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Open Access Research article

Genome mapping and characterization of the Anopheles gambiae heterochromatin

Maria V Sharakhova1, Phillip George1, Irina V Brusentsova2, Scotland C Leman3, Jeffrey A Bailey4, Christopher D Smith56 and Igor V Sharakhov1*

Author Affiliations

1 Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA

2 Department of Molecular and Cellular Biology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia

3 Department of Statistics, Virginia Tech, Blacksburg, VA 24061, USA

4 Program in Bioinformatics and Integrative Biology and Department of Medicine, Division of Transfusion Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA

5 Department of Biology, San Francisco State University, San Francisco, CA 94132, USA

6 Drosophila Heterochromatin Genome Project, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA

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BMC Genomics 2010, 11:459  doi:10.1186/1471-2164-11-459

Published: 4 August 2010

Abstract

Background

Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized.

Results

To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin.

Conclusions

Our results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.