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Anopheles gambiae: A genetic approach Karin Eiglmeier Unité de Biochimie et Biologie Moléculaire des Insectes Institut Pasteur
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Mosquitoes Order : Diptera ToxorhynchitinaeAnophelinaeCulicinae Family: Culicidae AedesCulexAnopheles
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Since when.......???? Anopheline fossile (20 Myr) http://www.uky.edu/AS/Geology/webdogs/am ber/critters/skeeter-b.html (Amber from the Dominican Republic) Dr. David Grimaldi Cretaceous carnivorous dinosaures (145-65Myr) Oldest Culicidae-like fossile: 76-79 Myr (canadian amber) FROM: www.dinozaury.ovh.org/ index.php?id=galeria
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Generalized mosquito life cycle The larvae feed on microorganisms and organic matter in the water. 4 -14 days The pupal stage: non-feeding stage of development, reacts to stimuli -> metamorphosis 1- 4 days Eggs hatch into larvae within 48 H. Larvae Pupa Eggs Adult modified from: www.edmonton.cal
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Mosquito facts CO 2, temperature, humidity, odor, colour (infra-red) mouvement Malaria West Nile virus filarial diseases dengue encephalitis yellow fever 1 -1.5 miles/hour 75 - 100 miles 20 - 35 meters DetectionTransmission Immunity Blood-meal endophage 4x weight
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Mosquito facts CO 2, temperature, humidity, odor, colour (infra-red) mouvement Malaria West Nile virus filarial diseases dengue encephalitis yellow fever 1 -1.5 miles/hour 75 - 100 miles 20 - 35 meters DetectionTransmission Immunity Blood-meal endophage 4x weight
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Malaria (“Paludisme”) - Vector: Anopheles gambiae - Parasite: protozoans of the genus Plasmodium > 90 countries (40% of the world’s population) - 90% malaria fatalities in sub-saharan Africa - 300 - 500 millions clinical cases/ year - 1.5 - 2.7 millions deaths
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Plasmodium life cycle Adapted from Waters, Science,301 (2003) ~13-18 days
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Anopheles mosquitoes Genus: Anopheles AfricaAsiaAmerica An. gambiae An. arabiensis An. funestus An. stephensi An. farauti An. sinensis An. tellessarus An. minimus An. albimanus An. quadrimaculatus An. darlingi An. freeborni Principal disease transmitting species: about 70 transmit malaria to humans about 20 are important vectors
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- An. gambiae M et S - An. arabiensis - An. melas - An. merus - An. bwambae - An. quadriannulatus - An. quadriannulatus B Anopheles gambiae complex Adapted from J.Mouchet & D.Fontenille
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Golden Path length ~ 273 Mb ( from: http://www2.ncid.cdc.gov/vector/vector.html) Anopheles gambiae chromosomes
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Whole genome assembly Genome size:- 278 Mb ( 273 Mb ) - 8987 scaffolds - 303 scaffolds => 91% of the genome - 18634 contigs Inter-scaffold gaps: - sequence gaps, no clones - repeat sequences - smaller scaffolds ? Y chromosome: - no assembly - ongoing ? 0.18Mb - high repeat content Current release AgamP3 last update: 2/2006 First draft: March 2002
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4961425324Mb Anopheles gambiae chromosomes ++ adapted from: http://www.ensembl.org
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Immediate results 20 genes (1999) 14700 genes (2005) Cross disciplinary research: - Drosophila community - Bioinformaticiens - other domains - BLAST Fieldwork: - Entomologists - Identification follow-up of mutations adapt strategy
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Gene prediction and annotation Several evidences: - Gene prediction programs: - open reading frame - signals: start codon, stop codon, poly-adenylation site - splice sites - bias in base composition - bias in base frequency - encoded peptide has similarity with known protein - encoded peptide has similarity with a protein domain or motif - « evolutionarily conserved sequences » - Ecores - cDNA, EST, SAGE biological evidences
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Annotation 15189 genes Celera pipeline (Otto) Ensembl pipeline “Ab inito gene finding” Homology 9896 transcripts14564 transcripts 24460 transcripts 15189 genes 13757840 5974 (identified exclusively) “consensus set”
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Does gene prediction correspond to real gene ? Problems: - real gene? => mono-exonic ! - small exons, intron-exon structure - first and last exon - untranscribed regions (“UTRs”) - genes for atypic or specific proteins - genes duplicated in tandem - pseudo-genes
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Comparison An. gambiae - D. melanogaster Common ancestor Anopheles gambiae Drosophila melanogaster 250 ~ 273 Mb 15189 annotated genes (13765 in AgamP3) ~ 130 Mb 14651 annotated genes
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Protein similarity 14000 12000 10000 8000 6000 4000 2000 DmAg 44,2% 11,0% 15,9% 10,3% 18,6% 47,2% 13,8% 17,9% 10,0% 11,1% species specific Homologs, best matches: - non-insects Homologs, best matches: - insects “Many-to-many” orthologs, duplications 1:1 Orthologs (6089 pairs) average identity: 56% 1388512981 increased speed of divergence : Orthologs Human - Fugu: average identity: 61% adapted from: Zdobnov E. Science (2002), 298, 149-159
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Starting point: Publication of the Anopheles gambiae genome 2002 - Genome sequence incomplete - First characterisation and annotation of genes of variable quality Problems:Post-genomic analysis difficult Gene detection Approach:Full-length enriched cDNA libraries: - developmental stages - different tissues Aims:- Identification of new genes - Improve description of gene structure (TSS, UTRs, Exon / Intron) - Alternative splicing recombinant proteins - Facilitate comparative genomics Genome, gene expression and annotation
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How to get more information?
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Experimental evidence: - Transcriptome - Proteome - Biochemistry - RNAi - Transgenesis
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Modified from Zhang MQ Nat. Rev. Genet.2002(9):698-709 and from Ben-Dor,S 1234 5 ATGSTOPPoly(A) site TTSTSS Promoter 12345 ATGSTOPPoly(A) site DNA Pre-mRNA mRNA 1342 AUG 5 STOP Poly(A) 5’UTR3’UTRCDS CAP From DNA to mRNA
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Modified from Zhang MQ Nat. Rev. Genet.2002(9):698-709 and from Ben-Dor,S 1234 5 ATGSTOPPoly(A) site TTSTSS Promoter 12345 ATGSTOPPoly(A) site DNA Pre-mRNA mRNA 1342 AUG 5 STOP Poly(A) 5’UTR3’UTRCDS CAP From DNA to mRNA
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AAAA Gppp p OH mRNA + CAP mRNA sans CAP AAAA Gppp OH AAAA p OH AAAA OH BAP treatment TAP treatment RNA ligation 5’-oligo « Oligo-capping » ( Maruyama & Sugano ) adapted from:Suzuki et al. Genome Res.(2001)11(5):677-84
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AAAA TTTT AAAA TTTT AAAA Ligation First strand synthesis Alkaline degradation PCR SfiI Digestion TTTT AAAA adapted from:Suzuki et al. Genome Res.(2001)11(5):677-84
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Banques ADNc « Full-length » modified from: www.edmonton.cal
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More genes to discover ? 67044 reads ~ 3700 clusters 85 % improved cDNAs - submitted to EMBL : 654 new genes Pilot project: Adult females 3032 Ensembl genes
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Perfect annotation Gene model cDNA data proteins - Ensembl -
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Improvement of annotation - Ensembl -
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600 new genes - how are they?
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”New” genes - Ensembl -
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Predictions and proof - Ensembl -
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Banques ADNc « Full-length »
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Clustering results: 5664 cluster - 869 new genes 175 21 6 12 256 37 401 Adulte females (4056) Embryos (1816) Larvae (1982)
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Available or planned cDNA libraries: Available/sequenced: Adult females Embryo Larves Salivary glands Planned: Pupa
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Plasmodium life cycle Adapted from Waters, Science,301 (2003) Adapted from: James, A.A., (2003),206:3817-3821
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Sporozoites - invasion, specific receptors - secretory cells - storage - influence normal functions Saliva - proteins involved in l’hematophagy - modulation of immune defense An. gambiae salivary glands
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Chromosome X, pos. 11070 kb: Anopheles-specific SG1 family AgamP3 Moz2a v.34 Adapted from: Arca et al. J.ExpBiol(2005), 208:3971
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What does genomics offer for malaria control ?
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Adapted from Waters, Science,301 (2003) Vector eradication
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Insecticides Monitoring of insecticide resistance genes - pyrethroid resistance - epidemiology Detoxifying enzymes Detox-chip New targets
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Adapted from Waters, Science,301 (2003) Host - vector relationship
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BehaviourCandidate genes: odorant - smell79 putative odorant receptors gustatory- taste76 putative gustatory receptors Attractant/Repellant - Host location Vectorial capacity Mating Oviposition Traps
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Adapted from Waters, Science,301 (2003) Transmission blocking - SM1
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SM1 = salivary gland and midgut peptide 1 (Gosh, et al. 2000) 12 amino acids transgenic mosquitoes: - midgut expression - blocking plasmodium - salivary gland expression - blocking invasion - selective advantage of transgenic mosquitoes - proof of principle => Marrelli et al., PNAS 104, 2007
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Adapted from Waters, Science,301 (2003) Immune system
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Natural efficient immune system - resistance against Plasmodium - melanotic incapsulation - several loci - identify genes - multiply/release naturally occuring resistant strains
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Adapted from Waters, Science,301 (2003) Salivary glands
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- cDNAs - RT-PCR - protein expression - SAGE analysis of transcriptome - proteomic studies of salivary glands and saliva salivary gland sporozoite relationships - saliva and humans: - immunomodulatory - function? - vaccine target?
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Where to go from now ?? Annotation = continuing process - new start for Anopheles research - Improvement of genomic annotation: - Sequence, gene models, promoters - genome arrays : -infected non-infected - Annotation at the protein level: - protein interaction networks - hypothesis experiments - comparative genomics - more insects (honey bee, Aedes) - transgenic mosquitoes, RNAi experiments
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Aedes aegypti - Start: September 2002 - Fin : Spring 2007 ? first assembly, version 0.5 - Public: - First annotations - cDNA sequences - Genome size: > 1300 Mb => in 4758 supercontigs - « Evolutionary distance » Anopheles - Aedes: ~ 27-62 Myr From: www.bg-sentinel.com
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Gene size comparison Anopheles Aedes
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Gene size comparison 4 kb 16 kb Anopheles Aedes
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Aedes aegypti annotation - genome size bigger than expected (780 Mb => 1300 Mb) - sequencing strategy different - cDNAs early in project - high content of repeat sequences (~68%) - gene prediction programs adapted - long genes, nested genes - Anopheles - Aedes - synteny between chromosome arms
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Data bases Ensembl Anopheles gambiae Aedes aegypti Anobase Anopheles gambiae Vectorbase Anopheles gambiae Aedes aegypti Ixodes scrapularis TIGR - The Institut for Genome Research
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Traps Identification Understanding - behaviour Genome/proteome caracterisation Promoter/expression Vector control strategies: - Transgenesis Genetically modified mosquitoes -reduced parasite transmission -functional genomics New insecticidal targets Vaccines Main orientations in mosquito research Immunity
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Collaborations Institut Pasteur BBMI - Paul Brey Charles Roth Inge Holm Pierre Dehoux (PF4) Shawn Gomez Sylvie Perrot Marie-Kim Chaveroche Jean Sautereau Plate-forme Genomique - PF1 Christiane Bouchier Anthony Lepelletier Genoscope Jean Weissenbach Beatrice Segurens Patrick Wincker Gabor Gyapay Corinne da Silva Betina Porcel AMSUD Network Sergio Verjovski-Almeida Universidade de Sao Paulo Hamza el Dorry Suely L. Gomes Carlos F.M. Menck Ana L. Nascimento
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