Inversions and Gene Order Shuffling in Anopheles gambiae and A. funestus

Abstract

In tropical Africa, Anopheles funestus is one of the three most important malaria vectors. We physically mapped 157 A. funestus complementary DNAs (cDNAs) to the polytene chromosomes of this species. Sequences of the cDNAs were mapped in silico to the A. gambiae genome as part of a comparative genomic study of synteny, gene order, and sequence conservation between A. funestus and A. gambiae. These species are in the same subgenus and diverged about as recently as humans and chimpanzees. Despite nearly perfect preservation of synteny, we found substantial shuffling of gene order along corresponding chromosome arms. Since the divergence of these species, at least 70 chromosomal inversions have been fixed, the highest rate of rearrangement of any eukaryote studied to date. The high incidence of paracentric inversions and limited colinearity suggests that locating genes in one anopheline species based on gene order in another may be limited to closely related taxa.

An Integrated Genetic and Physical Map for the Malaria Vector Anopheles funestus

“…The genetic order was generally consistent among the loci across all families and all markers were consistently assigned to the same linkage groups. A good concordance was observed between the genetic order from single family genetic map and the physical map of Sharakhov et al (2002Sharakhov et al ( , 2004.…”

“…Two of the markers were derived from the phosphoribosylaminoimidazole carboxylase gene, which has been physically mapped to the X chromosome (Sharakhov et al 2002), allowing us to anchor this group to the X chromosome. As Anopheles mosquitoes have heteromorphic sex chromosomes, with females being XX and males XY, only females are informative for X chromosome markers.…”

“…DNA extractions were performed using the LIVAK method as described previously (Collins et al 1987). Initially we used published primer sets (Sinkins et al 2000;Cohuet et al 2002;Sharakhov et al 2002;Soremekun et al 2004) to individually amplify 72 microsatellite markers from the parental and F 1 A. funestus genomic DNA. A tailed primer system, described by Oetting et al (1998), was used to label the PCR products with a fluorescent dye to reduce the genotyping costs.…”

“…Identification of SNP loci: Single nucleotide polymorphisms (SNPs) were identified within cytochrome P450 genes or within DNA fragments that had been physically mapped to A. funestus polytene chromosomes (Sharakhov et al 2002) (see Table 2 for more details). The sequences of the physically mapped cDNAs were retrieved from GenBank.…”

Remodelling of a homeobox gene cluster by multiple independent gene reunions in Drosophila

“…Here we performed a comprehensive analysis of the organization of the nine NK genes belonging to the putative ProtoNK cluster and their neighbouring genes. This was performed across 20 arthropods in order to: (i) ascertain the extent of conservation of NK clustering when multiple highly rearranged genomes, such as those in the Drosophila genus and Culicidae, are considered [19][20][21] ; (ii) understand the origin of differences in constituent genes that NK clusters show among different arthropod phyla by reconstructing the evolutionary history of NK gene rearrangements; and (iii) extract evolutionary patterns of how the organization of a paralogous gene cluster decays and is reshaped in animal genomes.…”