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

Xiaofang Jiang, Ashley Peery, A. Brantley Hall, Atashi Sharma, Xiao Guang Chen, Robert M. Waterhouse, Aleksey Komissarov, Michelle M. Riehle, Yogesh Shouche, Maria V. Sharakhova, Dan Lawson, Nazzy Pakpour, Peter Arensburger, Victoria L.M. Davidson, Karin Eiglmeier, Scott Emrich, Phillip George, Ryan C. Kennedy, Shrinivasrao P. Mane, Gareth MaslenChioma Oringanje, Yumin Qi, Robert Settlage, Marta Tojo, Jose M.C. Tubio, Maria F. Unger, Bo Wang, Kenneth D. Vernick, Jose M.C. Ribeiro, Anthony A. James, Kristin Michel, Michael A. Riehle, Shirley Luckhart, Igor V. Sharakhov, Zhijian Tu

Research output: Contribution to journalArticlepeer-review

84 Scopus citations


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.

Original languageEnglish (US)
Article number459
Pages (from-to)459
Number of pages1
JournalGenome biology
Issue number9
StatePublished - 2014

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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