title: 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.
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Jiang
authors.forename: Ashley
authors.initials: A
authors.lastname: Peery
authors.forename: A Brantley
authors.initials: AB
authors.lastname: Hall
authors.forename: Atashi
authors.initials: A
authors.lastname: Sharma
authors.forename: Xiao-Guang
authors.initials: XG
authors.lastname: Chen
authors.forename: Robert M
authors.initials: RM
authors.lastname: Waterhouse
authors.forename: Aleksey
authors.initials: A
authors.lastname: Komissarov
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Riehle
authors.forename: Yogesh
authors.initials: Y
authors.lastname: Shouche
authors.forename: Maria V
authors.initials: MV
authors.lastname: Sharakhova
authors.forename: Dan
authors.initials: D
authors.lastname: Lawson
authors.forename: Nazzy
authors.initials: N
authors.lastname: Pakpour
authors.forename: Peter
authors.initials: P
authors.lastname: Arensburger
authors.forename: Victoria L M
authors.initials: VL
authors.lastname: Davidson
authors.forename: Karin
authors.initials: K
authors.lastname: Eiglmeier
authors.forename: Scott
authors.initials: S
authors.lastname: Emrich
authors.forename: Phillip
authors.initials: P
authors.lastname: George
authors.forename: Ryan C
authors.initials: RC
authors.lastname: Kennedy
authors.forename: Shrinivasrao P
authors.initials: SP
authors.lastname: Mane
authors.forename: Gareth
authors.initials: G
authors.lastname: Maslen
authors.forename: Chioma
authors.initials: C
authors.lastname: Oringanje
authors.forename: Yumin
authors.initials: Y
authors.lastname: Qi
authors.forename: Robert
authors.initials: R
authors.lastname: Settlage
authors.forename: Marta
authors.initials: M
authors.lastname: Tojo
authors.forename: Jose M C
authors.initials: JM
authors.lastname: Tubio
authors.forename: Maria F
authors.initials: MF
authors.lastname: Unger
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Vernick
authors.forename: Jose M C
authors.initials: JM
authors.lastname: Ribeiro
authors.forename: Anthony A
authors.initials: AA
authors.lastname: James
authors.forename: Kristin
authors.initials: K
authors.lastname: Michel
authors.forename: Michael A
authors.initials: MA
authors.lastname: Riehle
authors.forename: Shirley
authors.initials: S
authors.lastname: Luckhart
authors.forename: Igor V
authors.initials: IV
authors.lastname: Sharakhov
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Tu
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D059006:Chromosomes, Insect / Q000235:genetics; D016000:Cluster Analysis; D019143:Evolution, Molecular; D049750:Genome, Insect; D006801:Humans; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism; D007303:Insect Vectors / Q000235:genetics*; D008288:Malaria / Q000635:transmission; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D026801:Synteny; D059467:Transcriptome; D014505:Urban Population
chemical_list: D019476:Insect Proteins