Highly evolvable malaria vectors: The genomes of 16
Anopheles
mosquitoes
Authors: Neafsey Daniel E. , Waterhouse Robert M. , Abai Mohammad R. , Aganezov Sergey S. , Alekseyev Max A. , Allen James E. , Amon James , Arcà Bruno , Arensburger Peter , Artemov Gleb , Assour Lauren A. , Basseri Hamidreza , Berlin Aaron , Birren Bruce W. , Blandin Stephanie A. , Brockman Andrew I. , Burkot Thomas R. , Burt Austin , Chan Clara S. , Chauve Cedric , Chiu Joanna C. , Christensen Mikkel , Costantini Carlo , Davidson Victoria L. M. , Deligianni Elena , Dottorini Tania , Dritsou Vicky , Gabriel Stacey B. , Guelbeogo Wamdaogo M. , Hall Andrew B. , Han Mira V. , Hlaing Thaung , Hughes Daniel S. T. , Jenkins Adam M. , Jiang Xiaofang , Jungreis Irwin , Kakani Evdoxia G. , Kamali Maryam , Kemppainen Petri , Kennedy Ryan C. , Kirmitzoglou Ioannis K. , Koekemoer Lizette L. , Laban Njoroge , Langridge Nicholas , Lawniczak Mara K. N. , Lirakis Manolis , Lobo Neil F. , Lowy Ernesto , MacCallum Robert M. , Mao Chunhong , Maslen Gareth , Mbogo Charles , McCarthy Jenny , Michel Kristin , Mitchell Sara N. , Moore Wendy , Murphy Katherine A. , Naumenko Anastasia N. , Nolan Tony , Novoa Eva M. , O’Loughlin Samantha , Oringanje Chioma , Oshaghi Mohammad A. , Pakpour Nazzy , Papathanos Philippos A. , Peery Ashley N. , Povelones Michael , Prakash Anil , Price David P. , Rajaraman Ashok , Reimer Lisa J. , Rinker David C. , Rokas Antonis , Russell Tanya L. , Sagnon N’Fale , Sharakhova Maria V. , Shea Terrance , Simão Felipe A. , Simard Frederic , Slotman Michel A. , Somboon Pradya , Stegniy Vladimir , Struchiner Claudio J. , Thomas Gregg W. C. , Tojo Marta , Topalis Pantelis , Tubio José M. C. , Unger Maria F. , Vontas John , Walton Catherine , Wilding Craig S. , Willis Judith H. , Wu Yi-Chieh , Yan Guiyun , Zdobnov Evgeny M. , Zhou Xiaofan , Catteruccia Flaminia , Christophides George K. , Collins Frank H. , Cornman Robert S. , Crisanti Andrea , Donnelly Martin J. , Emrich Scott J. , Fontaine Michael C. , Gelbart William , Hahn Matthew W. , Hansen Immo A. , Howell Paul I. , Kafatos Fotis C. , Kellis Manolis , Lawson Daniel , Louis Christos , Luckhart Shirley , Muskavitch Marc A. T. , Ribeiro José M. , Riehle Michael A. , Sharakhov Igor V. , Tu Zhijian , Zwiebel Laurence J. , Besansky Nora J. 
Published: November 2014

INTRODUCTION

Control of mosquito vectors has historically proven to be an effective means of eliminating malaria. Human malaria is transmitted only by mosquitoes in the genus
Anopheles
, but not all species within the genus, or even all members of each vector species, are efficient malaria vectors. Variation in vectorial capacity for human malaria among
Anopheles
mosquito species is determined by many factors, including behavior, immunity, and life history.

RATIONALE

This variation in vectorial capacity suggests an underlying genetic/genomic plasticity that results in variation of key traits determining vectorial capacity within the genus. Sequencing the genome of
Anopheles gambiae
, the most important malaria vector in sub-Saharan Africa, has offered numerous insights into how that species became highly specialized to live among and feed upon humans and how susceptibility to mosquito control strategies is determined. Until very recently, similar genomic resources have not existed for other anophelines, limiting comparisons to individual genes or sets of genomic markers with no genome-wide data to investigate attributes associated with vectorial capacity across the genus.

RESULTS

We sequenced and assembled the genomes and transcriptomes of 16 anophelines from Africa, Asia, Europe, and Latin America, spanning ~100 million years of evolution and chosen to represent a range of evolutionary distances from
An. gambiae
, a variety of geographic locations and ecological conditions, and varying degrees of vectorial capacity. Genome assembly quality reflected DNA template quality and homozygosity. Despite variation in contiguity, the assemblies were remarkably complete and searches for arthropod-wide single-copy orthologs generally revealed few missing genes. Genome annotation supported with RNA sequencing transcriptomes yielded between 10,738 and 16,149 protein-coding genes for each species. Relative to
Drosophila,
the closest dipteran genus for which equivalent genomic resources exist,
Anopheles
exhibits a dynamic genomic evolutionary profile. Comparative analyses show a fivefold faster rate of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses in
Anopheles
. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. We also document evidence of variation in important reproductive phenotypes, genes controlling immunity to
Plasmodium
malaria parasites and other microbes, genes encoding cuticular and salivary proteins, and genes conferring metabolic insecticide resistance. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

CONCLUSIONS

Anopheline mosquitoes exhibit a molecular evolutionary profile very distinct from
Drosophila
, and their genomes harbor strong evidence of functional variation in traits that determine vectorial capacity. These 16 new reference genome assemblies provide a foundation for hypothesis generation and testing to further our understanding of the diverse biological traits that determine vectorial capacity.

Geography, vector status, and molecular phylogeny of the 16 newly sequenced anopheline mosquitoes and selected other dipterans.
The maximum likelihood molecular phylogeny of all sequenced anophelines and two mosquito outgroups was constructed from the aligned protein sequences of 1085 single-copy orthologs. Shapes between branch termini and species names indicate vector status and are colored according to geographic ranges depicted on the map.