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Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Neil F Lobo1*, Djibril M Sangaré12, Allison A Regier3, Kyanne R Reidenbach1, David A Bretz1, Maria V Sharakhova15, Scott J Emrich3, Sekou F Traore2, Carlo Costantini4, Nora J Besansky1 and Frank H Collins13

Author Affiliations

1 Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA

2 Malaria Research and Training Center (MRTC), Bamako, Mali

3 Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA

4 Institut de Recherche pour le Développement, Unité de Recherche R016, Montpellier, France; and Organisation de Coordination pour la Lutte contre les Endémies en Afrique Centrale, Yaounde, Cameroon

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

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Malaria Journal 2010, 9:293  doi:10.1186/1475-2875-9-293

Published: 25 October 2010



Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies.


Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon.


The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations.


The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.