Overview and History of VectorBase Frank Collins March 31, 2015
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Overview and History of
VectorBase
Frank CollinsMarch 31, 2015
Outline
● History
● Organisms
● Types of Data
● Tools and Resources
History
The Anopheles gambiae Genome2001-2002
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 2001-2002
Aug 29 Sequencing initiated at Celera
Nov 11Sequencing complete at all centers
Dec 12First assembly results
Feb 11Final assembly complete
Mar 8 - Assembly submitted to public databases
May 1Consensus annotations complete and frozen for analysis.
May 16Annotations submitted to public databases
July-Aug - Manuscripts submitted
Aug 8NIAID UO1 awarded
Dec‘01
Feb‘02
Jun‘02
Oct‘01
Aug ‘01
Apr‘02
Aug ‘02
2002 - 2004
1 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
OrganismsAnopheles
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
OrganismsGlossina austeniG. brevipalpisG. fuscipesG. morsitansG. pallidipesG. 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
Lutzomyialongipalpis
- 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 vittatumS. sirbanumS. damnosumS. squamosumS. ochraeceumS. thyolenseS. sanctipauliS. woodiS. exigumS. 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
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