Overview and History of VectorBase Frank Collins March 31, 2015

Outline ●History ●Organisms ●Types of Data ●Tools and Resources

History

The Anopheles gambiae Genome Celera Genomics, University of Notre Dame, EMBL, Genoscope, TIGR, Institut Pasteur, IMBB, University of Iowa, University of Rome, Institute of Genetics and Cytology Novosibirsk

Project timeline Aug 29 Sequencing initiated at Celera Nov 11 Sequencing complete at all centers Dec 12 First assembly results Feb 11 Final assembly complete Mar 8 - Assembly submitted to public databases May 1 Consensus annotations complete and frozen for analysis. May 16 Annotations submitted to public databases July-Aug - Manuscripts submitted Aug 8 NIAID UO1 awarded Dec ‘01 Feb ‘02 Jun ‘02 Oct ‘01 Aug ‘01 Apr ‘02 Aug ‘02

genome Anopheles gambiae

1st contract: June 2004 to September 2009 Image from 2005, 2 genomes

Image from 2007, 5 genomes 2nd contract: October 2009 to September 2014

Image from 2015, 37 genomes 3rd contract: September 2014 to September 2015 (option to 2019)

37 Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans, Blackflies cluster and Sarcoptes scabei

Organisms Anopheles 19 “species” 21 genomes Aedes aegypti ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans, Blackflies cluster and Sarcoptes scabei Culex quinquefasciatus Aedes albopictus: we “may” receive the genome in the summer

Organisms Glossina austeni G. brevipalpis G. fuscipes G. morsitans G. pallidipes G. palpalis ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans, Blackflies cluster and Sarcoptes scabiei. Musca domestica Stomoxys calcitrans -Two genomes have being published -The annotation of the other 5 Glossina started this month (March 2015)

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans and Blackflies cluster Phlebotomus papatasi Lutzomyia longipalpis -Community is finishing the genome analyses and gene manual annotations. -The paper has started to being written this past month (Feb 2015).

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans, Blackflies cluster and Sarcoptes scabiei Ixodes scapularis -The genome paper will be submitted on April 30th (not accepted in Nature & Science in 2013) -It will potentially have 8 companion papers

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans and Blackflies cluster Pediculus humanus

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans and Blackflies cluster -The genome paper will be submitted to PNAS in early April (not accepted in Nature Genetics & Science in 2014) -The companion papers are being submitted to Insect Biochemistry and Molecular Biology. Rhodnius prolixus

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans and Blackflies cluster Biomphalaria glabrata -Analyses are done -We are working with them to finish manual gene annotations -A 1st draft of the paper will be circulated soon with the community

Organisms ●Mosquitoes ●Tsetse cluster ●Musca domestica ●Lutzomyia longipalpis and Phlebotomus papatasi ●Ixodes scapularis ●Pediculus humanus ●Rhodnius prolixus ●Biomphalaria glabrata ●Coming soon: Aedes albopictus, Stomoxys calcitrans and Blackflies cluster Simulium vittatum S. sirbanum S. damnosum S. squamosum S. ochraeceum S. thyolense S. sanctipauli S. woodi S. exigum S. yahense

Types of data Genes and Genomes Transcripts and Transcriptomes Proteins and Proteomes Mitochondrial Sequences Population Data

Types of data Genes and Genomes Transcripts and Transcriptomes Proteins and Proteomes -37 genomes -37 in silico transcriptomes and proteomes -9 experimental transcriptomes for Anopheles spp (Sanger and RNAseq) -2 experimental proteomes for An. gambiae (Mass spec) -69 microarray experiments ( 42 An g, 22 Aa, 1 Af and 1 Cq) -200 RNAseq experiments (24 species)

Types of data Mitochondrial Sequences Population Data -All GenBank sequences for Aedes, Anopheles, Culex and Ixodida. -Insecticide Resistance and other data … talk by Daniel Lawson

Tools and Resources

Thank you from the VectorBase team! European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) University of Notre Dame (+3 more not in the picture) Imperial College London Coming soon to …University of Cambridge