Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

SIMPLE SUMMARY: Anopheles darlingi mosquitoes are the main vectors of malaria in the Brazilian Amazon. To assign genomic DNA sequences to chromosomes of this species, we performed fluorescence in situ hybridization of DNA probes with salivary glands polytene chromosomes. We compared the physical locations of the An. darlingi probes with homologous sequences in other Anopheles species, namely Anopheles albimanus and Anopheles gambiae. The results demonstrated that substantial genome rearrangements occurred throughout the evolutionary history of these mosquitoes. The physical mapping data can be useful for improving the structural accuracy of the An. darlingi genome assembly and for understanding the chromosomal evolution of these mosquitoes. ABSTRACT: The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.