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.
Bibliographical noteFunding Information:
This work is supported by the Fralin Life Science Institute and the Virginia Experimental Station, and by NIH grants AI77680 and AI105575 to ZT, AI094289 and AI099528 to IVS, AI29746 to AAJ, AI095842 to KM, AI073745 to MAR, AI080799 and AI078183 to SL, and AI042361 and AI073685 to KDV. AP and IVS are supported in part by the Institute for Critical Technology and Applied Science and the NSF award 0850198. RMW is supported by Marie Curie International Outgoing Fellowship PIOF-GA-2011-303312. XC is supported by GDUPS (2009). This work was also supported in part by NSF grant CNS-0960081 and the HokieSpeed and BlueRidge supercomputers at Virginia Tech. YS thanks the Department of Biotechnology, Government of India for the financial support. Drew Cocrane provided assistance with in situ hybridization.