Project Information

Genome Analysis of Vectorial Capacity In Major Anopheles Vectors of Malaria Parasites

In September of 2008, the National Human Genome Research Institute (NHGRI) and the National Institute of Allergy and Infectious Diseases (NIAID) of the U.S. National Institutes of Health approved funding for the sequencing of the genomes and transcriptomes of thirteen Anopheles species, as described in the white paper: www.vectorbase.org/Help/Anopheles_species_cluster_white_paper

Although vector status was of prime importance in the selection of sequencing targets, choice was constrained by availability of colonies housed by the Malaria Research and Reference Reagent Resource Center (MR4), which will be a project and community resource for DNA, RNA and live mosquitoes from colonies. Since the initial whitepaper was approved, two additional species have been added to the project following the acquisition of available sequencing template: An. melas and An. christyi.

In addition to the approved goals of (1) high quality reference genome assemblies of each species and (2) transcriptome sequencing in support of gene annotation, a limited amount of SNP discovery based on wild specimens will augment these genome projects.  Illumina-based genome sequencing and assembly, RNAseq and SNP discovery will be managed by the Broad Institute (under the direction of Daniel Neafsey). Genome annotation will be based on contributions by the Broad Institute, VectorBase, and members of the scientific community, whose input is encouraged.  Once available, assemblies and gene models will be made accessible to the public. Production sequencing is beginning in spring 2011 and initial genome assemblies and annotations are expected to be available by late summer or early fall of 2011.  

Overall coordination of the project will be handled by Nora Besansky (nbesansk at nd.edu) and a Coordinating Committee (AGCC)1. In addition, as the need arises, individuals have agreed to serve as community liaisons2 between focal groups and the AGCC.  

This project was inspired by very ambitious goals: improved understanding of vectorial capacity, and the application of that understanding toward reducing malaria disease burden.  Accordingly, its success depends upon community input at all levels.  Please contact Nora Besansky or any members of the AGCC with questions, comments or suggestions. The AGCC is presently coordinating a community analysis strategy for the data to be generated under this whitepaper. The AGCC plan is to publish two flagship papers broadly covering the evolutionary genomics of the An. gambiae species group and the larger set of species in relation to malaria.  

The AGCC will also help coordinate community efforts to more deeply explore topics of special interest, for publication as focal papers. Parties interested in contributing to the initial analysis of these data, whether for the flagship manuscripts or the focal manuscripts or both, should send a brief email to Nora Besansky (nbesansk at nd.edu) describing the analysis topic of interest. To facilitate coordination, transparency, and maximal community engagement, the AGCC will coordinate a project wiki by late summer 2011 with available information about analysis efforts and who is leading them.

Anopheles Genomes Cluster (MODIFIED, UPDATED FROM WHITE PAPER).

Species

Classification

Reference Assembly (Geographic Source)

[Notes]

SNP Discovery (Geographic Source)

 

Subgenus Cellia

 

 

 

1. An. arabiensis

Series Pyretophorus

(Gambiae complex)

 

Dongola (Sudan)

[Isofemale subcolony, 2Rb/b homokaryotype]

Burkina Faso, Cameroon, Kenya

2. An. quadriannulatus A

(Gambiae complex)

SANGWE (South Africa)

[Isofemale subcolony, heterokaryotype X+f/f]

Zimbabwe

3.  An. merus

(Gambiae complex)

MAF (South Africa)

[Isofemale subcolony]

Kenya, South Africa

4. An. melas

(Gambiae complex)

NO COLONY

[sequencing from wild collected from Cameroon]

Bioko, Equatorial Guinea;
Ipono, Cameroon;
Ballingho, The Gambia

5. An. christyi

 

NO COLONY

[Sequencing from wild collected from Kenya]

-----

6. An. epiroticus

(Sundaicus complex)

NO COLONY

[Sequencing from wild collected from Vietnam]

Vietnam (resistance)

7. An. stephensi

Series Neocellia

SDA-500 (Pakistan)

[Isofemale subcolony]

TBD

8. An. maculatus (sp. B)

(Maculatus Subgroup)

COLONY Not AT MR4 (Kuala Lumpur)

[sequencing from preserved females]

-----

9. An. funestus

Series Myzomyia (Funestus Subgroup)

FUMOZ (Mozambique)

 

Burkina Faso (Folonzo & Kiribina)

10. An. minimus s.s.(sp. A)

(Minimus complex)

MINIMUS1 (Thailand)

 

Thailand (cline)

 

11. An. culicifacies A

(Culicifacies Subgroup)

NO COLONY

[sequencing from wild collected from Iran]

Iran (species A, species D, species A-like)

12. An. farauti 1

Series Neomyzomyia

FAR1 (Papua New Guinea)

[Isofemale subcolony]

TBD

13. An. dirus s.s. (sp. A)

(Dirus complex)

WRAIR2 (Thailand)

[Isofemale subcolony]

Thailand (species A/D)

14. An. atroparvus

Subgenus Anopheles

EBRO (Spain)

[Isofemale subcolony]

----

15.  An. albimanus

Subgenus Nyssorhynchus

STECLA (El Salvador)

[Isofemale subcolony]

TBD

16. An. sinensis

(Hyrcanus Group)

CHONGQING (China)

[Isofemale subcolony]

TBD

 

Samples are in sequencing; check back later for data. 

 

1Anopheles Genomes Cluster Coordinating Committee (AGCC):

George Christophides: g.christophides at imperial.ac.uk; Frank Collins: frank at nd.edu; Scott Emrich: semrich at nd.edu; William Gelbart: gelbart at morgan.harvard.edu; Matthew Hahn: mwh at indiana.edu; Paul Howell: bsr7 at cdc.gov; Fotis Kafatos: f.kafatos at imperial.ac.uk; Daniel Lawson: Lawson at ebi.ac.uk; Marc Muskavitch: marc.muskavitch at bc.edu; Daniel Neafsey: neafsey at broadinstitute.org; Nora Besansky: nbesansk at nd.edu.

2Community Liaisons:

An. gambiae and sibling species: Dr. Nora Besansky (nbesansk at nd.edu); An. funestus: Drs. N?Fale Sagnon (n.fale.cnlp at fasonet.bf) and W. Guelbeogo  (guelbeogo.cnrfp at fasonet.bf); An. stephensi: Drs. Igor Sharakhov (igor at vt.edu) and Jake Tu (jaketu at vt.edu); An. farauti: Dr. Nigel Beebe (n.beebe at uq.edu.au); An. dirus, An. minimus: Dr. Catherine Walton (Catherine.Walton at manchester.ac.uk); An. atroparvus: Drs. Maria Sharakhova (msharakh at vt.edu) and Igor Sharakhov (igor at vt.edu); An. albimanus: Dr. Martinez Barnetche (jmbarnet at correo.insp.mx).