University, Corvallis, Oregon 97331
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David J. Begun
Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616
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  • Search for this author on this site

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