Anopheles gambiae

PopGenBaseGroundwork for a vector

population genetics database

UC Davis - UCLA

Anopheles gambiae s.l.

One of major vectors for malaria transmission in

Africa

Different species and forms of An. gambiae s.l. are

identical in morphology.

Researches have shown that different

subpopulations of An. gambiae s.s. exhibit different

response to important phenotype such as insecticide

resistance.

Genetic markers are not randomly distributed.

Mali

Distribution of the kdr SNP among An. gambiae s.s. in Mali

Distribution of the kdr SNP among populations of the M and S molecular forms of An. gambiae at four sites in Mali at which the two forms occur in sympatry. The "rr" refers homozygote of kdr SNP; the "rs" refersheterozygotes; and "ss" refers wild-type homozygote. From Tripet et al. (2007)

Beginning In 2004, our Anopheles gambiae population genetics

study demanded a data repository tool that organizes population, geographical, ecological and genetic information.

Collaborators among multiple campuses desired a better way to share data than sending spreadsheet files.

Progress

Anopheles gambiae Population genomics DB (In-group DB) Online data upload Summary pages for each country Query pages Interactive Google map of collection sites Chromosome Image links for verification Data output to fit into specific analysis programs Documentation regarding data structure and naming

conventions

ER Diagram of in-group PopGenBase

Genetic data for each individual

A table for each experiment or protocol

ScottTest

Karyotypemos_id

2La2Rj

Species Mosquitoid

ResearcherID

Name

FaviaFanelloTest

MicrosatDatamos_id

Length A

Microsat ID

Referencing attribute referenced attribute

MicrosatListID

Collection siteCollection date

Tube num

mos_id

X

Chrom form

Researcher ID

Researcher ID

Researcher ID

Last modified byLast_modified

Sites

villageID

molecular formmos_id

Researcher ID

PrecipitationRecording station

ChromosomeImagefile ID

chromosomemos_id

comment2Rb2Rc2Rd2Rd

chromosomeGenebank name

Length B

Last_modifiedLast_modified by

comment

Last_modifiedLast_modified by

comment

Last_modifiedLast_modified by

comment

LabInstitutionPositionE-mail

comment

countrylatitude

longitudeelevation Meteorology Stations

nameID

countrylatitude

longitude

Recording dateprecipitation

Goals of PopGenBase Provide encouragement to the vector population genetics

community to use PopGenBase, much in the manner of many of the public data resources of NCBI and EMBL-EBI.

Bring some standardization of genetic markers and inter-study compatibility to the field of vector population genetics.

Directly link markers used in population studies with emerging knowledge of the genome, generating far more powerful population data sets.

Encourage studies in other areas of vector biology, like ecology, behavior and epidemiology, to incorporate genetic information, in order to identify genes affecting complex phenotypes.

Current Progress https://grassi2.ucdavis.edu

[Current status]

Query page

[Current status]

Various query output format

[Current status]

Chromosome Images

[Current status]

GoogleMaps API

[Current status]

Documentation

To Do List Stage 2 PopGenBase

Nov. 2008 – Jun. 2009 Incorporation of other

genetic data such as microsatellite genotypes.

A pilot “Work Bench” implementation and soliciting other research group as test groups.

Improvement of GoogleMap API interface

Define ‘Sample’ schema to aid cross-link among other vector databases.