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

Xiaofang Jiang (1, 2) , Ashley Peery (3) , A Hall (1, 2) , Atashi Sharma (3) , Xiao-Guang Chen (4) , Robert M Waterhouse (5, 6, 7, 8) , Aleksey Komissarov (9, 10) , Michelle M Riehl (11) , Yogesh Shouche (12) , Maria V Sharakhova (3) , Dan Lawson (13) , Nazzy Pakpour (14) , Peter Arensburger (15) , Victoria L M Davidson (16) , Karin Eiglmeier (17) , Scott Emrich (18) , Phillip George (3) , Ryan C Kennedy (19) , Shrinivasrao P Mane (20) , Gareth Maslen (12) , Chioma Oringanje (21) , Yumin Qi (2) , Robert Settlage (22) , Marta Tojo (21) , Jose M C Tubio (23) , Maria F Unger (24) , Bo Wang (14) , Kenneth D Vernick (17) , Jose M C Ribeiro (25) , Anthony A James (26) , Kristin Michel (17) , Michael A Riehle (21) , Shirley Luckhart (14) , Igor V Sharakhov (1, 3) , Zhijian Tu (1, 2)

1 Department of Biochemistry [Blacksburg]
2 GBCB - Program of Genetics, Bioinformatics, and Computational Biology [Blacksburg]
3 Department of Entomology [Blacksburg]
4 Department of Pathogen Biology
5 Department of Genetic Medicine and Development
6 SIB - Swiss Institute of Bioinformatics [Genève]
7 CSAIL - Computer Science and Artificial Intelligence Laboratory [Cambridge]
8 BROAD INSTITUTE - Broad Institute of MIT and Harvard
9 Theodosius Dobzhansky Center for Genome Bioinformatics
10 Institute of Cytology
11 Department of Microbiology
12 National Center for Cell Science
13 EMBL-EBI - European Bioinformatics Institute [Hinxton]
14 Department of Medical Microbiology and Immunology
15 Department of Biological Sciences [Pomona]
16 Division of Biology
17 Génétique et Génomique des Insectes vecteurs
18 Department of Computer Science and Engineering
19 Department of Bioengineering and Therapeutic Sciences
20 Virginia Bioinformatics Institute
21 Department of Entomology
22 Department of Physiology, School of Medicine – CIMUS
23 The Wellcome Trust Sanger Institute [Cambridge]
24 Department of Biological Sciences [Notre Dame]
25 Vector Molecular Biology Section, Laboratory of Malaria and Vector Research
26 Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry

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.ResultsHere, 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.ConclusionsThe 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.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]; Life Sciences [q-bio]; Genetics

Xiaofang Jiang, Ashley Peery, A Hall, Atashi Sharma, Xiao-Guang Chen, et al.. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.. Genome Biology, 2014, 15 (9), pp.459. ⟨10.1186/s13059-014-0459-2⟩. ⟨pasteur-01074253⟩