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Background  Malaria mosquitoes have had a remarkable stability in the number of chromosomes in their karyotype (2n = 6) during 100 million years of evolution. Moreover, autosomal arms were assumed to maintain their integrity even if their associations with each other changed via whole-arm translocations. Here we use high-coverage comparative physical genome mapping of three  Anopheles  species to test the extent of evolutionary conservation of chromosomal arms in malaria mosquitoes.    Results  In this study, we developed a physical genome map for  Anopheles atroparvus,  one of the dominant malaria vectors in Europe. Using fluorescence in situ hybridization (FISH) of DNA probes with the ovarian nurse cell polytene chromosomes and synteny comparison, we anchored 56 genomic scaffolds to the  An. atroparvus  chromosomes. The obtained physical map represents 89.6% of the  An. atroparvus  genome. This genome has the second highest mapping coverage among Anophelinae assemblies after  An. albimanus , which has 98.2% of the genome assigned to its chromosomes. A comparison of the  An. atroparvus ,  An. albimanus , and  An. gambiae  genomes identified partial-arm translocations between the autosomal arms that break down the integrity of chromosome elements in evolution affecting the structure of the genetic material in the pericentromeric regions. Unlike  An. atroparvus  and  An. albimanus , all chromosome elements of  An. gambiae  are fully syntenic with chromosome elements of the putative ancestral  Anopheles  karyotype. We also detected nonrandom distribution of large conserved synteny blocks and confirmed a higher rate of inversion fixation in the X chromosome compared with autosomes.    Conclusions  Our study demonstrates the power of physical mapping for understanding the genome evolution in malaria mosquitoes. The results indicate that syntenic relationships among chromosome elements of  Anopheles  species have not been fully preserved because of multiple partial-arm translocations.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4663-4) contains supplementary material, which is available to authorized users.

Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome