High Rates of Genome Rearrangements in Malaria Mosquitoes, Anopheles gambiae and A. funestus

Monday, October 20, 2003 - 4:00pm - 4:20pm
Keller 3-180
Igor Sharakhov (University of Notre Dame)
The rates of chromosomal evolution vary among different genomic segments and eukaryotic lineages [1]. A comparative genomic study between Drosophila melanogaster and Anopheles gambiae shows extensive reshuffling of gene order within chromosomes [2]. Genus Drosophila has a very high rate of paracentric inversions [3]. Our study determines rates of chromosomal rearrangement in genus Anopheles. Anopheles gambiae and A. funestus, important vectors of malaria in tropical Africa, are in the same subgenus and diverged about as recently as humans and chimpanzees (~5 million years ago) [4]. Using fluorescence in situ hybridization (FISH), we mapped A. funestus cDNA clones on the five arms of the polytene chromosome complement. Of 157 cDNAs used as probes, 116 mapped to single chromosomal locations on the A. funestus cytogenetic map, and the remainder hybridized in multiple locations. Those 116 cDNAs were mapped in silico to the completely sequenced A. gambiae genome. The relative positions of sequences with unique map locations in both species support the hypothesized chromosome arm homologies and the reciprocal whole arm translocation between 2L and 3R, postulated previously on the basis of relative length and banding pattern [5]. Correspondence between chromosome arms was contradicted by only two of the cDNAs examined in this study. Within corresponding arms, paracentric inversions have had a major impact on genome architecture since the divergence of these species. Gene order has not been preserved along the length of any chromosome arm, although there are conserved segments in some regions near centromeres where the rate of meiotic recombination may be reduced. Inversions have involved large as well as relatively small chromosomal segments. One of three small inversions at the distal end of 2R includes a rearrangement involving the 8C region in A. gambiae that contains the major Plasmodium-refractoriness locus Pen1 [6]. What has been the extent of rearrangement of gene order between these species? The number of inversion events can be estimated by considering the mean length of conserved segments, because this length decreases with each inversion fixed since the divergence of A. gambiae and A. funestus from a common ancestor. The method of Nadeau and Taylor [7] was applied to estimate mean lengths of all conserved segments in the genome, based on the nucleotide distance in A. gambiae between the outermost markers that defined the segments observed in our sample. An assumption of the method, that rearrangements fixed during evolution are randomly distributed in the genome, seems unlikely given the extraordinary concentration of polymorphic inversions on 2R in both lineages. Of eight polymorphic inversions described in A. gambiae, seven occur on chromosome 2R [8]. Similarly, 11 of 15 polymorphic inversions found in A. funestus involve 2R [9]. Accordingly, we assessed each arm independently. The estimated mean lengths of all conserved segments on each arm, defined with respect to A. gambiae, were X, 2.0 ± 0.2 megabases (Mb); 2R, 0.9 ± 0.2 Mb; 2L, 2.2 ± 0.4 Mb; 3R, 2.2 ± 1.0 Mb; and 3L, 1.1 ± 0.4 Mb. In a slight departure from Nadeau and Taylor [7], each rearrangement was assumed to be an inversion requiring two disruption events. Therefore, n inversions result in 2n + 1 conserved segments. The number of inversions on each arm was 5 ± 1, 36 ± 9, 11 ± 3, 11 ± 3, and 19 ± 5, respectively. Assuming a divergence time of 5 million years [4], the rate of fixation per My for each chromosome arm can be estimated as 0.5, 3.6, 1.1, 1.1, and 1.9, respectively (or 7 when estimated across the genome). When normalized to account for differences in chromosome length, the number of inversions per Mb per My for X, 2R, 2L, 3R, and 3L was estimated as 0.023, 0.057, 0.022, 0.021, and 0.044, respectively (0.031 genome-wide). This rate is even more extreme than the genome-wide estimate for Drosophila [3]. Moreover, our results indicate that 2R has a higher rate of rearrangement than other arms. It is clear that tightly linked genes in A. gambiae are unlikely to be similarly linked in A. funestus, particularly on 2R. The estimate of mean conserved segment length derived for each arm can be used to predict the probability of linkage in A. funestus, given the known distance between genes in A. gambiae and the assumption of random distribution of breakpoints [7]. As an example, the probability that genes 1 Mb apart on 2R in A. gambiae are linked on 2R in A. funestus is only 0.31. Polymorphic inversions on chromosome 2R are widespread within the A. gambiae and A. funestus and are believed to indicate adaptations to different environmental niches [8, 9]. Identification of genes encoded within these inversions could provide clues to factors determining mosquito behavior and vectorial capacity. Thus, the main features of genome rearrangements in malaria mosquitoes, A. gambiae and A. funestus, can be summarized as following: (1) the reciprocal whole arm translocation has preserved a synteny (the occurrence of genes) at the whole-arm level; (2) high rate of paracentric inversions, especially on 2R, have had a major impact on extensive gene order reshuffling. Our results suggest that the success of positional cloning or interspecific microarray experiments may be limited to either very closely related anopheline species or small genomic fragments. Further comparative studies of these two genomes will provide valuable insights into the mechanism and effects of chromosomal rearrangements. This study was supported by grants from NIH (AI48842) to N.J.B. and from the Indiana 21st Century Research & Technology Fund to F.H.C.


1. E. Eichler, D. Sankoff, Science 301, 5634 (2003).
2. E. M. Zdobnov et al., Science 298, 149 (2002).
3. J. González, J. M. Ranz, A. Ruiz, Genetics 161, 1137 (2002)
4. I. V. Sharakhov et al., Science 298, 182 (2002).
5. I. V. Sharakhov, M. V. Sharakhova, C. M. Mbogo, L. L. Koekemoer, G. Yan, Genetics 159, 211 (2001)
6. L. Zheng, et al., Science 276, 425 (1997)
7. J. H. Nadeau and B. A. Taylor, Proc. Natl. Acad. Sci. U.S.A. 81, 814 (1984)
8. M. Coluzzi, A. Sabatini, V. Petrarca, M. A. Di Deco, Trans. R. Soc. Trop. Med. Hyg. 73, 483 (1979)
9. I. Dia, D. Boccolini, C. Antonio-Nkondjio, C. Costantini, D. Fontenille, Parassitologia 42, 227 (2000)

Joint work with Andrew C. Serazin (1), Olga G. Grushko (1), Ali Dana (1), Neil Lobo (1), Maureen E. Hillenmeyer (1), Richard Westerman (2), Jeanne Romero-Severson (3), Carlo Costantini (4), N'Fale Sagnon (4) Frank H. Collins (1), Nora J. Besansky (1)

(1) Center for Tropical Disease Research and Training, University of Notre Dame, Notre Dame, IN 46556-0369, USA.
(2) Horticulture Department, Purdue University, West Lafayette, IN 47907-1159, USA.
(3) Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907-1165, USA.
(4) Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.