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Panara V, Monteiro R, Koltowska K. Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development-New Insights From Technical Advances. Front Cell Dev Biol 2022; 10:891538. [PMID: 35615697 PMCID: PMC9125237 DOI: 10.3389/fcell.2022.891538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/10/2022] [Indexed: 01/09/2023] Open
Abstract
Epigenetic regulation is integral in orchestrating the spatiotemporal regulation of gene expression which underlies tissue development. The emergence of new tools to assess genome-wide epigenetic modifications has enabled significant advances in the field of vascular biology in zebrafish. Zebrafish represents a powerful model to investigate the activity of cis-regulatory elements in vivo by combining technologies such as ATAC-seq, ChIP-seq and CUT&Tag with the generation of transgenic lines and live imaging to validate the activity of these regulatory elements. Recently, this approach led to the identification and characterization of key enhancers of important vascular genes, such as gata2a, notch1b and dll4. In this review we will discuss how the latest technologies in epigenetics are being used in the zebrafish to determine chromatin states and assess the function of the cis-regulatory sequences that shape the zebrafish vascular network.
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Affiliation(s)
- Virginia Panara
- Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom,Birmingham Centre of Genome Biology, University of Birmingham, Birmingham, United Kingdom
| | - Katarzyna Koltowska
- Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden,*Correspondence: Katarzyna Koltowska,
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Cohuet A, Krishnakumar S, Simard F, Morlais I, Koutsos A, Fontenille D, Mindrinos M, Kafatos FC. SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system. BMC Genomics 2008; 9:227. [PMID: 18489733 PMCID: PMC2405807 DOI: 10.1186/1471-2164-9-227] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 05/19/2008] [Indexed: 01/10/2023] Open
Abstract
Background Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide insights into the evolutionary forces that condition pathogen-vector interactions. The discovery of polymorphisms is an essential step towards association studies of susceptibility to infection. Results We sequenced coding fragments of 72 immune related genes in natural populations of Anopheles gambiae and of 37 randomly chosen genes to provide a background measure of genetic diversity across the genome. Mean nucleotide diversity (π) was 0.0092 in the A. gambiae S form, 0.0076 in the M form and 0.0064 in A. arabiensis. Within each species, no statistically significant differences in mean nucleotide diversity were detected between immune related and non immune related genes. Strong purifying selection was detected in genes of both categories, presumably reflecting strong functional constraints. Conclusion Our results suggest similar patterns and rates of molecular evolution in immune and non-immune genes in A. gambiae. The 3,214 Single Nucleotide Polymorphisms (SNPs) that we identified are the first large set of Anopheles SNPs from fresh, field-collected material and are relevant markers for future phenotype-association studies.
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Affiliation(s)
- Anna Cohuet
- Institut de Recherche pour le Développement, UR 016, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
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Wang-Sattler R, Blandin S, Ning Y, Blass C, Dolo G, Touré YT, Torre AD, Lanzaro GC, Steinmetz LM, Kafatos FC, Zheng L. Mosaic genome architecture of the Anopheles gambiae species complex. PLoS One 2007; 2:e1249. [PMID: 18043756 PMCID: PMC2082662 DOI: 10.1371/journal.pone.0001249] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 11/02/2007] [Indexed: 01/05/2023] Open
Abstract
Background Attempts over the last three decades to reconstruct the phylogenetic history of the Anopheles gambiae species complex have been important for developing better strategies to control malaria transmission. Methodology We used fingerprint genotyping data from 414 field-collected female mosquitoes at 42 microsatellite loci to infer the evolutionary relationships of four species in the A. gambiae complex, the two major malaria vectors A. gambiae sensu stricto (A. gambiae s.s.) and A. arabiensis, as well as two minor vectors, A. merus and A. melas. Principal Findings We identify six taxonomic units, including a clear separation of West and East Africa A. gambiae s.s. S molecular forms. We show that the phylogenetic relationships vary widely between different genomic regions, thus demonstrating the mosaic nature of the genome of these species. The two major malaria vectors are closely related and closer to A. merus than to A. melas at the genome-wide level, which is also true if only autosomes are considered. However, within the Xag inversion region of the X chromosome, the M and two S molecular forms are most similar to A. merus. Near the X centromere, outside the Xag region, the two S forms are highly dissimilar to the other taxa. Furthermore, our data suggest that the centromeric region of chromosome 3 is a strong discriminator between the major and minor malaria vectors. Conclusions Although further studies are needed to elucidate the basis of the phylogenetic variation among the different regions of the genome, the preponderance of sympatric admixtures among taxa strongly favor introgression of different genomic regions between species, rather than lineage sorting of ancestral polymorphism, as a possible mechanism.
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Affiliation(s)
- Rui Wang-Sattler
- European Molecular Biology Laboratory, Heidelberg, Germany
- * To whom correspondence should be addressed. E-mail: (RW); (FK)
| | | | - Ye Ning
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claudia Blass
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Guimogo Dolo
- Faculté de Médicine, de Pharmacie et d'Odonto-Stomatologie, Université du Mali, Bamako, Mali
| | - Yeya T. Touré
- Faculté de Médicine, de Pharmacie et d'Odonto-Stomatologie, Université du Mali, Bamako, Mali
| | - Alessandra della Torre
- Dipartimento di Scienze di Sanità Pubblica, Sezione di Parassitologia, Università degli Studi di Roma-La Sapienza, Roma, Italy
| | - Gregory C. Lanzaro
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California at Davis, Davis, California, United States of America
| | | | - Fotis C. Kafatos
- Section of Infection and Immunity, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (RW); (FK)
| | - Liangbiao Zheng
- Shanghai Institute of Plant Physiology and Ecology, Shanghai, China
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Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH. Update of the Anopheles gambiae PEST genome assembly. Genome Biol 2007; 8:R5. [PMID: 17210077 PMCID: PMC1839121 DOI: 10.1186/gb-2007-8-1-r5] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 10/24/2006] [Accepted: 01/08/2007] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The genome of Anopheles gambiae, the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific community was complicated by the presence of assembly issues, such as scaffolds with no chromosomal location, no sequence data for the Y chromosome, haplotype polymorphisms resulting in two different genome assemblies in limited regions and contaminating bacterial DNA. RESULTS Polytene chromosome in situ hybridization with cDNA clones was used to place 15 unmapped scaffolds (sizes totaling 5.34 Mbp) in the pericentromeric regions of the chromosomes and oriented a further 9 scaffolds. Additional analysis by in situ hybridization of bacterial artificial chromosome (BAC) clones placed 1.32 Mbp (5 scaffolds) in the physical gaps between scaffolds on euchromatic parts of the chromosomes. The Y chromosome sequence information (0.18 Mbp) remains highly incomplete and fragmented among 55 short scaffolds. Analysis of BAC end sequences showed that 22 inter-scaffold gaps were spanned by BAC clones. Unmapped scaffolds were also aligned to the chromosome assemblies in silico, identifying regions totaling 8.18 Mbp (144 scaffolds) that are probably represented in the genome project by two alternative assemblies. An additional 3.53 Mbp of alternative assembly was identified within mapped scaffolds. Scaffolds comprising 1.97 Mbp (679 small scaffolds) were identified as probably derived from contaminating bacterial DNA. In total, about 33% of previously unmapped sequences were placed on the chromosomes. CONCLUSION This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.
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Affiliation(s)
- Maria V Sharakhova
- Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556-0369, USA.
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Vernick KD, Oduol F, Lazzaro BP, Glazebrook J, Xu J, Riehle M, Li J. Molecular genetics of mosquito resistance to malaria parasites. Curr Top Microbiol Immunol 2006; 295:383-415. [PMID: 16265899 DOI: 10.1007/3-540-29088-5_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Malaria parasites are transmitted by the bite of an infected mosquito, but even efficient vector species possess multiple mechanisms that together destroy most of the parasites present in an infection. Variation between individual mosquitoes has allowed genetic analysis and mapping of loci controlling several resistance traits, and the underlying mechanisms of mosquito response to infection are being described using genomic tools such as transcriptional and proteomic analysis. Malaria infection imposes fitness costs on the vector, but various forms of resistance inflict their own costs, likely leading to an evolutionary tradeoff between infection and resistance. Plasmodium development can be successfully completed onlyin compatible mosquito-parasite species combinations, and resistance also appears to have parasite specificity. Studies of Drosophila, where genetic variation in immunocompetence is pervasive in wild populations, offer a comparative context for understanding coevolution of the mosquito-malaria relationship. More broadly, plants also possess systems of pathogen resistance with features that are structurally conserved in animal innate immunity, including insects, and genomic datasets now permit useful comparisons of resistance models even between such diverse organisms.
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Affiliation(s)
- K D Vernick
- Department of Microbiology, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Avenue, St. Paul, MN 55108, USA.
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Xu W, Huang FS, Hao HX, Duan JH, Qiu ZW. Two serine proteases from Anopheles dirus haemocytes exhibit changes in transcript abundance after infection of an incompatible rodent malaria parasite, Plasmodium yoelii. Vet Parasitol 2006; 139:93-101. [PMID: 16567047 DOI: 10.1016/j.vetpar.2006.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 02/15/2006] [Accepted: 02/17/2006] [Indexed: 11/22/2022]
Abstract
Serine proteases are involved in regulation of innate immune responses, such as haemolymph coagulation, melanization reaction and antimicrobial peptide synthesis. Although several serine proteases have been characterized in Anopheles gambiae (A. gambiae), few were cloned from other malaria vectors. In this study, we identified three cDNA fragments of serine proteases (AdSp1, AdSp2 and AdSp3) from haemocytes of an oriental malaria vector, Anopheles dirus (A. dirus), by cloning of fragments amplified with degenerate primers into the T-vector. RT-PCR analysis demonstrated that both AdSp1 and AdSp3 genes were also expressed in salivary gland. Basic local alignment search tool (BLAST) search found that both AdSp1 and AdSp3 were highly similar in sequence to A. gambiae Sp14A and Sp14D2, insects prophenoloxidase activating enzyme (PPAE) and Drosophila protease easter. Semi-quantitative RT-PCR indicated the transcription level of both AdSp1 and AdSp3 in haemocytes of A. dirus infected with Plasmodium yoelii (P. yoelii) was significant higher than that fed on 5% glucose or normal mouse blood at 7 days after the infectious meal (p<0.05), when P. yoelii oocysts began to be melanized by A. dirus. Our results indicated that both AdSp1 and AdSp3 might play an important role during melanotic encapsulation of P. yoelii by A. dirus.
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Affiliation(s)
- Wenyue Xu
- Department of Pathobiology, The Third Military Medical University, Chongqing 400038, PR China.
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Menge DM, Zhong D, Guda T, Gouagna L, Githure J, Beier J, Yan G. Quantitative trait loci controlling refractoriness to Plasmodium falciparum in natural Anopheles gambiae mosquitoes from a malaria-endemic region in western Kenya. Genetics 2006; 173:235-41. [PMID: 16510784 PMCID: PMC1461423 DOI: 10.1534/genetics.105.055129] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural anopheline populations exhibit much variation in ability to support malaria parasite development, but the genetic mechanisms underlying this variation are not clear. Previous studies in Mali, West Africa, identified two quantitative trait loci (QTL) in Anopheles gambiae mosquitoes that confer refractoriness (failure of oocyst development in mosquito midguts) to natural Plasmodium falciparum parasites. We hypothesize that new QTL may be involved in mosquito refractoriness to malaria parasites and that the frequency of natural refractoriness genotypes may be higher in the basin region of Lake Victoria, East Africa, where malaria transmission intensity and parasite genetic diversity are among the highest in the world. Using field-derived F2 isofemale families and microsatellite marker genotyping, two loci significantly affecting oocyst density were identified: one on chromosome 2 between markers AG2H135 and AG2H603 and the second on chromosome 3 near marker AG3H93. The first locus was detected in three of the five isofemale families studied and colocalized to the same region as Pen3 and pfin1 described in other studies. The second locus was detected in two of the five isofemale families, and it appears to be a new QTL. QTL on chromosome 2 showed significant additive effects while those on chromosome 3 exhibited significant dominant effects. Identification of P. falciparum-refractoriness QTL in natural An. gambiae mosquitoes is critical to the identification of the genes involved in malaria parasite transmission in nature and for understanding the coevolution between malaria parasites and mosquito vectors.
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Affiliation(s)
- David M Menge
- Program in Public Health, University of California, Irvine 92697, USA.
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Lobo NF, Behura SK, Aggarwal R, Chen MS, Collins FH, Stuart JJ. Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13. BMC Genomics 2006; 7:7. [PMID: 16412254 PMCID: PMC1352350 DOI: 10.1186/1471-2164-7-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Accepted: 01/16/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To have an insight into the Mayetiola destructor (Hessian fly) genome, we performed an in silico comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases. RESULTS Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene vH13. These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study. In silico gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, and to infer evolutionary relationships. CONCLUSION This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.
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Affiliation(s)
- Neil F Lobo
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Galvin Life Sciences Building, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Susanta K Behura
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Entomology, 505 S Goodwin Ave., University of Illinois, Urbana-Champaign, Il 61801, USA
| | - Rajat Aggarwal
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ming-Shun Chen
- Department of Entomology, 505 S Goodwin Ave., University of Illinois, Urbana-Champaign, Il 61801, USA
| | - Frank H Collins
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Galvin Life Sciences Building, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jeff J Stuart
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
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9
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Eiglmeier K, Wincker P, Cattolico L, Anthouard V, Holm I, Eckenberg R, Quesneville H, Jaillon O, Collins FH, Weissenbach J, Brey PT, Roth CW. Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2005; 35:799-814. [PMID: 15944077 DOI: 10.1016/j.ibmb.2005.02.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/10/2005] [Accepted: 02/15/2005] [Indexed: 05/02/2023]
Abstract
The only natural mechanism of malaria transmission in sub-Saharan Africa is the mosquito, generally Anopheles gambiae. Blocking malaria parasite transmission by stopping the development of Plasmodium in the insect vector would provide a useful alternative to the current methods of malaria control. Toward this end, it is important to understand the molecular basis of the malaria parasite refractory phenotype in An. gambiae mosquito strains. We have selected and sequenced six bacterial artificial chromosome (BAC) clones from the Pen-1 region that is the major quantitative trait locus involved in Plasmodium encapsulation. The sequence and the annotation of five overlapping BAC clones plus one adjacent, but not contiguous clone, totaling 585kb of genomic sequence from the centromeric end of the Pen-1 region of the PEST strain were compared to that of the genome sequence of the same strain produced by the whole genome shotgun technique. This project identified 23 putative mosquito genes plus putative copies of the retrotransposable elements BEL12 and TRANSIBN1_AG in the six BAC clones. Nineteen of the predicted genes are most similar to their Drosophila melanogaster homologs while one is more closely related to vertebrate genes. Comparison of these new BAC sequences plus previously published BAC sequences to the cognate region of the assembled genome sequence identified three retrotransposons present in one sequence version but not the other. One of these elements, Indy, has not been previously described. These observations provide evidence for the recent active transposition of these elements and demonstrate the plasticity of the Anopheles genome. The BAC sequences strongly support the public whole genome shotgun assembly and automatic annotation while also demonstrating the benefit of complementary genome sequences and of human curation. Importantly, the data demonstrate the differences in the genome sequence of an individual mosquito compared to that of a hypothetical, average genome sequence generated by whole genome shotgun assembly.
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Affiliation(s)
- Karin Eiglmeier
- Biochimie et Biologie Moléculaire des Insectes, CNRS-FRE 2849, Institut Pasteur, 25, rue du Dr. Roux, F-75724 Paris Cedex 15, France
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Campbell CL, Vandyke KA, Letchworth GJ, Drolet BS, Hanekamp T, Wilson WC. Midgut and salivary gland transcriptomes of the arbovirus vector Culicoides sonorensis (Diptera: Ceratopogonidae). INSECT MOLECULAR BIOLOGY 2005; 14:121-136. [PMID: 15796745 DOI: 10.1111/j.1365-2583.2004.00537.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Numerous Culicoides spp. are important vectors of livestock or human disease pathogens. Transcriptome information from midguts and salivary glands of adult female Culicoides sonorensis provides new insight into vector biology. Of 1719 expressed sequence tags (ESTs) from adult serum-fed female midguts harvested within 5 h of feeding, twenty-eight clusters of serine proteases were derived. Four clusters encode putative iron binding proteins (FER1, FERL, PXDL1, PXDL2), and two clusters encode metalloendopeptidases (MDP6C, MDP6D) that probably function in bloodmeal catabolism. In addition, a diverse variety of housekeeping cDNAs were identified. Selected midgut protease transcripts were analysed by quantitative real-time PCR (q-PCR): TRY1_115 and MDP6C mRNAs were induced in adult female midguts upon feeding, whereas TRY1_156 and CHYM1 were abundant in midguts both before and immediately after feeding. Of 708 salivary gland ESTs analysed, clusters representing two new classes of protein families were identified: a new class of D7 proteins and a new class of Kunitz-type protease inhibitors. Additional cDNAs representing putative immunomodulatory proteins were also identified: 5' nucleotidases, antigen 5-related proteins, a hyaluronidase, a platelet-activating factor acetylhydrolase, mucins and several immune response cDNAs. Analysis by q-PCR showed that all D7 and Kunitz domain transcripts tested were highly enriched in female heads compared with other tissues and were generally absent from males. The mRNAs of two additional protease inhibitors, TFPI1 and TFPI2, were detected in salivary glands of paraffin-embedded females by in situ hybridization.
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Affiliation(s)
- C L Campbell
- USDA, ARS, Arthropod-Borne Animal Diseases Research Laboratory, College of Agriculture, Department 3354, 1000 E. University, Laramie, WY 82071, USA.
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Meister S, Koutsos AC, Christophides GK. The Plasmodium parasite--a 'new' challenge for insect innate immunity. Int J Parasitol 2005; 34:1473-82. [PMID: 15582524 DOI: 10.1016/j.ijpara.2004.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 09/17/2004] [Accepted: 10/01/2004] [Indexed: 11/23/2022]
Abstract
Though lacking adaptive immunity, insects possess a powerful innate immune system, a genome-encoded defence machinery used to confront infections. Studies in the fruit fly Drosophila melanogaster revealed a remarkable capacity of the innate immune system to differentiate between and subsequently respond to different bacteria and fungi. However, hematophagous compared to non-hematophagous insects encounter additional blood-borne infectious agents, such as parasites and viruses, during their lifetime. Anopheles mosquitoes become infected with the malaria parasite Plasmodium during feeding on infected human hosts and may then transmit the parasite to new hosts during subsequent bites. Whether Anopheles has developed mechanisms to confront these infections is the subject of this review. Initially, we review our current understanding of innate immune reactions and give an overview of the Anopheles immune system as revealed through comparative genomic analyses. Then, we examine and discuss the capacity of mosquitoes to recognize and respond to infections, especially to Plasmodium, and finally, we explore approaches to investigate and potentially utilize the vector immune competence to prevent pathogen transmission. Such approaches constitute a new challenge for insect immunity research, a challenge for global health.
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Affiliation(s)
- S Meister
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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12
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Tripoli G, D'Elia D, Barsanti P, Caggese C. Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae. Genome Biol 2005; 6:R11. [PMID: 15693940 PMCID: PMC551531 DOI: 10.1186/gb-2005-6-2-r11] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 12/08/2004] [Accepted: 01/07/2005] [Indexed: 01/16/2023] Open
Abstract
An analysis of nuclear-encoded oxidative phosphorylation genes in Drosophila and Anopheles reveals that pairs of duplicated genes have strikingly different expression patterns. Background In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set of genes correlated by function and subcellular localization of their products. Results We have identified and annotated the Drosophila melanogaster, D. pseudoobscura and Anopheles gambiae orthologs of 78 nuclear genes encoding mitochondrial proteins involved in oxidative phosphorylation by a comparative analysis of their genomic sequences and organization. We have also identified 47 genes in these three dipteran species each of which shares significant sequence homology with one of the above-mentioned OXPHOS orthologs, and which are likely to have originated by duplication during evolution. Gene structure and intron length are essentially conserved in the three species, although gain or loss of introns is common in A. gambiae. In most tissues of D. melanogaster and A. gambiae the expression level of the duplicate gene is much lower than that of the original gene, and in D. melanogaster at least, its expression is almost always strongly testis-biased, in contrast to the soma-biased expression of the parent gene. Conclusions Quickly achieving an expression pattern different from the parent genes may be required for new OXPHOS gene duplicates to be maintained in the genome. This may be a general evolutionary mechanism for originating phenotypic changes that could lead to species differentiation.
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Affiliation(s)
- Gaetano Tripoli
- University of Bari, DAPEG Section of Genetics, via Amendola 165/A, 70126 Bari, Italy
| | - Domenica D'Elia
- CNR, Institute of Biomedical Technology, Section of Bari, via Amendola 122/D, 70126 Bari, Italy
| | - Paolo Barsanti
- University of Bari, DAPEG Section of Genetics, via Amendola 165/A, 70126 Bari, Italy
| | - Corrado Caggese
- University of Bari, DAPEG Section of Genetics, via Amendola 165/A, 70126 Bari, Italy
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Carton Y, Nappi AJ, Poirie M. Genetics of anti-parasite resistance in invertebrates. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2005; 29:9-32. [PMID: 15325520 DOI: 10.1016/j.dci.2004.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Revised: 04/21/2004] [Accepted: 05/12/2004] [Indexed: 05/24/2023]
Abstract
This review summarizes and compares available data on genetic and molecular aspects of resistance in four well-described invertebrate host-parasite systems: snail-schistosome, mosquito-malaria, mosquito-filarial worm, and Drosophila-wasp associations. It underlies that the major components of the immune reaction, such as hemocyte proliferation and/or activation, and production of cytotoxic radicals are common to invertebrate hosts. Identifying genes responsible for naturally occurring resistance will then be helpful to understand the mechanisms of invertebrate immune defenses and to determine how virulence factors are used by parasites to overcome host resistance. Based on these four well-studied models, invertebrate resistance appears as generally determined by one major locus or a few loci, displaying at least partial dominance. Interestingly, specificity of resistance is highly variable and would involve processes other than simple recognition mechanisms. Finally, resistance was shown to be generally costly but is nevertheless observed at high frequencies in many natural populations, suggesting a high potential for host parasite coevolution.
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Affiliation(s)
- Y Carton
- Laboratoire Populations, Génétique et Evolution, CNRS, 91198 Gif, Yvette, France.
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Christophides GK, Vlachou D, Kafatos FC. Comparative and functional genomics of the innate immune system in the malaria vector Anopheles gambiae. Immunol Rev 2004; 198:127-48. [PMID: 15199960 DOI: 10.1111/j.0105-2896.2004.0127.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In much of Africa, the mosquito Anopheles gambiae is the major vector of human malaria, a devastating infectious disease caused by Plasmodium parasites. Vector and parasite interact at multiple stages and locations, and the nature and effectiveness of this reciprocal interaction determines the success of transmission. Many of the interactions engage the mosquito's innate immunity, a primitive but very effective defense system. In some cases, the mosquito kills the parasite, thus blocking the transmission cycle. However, not all interactions are antagonistic; some represent immune evasion. The sequence of the A. gambiae genome revealed numerous potential components of the innate immune system, and it established that they evolve rapidly, as summarized in the present review. Their rapid evolution by gene family expansion diversification as well as the prevalence of haplotype alleles in the best-studied families may reflect selective adaptation of the immune system to the exigencies of multiple immune challenges in a variety of ecologic niches. As a follow-up to the comparative genomic analysis, the development of functional genomic methodologies has provided novel opportunities for understanding the immune system and the nature of its interactions with the parasite. In this context, identification of both Plasmodium antagonists and protectors in the mosquito represents a significant conceptual advance. In addition to providing fundamental understanding of primitive immune systems, studies of mosquito interactions with the parasite open unprecedented opportunities for novel interventions against malaria transmission. The generation of transgenic mosquitoes that resist malaria infection in the wild and the development of antimalarial 'smart sprays' capable of disrupting interactions that are protective of the parasite, or reinforcing others that are antagonistic, represent technical challenges but also immense opportunities for improvement of global health.
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Sinkins SP, Hastings IM. Male-specific insecticide resistance and mosquito transgene dispersal. Trends Parasitol 2004; 20:413-6. [PMID: 15324731 DOI: 10.1016/j.pt.2004.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There is a need to develop methods to spread disease-blocking transgenes through mosquito populations. This article discusses the possibility of linking transgenes to insecticide-resistant alleles engineered to be expressed only in males. The resulting increase in mean longevity of males carrying the construct under insecticide treatment could easily outweigh any fitness costs in females, so that the construct would spread rapidly. It should be possible to produce constructs where any potential risk of loss of male-specific expression would be negligible.
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Affiliation(s)
- Steven P Sinkins
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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16
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Osta MA, Christophides GK, Vlachou D, Kafatos FC. Innate immunity in the malaria vector Anopheles gambiae:comparative and functional genomics. J Exp Biol 2004; 207:2551-63. [PMID: 15201288 DOI: 10.1242/jeb.01066] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
The resurgence of malaria is at least partly attributed to the absence of an effective vaccine, parasite resistance to antimalarial drugs and resistance to insecticides of the anopheline mosquito vectors. Novel strategies are needed to combat the disease on three fronts: protection (vaccines),prophylaxis/treatment (antimalarial drugs) and transmission blocking. The latter entails either killing the mosquitoes (insecticides), preventing mosquito biting (bednets and repellents), blocking parasite development in the vector (transmission blocking vaccines), genetic manipulation or chemical incapacitation of the vector. During the past decade, mosquito research has been energized by several breakthroughs, including the successful transformation of anopheline vectors, analysis of gene function by RNAi,genome-wide expression profiling using DNA microarrays and, most importantly,sequencing of the Anopheles gambiae genome. These breakthroughs helped unravel some of the mechanisms underlying the dynamic interactions between the parasite and the vector and shed light on the mosquito innate immune system as a set of potential targets to block parasite development. In this context, putative pattern recognition receptors of the mosquito that act as positive and negative regulators of parasite development have been identified recently. Characterizing these molecules and others of similar function, and identifying their ligands on the parasite surface, will provide clues on the nature of the interactions that define an efficient parasite–vector system and open up unprecedented opportunities to control the vectorial capacity of anopheline mosquitoes.
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Affiliation(s)
- Mike A Osta
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Lobo NF, Ton LQ, Hill CA, Emore C, Romero-Severson J, Hunt GJ, Collins FH. Genomic analysis in the sting-2 quantitative trait locus for defensive behavior in the honey bee, Apis mellifera. Genome Res 2004; 13:2588-93. [PMID: 14656966 PMCID: PMC403800 DOI: 10.1101/gr.1634503] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have sequenced an 81-kb genomic region from the honey bee, Apis mellifera, associated with a quantitative trait locus (QTL) sting-2 for aggressive behavior. This sequence represents the first extensive study of the honey-bee genome structure encompassing putative genes in a QTL for a behavioral trait. Expression of 13 putative genes, as well as two transcripts that were present in a honey-bee EST database, was confirmed through reverse transcription analysis of mRNA from the honey-bee head. Whereas most transcripts exhibited little or no variation between European and Africanized honey-bee alleles, one transcript demonstrated significant nonsynonymous substitutions, deletions, and insertions. All 13 putative genes lacked similarity to known invertebrate or vertebrate proteins or transcripts. This observation may be reflective of the processes that determine the genomic evolution of an insect with social behavior and/or haplo-diploidy and are an indication of the unique nature of the honey-bee genome. These results make this sequence an invaluable research tool for the ongoing honey-bee whole-genome sequencing effort.
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Affiliation(s)
- Neil F Lobo
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana 46556, USA
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18
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Zheng L, Wang S, Romans P, Zhao H, Luna C, Benedict MQ. Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon. BMC Genet 2003; 4:16. [PMID: 14577840 PMCID: PMC280672 DOI: 10.1186/1471-2156-4-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2003] [Accepted: 10/24/2003] [Indexed: 11/21/2022] Open
Abstract
Background Anopheles gambiae females are the world's most successful vectors of human malaria. However, a fraction of these mosquitoes is refractory to Plasmodium development. L3-5, a laboratory selected refractory strain, encapsulates transforming ookinetes/early oocysts of a wide variety of Plasmodium species. Previous studies on these mosquitoes showed that one major (Pen1) and two minor (Pen2, Pen3) autosomal dominant quantitative trait loci (QTLs) control the melanotic encapsulation response against P. cynomolgi B, a simian malaria originating in Malaysia. Results We have investigated the response of L3-5 to infection with P. cynomolgi Ceylon, a different but related parasite species, in crosses with the susceptible strain 4Arr. Refractoriness to this parasite is incompletely recessive. Infection and genotyping of F2 intercross females at genome-spanning microsatellite loci revealed that 3 autosomal QTLs control encapsulation of this species. Two loci map to the regions containing Pen2 and Pen3. The novel QTL maps to chromosome 3R, probably to polytene division 32 or 33. Thus the relative contribution of any QTL to oocyst encapsulation varies with the species of parasite. Further, different QTLs were most readily identified in different F2 families. This, like the F1 data, suggests that L3-5 is not genetically homogeneous and that somewhat different pathways may be used to achieve an encapsulation response. Conclusion We have shown here that different QTLs are involved in responses against different Plasmodium parasites.
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Affiliation(s)
- Liangbiao Zheng
- Yale University School of Medicine, Department of Epidemiology and Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Shuang Wang
- Yale University School of Medicine, Department of Epidemiology and Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Patricia Romans
- Department of Zoology, University of Toronto, Toronto, ON, Canada M5S 3G5
| | - Hongyu Zhao
- Yale University School of Medicine, Department of Epidemiology and Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Coralia Luna
- Yale University School of Medicine, Department of Epidemiology and Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Mark Q Benedict
- Centers for Disease Control and Prevention, Mailstop F22, Chamblee, GA 30334, USA
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19
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Hong YS, Hogan JR, Wang X, Sarkar A, Sim C, Loftus BJ, Ren C, Huff ER, Carlile JL, Black K, Zhang HB, Gardner MJ, Collins FH. Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae. Mol Genet Genomics 2003; 268:720-8. [PMID: 12655398 DOI: 10.1007/s00438-003-0813-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Accepted: 01/06/2003] [Indexed: 11/28/2022]
Abstract
A Bacterial Artificial Chromosome (BAC) genomic DNA library of Anopheles gambiae, the major human malaria vector in sub-Saharan Africa, was constructed and characterized. This library (ND-TAM) is composed of 30,720 BAC clones in eighty 384-well plates. The estimated average insert size of the library is 133 kb, with an overall genome coverage of approximately 14-fold. The ends of approximately two-thirds of the clones in the library were sequenced, yielding 32,340 pair-mate ends. A statistical analysis (G-test) of the results of PCR screening of the library indicated a random distribution of BACs in the genome, although one gap encompassing the white locus on the X-chromosome was identified. Furthermore, combined with another previously constructed BAC library (ND-1), ~2,000 BACs have been physically mapped by polytene chromosomal in situ hybridization. These BAC end pair mates and physically mapped BACs have been useful for both the assembly of a fully sequenced A. gambiae genome and for linking the assembled sequence to the three polytene chromosomes. This ND-TAM library is now publicly available at both http://www.malaria.mr4.org/mr4pages/index.html/ and http://hbz.tamu.edu/, providing a valuable resource to the mosquito research community.
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Affiliation(s)
- Y S Hong
- Center for Tropical Disease Research and Training, Department of Biological Sciences, University of Notre Dame, IN 46556, USA
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Abstract
Anopheles gambiae is the mosquito vector responsible for transmitting Plasmodium falciparum, a malaria parasite of humans. With the emergence of genome projects for a variety of prokaryotic and eukaryotic microorganisms, there has been a long-standing interest in sequencing the genomes of the malaria parasite and its insect vector. This tour de force effort has now been completed and reported. The alignment of putative orthologs in An. gambiae with those of Drosophila melanogaster highlights several similarities and differences. These findings could have implications in: (1) identifying new targets for insecticide development; (2) strengthening our understanding of the developmental biology of mosquitoes; and (3) possibly controlling pathogen transmission. A brief overview of these interesting findings and the implications for further studies will be discussed here.
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Affiliation(s)
- Kirkwood M Land
- Sandler Center for Basic Research in Parasitic Diseases, University of California, San Francisco, CA 94143, USA.
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21
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Abstract
Insects' resistance to infectious agents is essential for their own survival and also for the health of the plant, animal and human populations with which they closely interact. Several of the major human diseases are spread by insects and are rapidly expanding as a result of the development of insecticide resistance in vectors and drug resistance in parasites. A vector insects' permissiveness to a pathogen, and hence the spread of the disease, will largely depend on the compatibility of the molecular interactions between the two species and the capability of the insect immune system to recognize and kill the pathogen. The innate immune system comprises a variety of components and mechanisms that can discriminate between different microorganisms and mount specific responses to control pathogenic infections. An impressive body of knowledge on the insects' innate immunity has been generated from studies in the model organism Drosophila. These studies are now guiding the exploration of the immune system in the vector mosquito of human malaria, Anopheles, and its implication in the elimination of parasites. Anopheles immune responses have been linked to parasite losses and some refractory mosquitoes can kill all parasites through specific defence mechanisms. The recently sequenced Drosophila and Anopheles genomes provide a detailed and comparative view on their immune gene repertoires that in combination with post-genomic analyses is used to further dissect the complex mechanisms of Plasmodium killing in the mosquito.
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Affiliation(s)
- George Dimopoulos
- Centre for Molecular Microbiology and Infection, Department of Biological Sciences, Imperial College of Science, Technology and Medicine, SW7 2AZ London, UK.
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Nayar JK, Knight JW. Isoenzyme variation in Aedes aegypti correlated with Dirofilaria immitis infectability. MEDICAL AND VETERINARY ENTOMOLOGY 2002; 16:424-429. [PMID: 12510895 DOI: 10.1046/j.1365-2915.2002.00399.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
From the Vero Beach strain of the mosquito Aedes (Stegomyia) aegypti (L.) (Diptera: Culicidae), substrains were selected for susceptibility (SS) and refractoriness (RR) to the dog heartworm Dirofilaria immitis (Leidy) (Filarioidea: Onchocercidae). These two lines and their reciprocal F1 hybrids were analysed for genetic variation at 14 enzyme loci, using polyacrylamide gel electrophoresis. Six of the enzyme loci showed variation (sample size 48 alleles/locus/line). Three of these were monomorphic in the refractory line but polymorphic in the susceptible, i.e. aconitase hydratase (Acoh), isocitrate dehydrogenase-1 (Idh-1) and phosphoglucomutase (Pgm). The other three loci, glucose-6-phosphate isomerase (Gpi), hexokinase-1 (Hk-1) and isocitrate dehydrogenase-2 (Idh-2), were polymorphic in both SS and RR lines and their hybrids. At two loci (Hk-1, Pgm) three alleles were detected, whereas the other polymorphic loci had only two alleles. For Hk-1, the most frequent allele was Hk-1(80) (0.563) in refractory and Hk-1(100) in the susceptible (0.521) and F1 hybrids. For Pgm the most frequent alleles were Pgm125 in the susceptible line (0.646) and Pgm100 in the F1 hybrids (0.563 and 0.604) and refractory line (1.000). The mean observed heterozygosity (Ho), the mean Hardy-Weinberg expected heterozygosity (He) and the mean number of alleles per locus in the refractory line were lower, but not significantly so, than in the susceptible line and their reciprocal F1 hybrids; the proportion of polymorphic loci was significantly lower in the refractory than in the susceptible line and their F1 hybrids. Within both lines all polymorphisms were in Hardy-Weinberg equilibrium, whereas significant departures from predicted frequencies were observed in SS x RR hybrids at four polymorphic loci (Acoh, Gpi, Hk-1, Pgm) and at three polymorphic loci (Acoh, Hk-1, Pgm) in RR x SS hybrids. The average Nei's and modified Rogers' genetic distances between the lines were 0.024 and 0.139, respectively. These electrophoretic data show that the refractory line (putatively lacking fi allele) can be distinguished from the susceptible line (fi/fi) and their hybrids (heterozygous fi) by isozyme marker frequencies, but it remains to be seen whether this difference is causal or chance linkage. In any case, this model system of Ae. aegypti/D. immitis provides opportunities to better understand and manipulate the molecular biology of filariasis transmission.
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Affiliation(s)
- J K Nayar
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach 32962-4699, USA.
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23
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Abstract
The Anopheles gambiae genome sequence will accelerate identification of new insect vector target genes leading to improved strategies for malaria control.
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Affiliation(s)
- Carlos M Morel
- Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, 20 Avenue Appia, CH-1211 Geneva 27, Switzerland.
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Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 2002; 298:149-59. [PMID: 12364792 DOI: 10.1126/science.1077061] [Citation(s) in RCA: 392] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.
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Affiliation(s)
- Evgeny M Zdobnov
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002; 298:129-49. [PMID: 12364791 DOI: 10.1126/science.1076181] [Citation(s) in RCA: 1399] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
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Affiliation(s)
- Robert A Holt
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
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Koella JC, Sørense FL. Effect of adult nutrition on the melanization immune response of the malaria vector Anopheles stephensi. MEDICAL AND VETERINARY ENTOMOLOGY 2002; 16:316-320. [PMID: 12243233 DOI: 10.1046/j.1365-2915.2002.00381.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two dietary resources - blood and sugar - were assessed for effects on the melanization immune response of the mosquito Anopheles stephensi Liston (Diptera: Culicidae) towards inoculated Sephadex beads (negatively charged C-25). This melanization is conferred by genetic factors capable of making the mosquito refractory to malaria parasites. If An. stephensi females had obtained a bloodmeal one day before inoculation with a bead, the efficacy of their immune response increased with the concentration of sugar ingested. At the highest sugar concentration (6%) tested, 38% of the mosquitoes completely melanized their bead, whereas at the lowest sugar concentration (2%), none of the mosquitoes were able to melanize their bead completely. Among mosquitoes not having a bloodmeal, the immuno-competence was low (c. 9% of the mosquitoes completely melanized their bead) and independent of sugar concentration. The observed interaction between these two resources indicates that both resources are required for the Anopheles female to develop an effective melanization immune response.
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Affiliation(s)
- J C Koella
- Laboratoire de Parasitologie Evolutive, UMR 7103, Université Pierre & Marie Curie, Paris, France.
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27
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Bergman CM, Pfeiffer BD, Rincón-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol 2002; 3:RESEARCH0086. [PMID: 12537575 PMCID: PMC151188 DOI: 10.1186/gb-2002-3-12-research0086] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2002] [Revised: 11/25/2002] [Accepted: 12/05/2002] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. RESULTS We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. CONCLUSIONS Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.
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Affiliation(s)
- Casey M Bergman
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- These authors contributed equally to this work
| | - Barret D Pfeiffer
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- These authors contributed equally to this work
| | - Diego E Rincón-Limas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Current address: Departamento de Biologia Molecular, Universidad Autonoma de Tamaulipas-UAMRA, Reynosa, CP 88740, Mexico
| | - Roger A Hoskins
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | | | - Chris J Mungall
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Adrienne M Wang
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Current address: Department of Physiology, University of California, San Francisco, CA 94143, USA
| | - Brent Kronmiller
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Current address: Department of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Joanne Pacleb
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Soo Park
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Mark Stapleton
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Kenneth Wan
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Reed A George
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Pieter J de Jong
- Children's Hospital and Research Center at Oakland, Oakland, CA 94609, USA
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gerald M Rubin
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448418 DOI: 10.1002/cfg.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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