Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Abstract

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

“…gambiae genome (27,33), yet a mere 0.18 Mb of unordered sequences have previously been assigned to the Y in the PEST reference genome assembly [https:// www.vectorbase.org (34)]. Similarly, a recent Anopheles stephensi genome project identified only 57 short unordered Y sequences spanning ∼50 kb from genomic reads, and 11 contigs spanning ∼200 kb from BAC clones that were assigned to the Y chromosome (35). To overcome this impediment, we developed a strategy based on long-read, PacBio single molecule real-time sequencing (36).…”

Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquitoAnopheles stephensi

“…The target gene is located autosomally on 3L of the An. stephensi linkage map (15), and we refer to it as kynurenine hydroxylase white (kh w ) to indicate orthology with a gene in Aedes aegypti, which has a recessive white-eye phenotype (27)(28)(29). The pAsMCRkh2 construct has the following elements: (i) an An.…”

“…Critical to this approach are the development of a gene that confers resistance to the transmission of the parasites, transgenesis tools for introducing the genes into mosquito strains, and a mechanism to spread the genes at epidemiologically significant rates into the target populations. Working with Anopheles stephensi, a vector of malaria in the Indian subcontinent (15), we now have demonstrated proof of principle for all of these components.…”

MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi

“…aegypti (Nene et al, 2007) is approximately five-fold larger than the genome of An. stephensi (Jiang et al, 2014). Our analysis has enabled the comparison of the number of lineage-specific miRNAs and the mechanisms to generate novel miRNAs between two mosquitos of divergent genomes.…”