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Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

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Abstract

Background

Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly.

Results

WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm.

Conclusions

Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.

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Acknowledgements

We thank Sima Misra and Casey Bergman for helpful discussions; Andrew Skora, Christopher Yan, and David Acevedo for assistance with FISH experiments; Robert Svirskas, John Tupy, Pavel Hradecky, Colin Wiel, Bruno Ribeiro, Marcelo Alvim and Maria Vibranovski for assistance with informatics; Erwin Frise, Eric Smith and Dave Hurley for computer systems support; and Catherine Nelson for editing the manuscript. This work was supported by Celera Genomics, the Howard Hughes Medical Institute, NSF grant MCB0213163 to B.T.W., fellowships from the CNPq and the Pew Latin American Fellows Program to A.B.C., NIH grant R01 HG00747 to G.H.K. and NIH grant P50 HG00750 to G.M.R. The work supported by P50-HG00750 was carried out under Department of Energy Contract DE-AC0376SF00098, University of California.

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Authors and Affiliations

  1. Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Roger A Hoskins, Joseph W Carlson, Susan E Celniker & Gerald M Rubin

  2. Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA

    Christopher D Smith, Joshua S Kaminker & Gerald M Rubin

  3. Departamento de Genética, Universidade Federal do Rio de Janeiro, CEP 21944-970, Rio de Janeiro, Brazil

    A Bernardo Carvalho

  4. Celera Genomics, 45 West Gude Drive, Rockville, MD, 20850, USA

    Aaron Halpern, Granger G Sutton & Eugene W Myers

  5. Molecular and Cell Biology Laboratory, Salk Institute, La Jolla, CA, 92037, USA

    Cameron Kennedy, Beth A Sullivan & Gary H Karpen

  6. Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA

    Chris J Mungall & Gerald M Rubin

  7. Department of Zoology, University of Washington, Seattle, WA, 98195, USA

    Jiro C Yasuhara & Barbara T Wakimoto

  8. These authors contributed equally to this work, USA

    Roger A Hoskins & Christopher D Smith

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  1. Roger A Hoskins
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  2. Christopher D Smith
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Correspondence to Roger A Hoskins.

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Hoskins, R.A., Smith, C.D., Carlson, J.W. et al. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol 3, research0085.1 (2002). https://doi.org/10.1186/gb-2002-3-12-research0085

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