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Background    Anopheles sinensis  is a dominant natural vector of  Plasmodium vivax  in China, Taiwan, Japan, and Korea. Recent genome sequencing of  An. sinensis  provides important insights into the genomic basis of vectorial capacity. However, the lack of a physical genome map with chromosome assignment and orientation of sequencing scaffolds hinders comparative analyses with other genomes to infer evolutionary changes relevant to the vector capacity.    Results  Here, a physical genome map for  An. sinensis  was constructed by assigning 52 scaffolds onto the chromosomes using fluorescence in situ hybridization (FISH). This chromosome-based genome assembly composes approximately 36% of the total  An. sinensis  genome. Comparisons of 3955 orthologous genes between  An. sinensis  and  Anopheles gambiae  identified 361 conserved synteny blocks and 267 inversions fixed between these two lineages. The rate of gene order reshuffling on the X chromosome is approximately 3.2 times higher than that on the autosomes.    Conclusions  The physical map will facilitate detailed genomic analysis of  An. sinensis  and contribute to understanding of the patterns and mechanisms of large-scale genome rearrangements in anopheline mosquitoes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-017-1888-7) contains supplementary material, which is available to authorized users.

Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae