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Abraham EM, Ganopoulos I, Madesis P, Mavromatis A, Mylona P, Nianiou-Obeidat I, Parissi Z, Polidoros A, Tani E, Vlachostergios D. The Use of Lupin as a Source of Protein in Animal Feeding: Genomic Tools and Breeding Approaches. Int J Mol Sci 2019; 20:ijms20040851. [PMID: 30781397 PMCID: PMC6413129 DOI: 10.3390/ijms20040851] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 12/05/2022] Open
Abstract
Livestock production in the European Union EU is highly dependent on imported soybean, exposing the livestock farming system to risks related to the global trade of soybean. Lupin species could be a realistic sustainable alternative source of protein for animal feeding. Lupinus is a very diverse genus with many species. However, only four of them—namely, L. albus, L. angustifolius, L. luteus and L. mutabilis—are cultivated. Their use in livestock farming systems has many advantages in relation to economic and environmental impact. Generally, lupin grains are characterized by high protein content, while their oil content is relatively low but of high quality. On the other hand, the presence of quinolizidine alkaloids and their specific carbohydrate composition are the main antinutritional factors that prevent their use in animal feeding. This research is mainly related to L. albus and to L. angustifolius, and to a lesser extent, to L. lauteus and L. mutabilis. The breeding efforts are mostly focused on yield stabilization, resistance to biotic and abiotic stresses, biochemical structure associated with seed quality and late maturing. Progress is made in improving lupin with respect to the seed quality, as well as the tolerance to biotic and abiotic stress. It has to be noted that modern cultivars, mostly of L. albus and L. angustifolius, contain low levels of alkaloids. However, for future breeding efforts, the implementation of marker-assisted selection and the available genomic tools is of great importance.
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Affiliation(s)
- Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | | | - Athanasios Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Photini Mylona
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Zoi Parissi
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Alexios Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. PLoS One 2013; 7:e52257. [PMID: 23284958 PMCID: PMC3527410 DOI: 10.1371/journal.pone.0052257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 11/09/2012] [Indexed: 11/19/2022] Open
Abstract
Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.
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Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Nat Protoc 2012; 7:479-99. [PMID: 22343430 DOI: 10.1038/nprot.2011.456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine animals, insects, algae and microbes. These libraries have been used globally for different aspects of genomics research. Here we describe the procedure with the latest improvements that we have made and used for construction of BIBAC libraries. The procedure includes the preparation of BIBAC vectors, the preparation of clonable fragments of the desired size from the source DNA, the construction and transformation of BIBACs and, finally, the characterization and assembly of BIBAC libraries. We also specify the modifications necessary for construction of BAC libraries using the protocol. The entire protocol takes ∼7 d.
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Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, Zhang HB. Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nat Protoc 2012; 7:467-78. [PMID: 22343429 DOI: 10.1038/nprot.2011.455] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Megabase-sized DNA is crucial to modern genomics research of all organisms. Among the preparation methods developed, the nuclei method is the simplest and most widely used for preparing high-quality megabase-sized DNA from divergent organisms. In this method, nuclei are first isolated by physically grinding the source tissues. The nontarget cytoplast organellar genomes and metabolites are removed by centrifugation and washing, thus maximizing the utility of the method and substantially improving the digestibility and clonability of the resultant DNA. The nuclei are then embedded in an agarose matrix containing numerous pores, allowing the access of restriction enzymes while preventing the DNA from physical shearing. DNA is extracted from the nuclei, purified and subsequently manipulated in the agarose matrix. Here we describe the nuclei method that we have successfully used to prepare high-quality megabase-sized DNA from hundreds of plant, animal, fish, insect, algal and microbial species. The entire protocol takes ∼3 d.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA
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Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Pląder W, Seroczyńska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpiński S, Malepszy S, Przybecki Z. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 2011; 6:e22728. [PMID: 21829493 PMCID: PMC3145757 DOI: 10.1371/journal.pone.0022728] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 07/05/2011] [Indexed: 01/01/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.
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MESH Headings
- Adaptation, Physiological
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/genetics
- Cucumis sativus/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Genome, Plant
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Regulatory Sequences, Nucleic Acid
- Sequence Analysis, DNA
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Affiliation(s)
- Rafał Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Justyna Witkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Joanna Dąbrowska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Alexandre Lomsadze
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Kohei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Anna Seroczyńska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Mieczysław Śmiech
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Gutman
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University, Higashi-ku, Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, Tokai University, Minamiaso-mura, Kumamoto, Japan
| | - Mark Borodovsky
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
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Muñoz-Torres MC, Saski C, Blackmon B, Romero-Severson J, Werren JH. Development of bacterial artificial chromosome library resources for parasitoid Hymenoptera (Nasonia vitripennis and Nasonia giraulti: Pteromalidae). INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 1:181-187. [PMID: 20167027 DOI: 10.1111/j.1365-2583.2009.00962.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The species of the genus Nasonia possess qualities that make them excellent candidates for genetic and genomic studies. To increase the wealth of genomic resources for the genus we constructed publicly available bacterial artificial chromosome (BAC) libraries for Nasonia vitripennis and Nasonia giraulti. Libraries have 36 864 clones each, empty-vector contents of approximately 2% and average insert sizes of 113.1 and 97.7 Kb, respectively, representing 12 and 11 genome equivalents. The N. vitripennis library was used for genome sequence assembly and in efforts at positional cloning of a developmental gene. The genome assembly of N. vitripennis is currently composed on 6181 un-joined scaffolds. These BAC libraries can be used to identify and close regions between scaffolds of the genome assemblies of both species.
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Wondji CS, Irving H, Morgan J, Lobo NF, Collins FH, Hunt RH, Coetzee M, Hemingway J, Ranson H. Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector. Genes Dev 2009; 19:452-9. [PMID: 19196725 PMCID: PMC2661802 DOI: 10.1101/gr.087916.108] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 12/08/2008] [Indexed: 11/24/2022]
Abstract
Pyrethroid resistance in Anopheles funestus is a potential obstacle to malaria control in Africa. Tools are needed to detect resistance in field populations. We have been using a positional cloning approach to identify the major genes conferring pyrethroid resistance in this vector. A quantitative trait locus (QTL) named rp1 explains 87% of the genetic variance in pyrethroid susceptibility in two families from reciprocal crosses between susceptible and resistant strains. Two additional QTLs of minor effect, rp2 and rp3, were also detected. We sequenced a 120-kb BAC clone spanning the rp1 QTL and identified 14 protein-coding genes and one putative pseudogene. Ten of the 14 genes encoded cytochrome P450s, and expression analysis indicated that four of these P450s were differentially expressed between susceptible and resistant strains. Furthermore, two of these genes, CYP6P9 and CYP6P4, which are 25 and 51 times overexpressed in resistant females, are tandemly duplicated in the BAC clone as well as in laboratory and field samples, suggesting that P450 gene duplication could contribute to pyrethroid resistance in An. funestus. Single nucleotide polymorphisms (SNPs) were identified within CYP6P9 and CYP6P4, and genotyping of the progeny of the genetic crosses revealed a maximum penetrance value f(2) = 1, confirming that these SNPs are valid resistance markers in the laboratory strains. This serves as proof of principle that a DNA-based diagnostic test could be designed to trace metabolic resistance in field populations. This will be a major advance for insecticide resistance management in malaria vectors, which requires the early detection of resistance alleles.
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Affiliation(s)
- Charles S Wondji
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, United Kingdom.
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Suetsugu Y, Minami H, Shimomura M, Sasanuma SI, Narukawa J, Mita K, Yamamoto K. End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries. BMC Genomics 2007; 8:314. [PMID: 17822570 PMCID: PMC2014780 DOI: 10.1186/1471-2164-8-314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 09/07/2007] [Indexed: 11/24/2022] Open
Abstract
Background We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori). Results More than 94000 BAC end sequences (BESs), comprising more than 55 Mbp and covering about 10.4% of the silkworm genome, were sequenced. Repeat-sequence analysis with known repeat sequences indicated that the long interspersed nuclear elements (LINEs) were abundant in BamHI BESs, whereas DNA-type elements were abundant in EcoRI BESs. Repeat-sequence analysis revealed that the abundance of LINEs might be due to a GC bias of the restriction sites and that the GC content of silkworm LINEs was higher than that of mammalian LINEs. In a BLAST-based sequence analysis of the BESs against two available whole-genome shotgun sequence data sets, more than 70% of the BESs had a BLAST hit with an identity of ≥ 99%. About 14% of EcoRI BESs and about 8% of BamHI BESs were paired-end clones with unique sequences at both ends. Cluster analysis of the BESs clarified the proportion of BESs containing protein-coding regions. Conclusion As a result of this characterization, the identified BESs will be a valuable resource for genomic research on Bombyx mori, for example, as a base for construction of a BAC-based physical map. The use of multiple complementary BAC libraries constructed with different restriction enzymes also makes the BESs a more valuable genomic resource. The GenBank accession numbers of the obtained end sequences are DE283657–DE378560.
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Affiliation(s)
- Yoshitaka Suetsugu
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroshi Minami
- Mitsubishi Space Software Co. Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Michihiko Shimomura
- Mitsubishi Space Software Co. Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Shun-ichi Sasanuma
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Junko Narukawa
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kazuei Mita
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kimiko Yamamoto
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
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Coulibaly MB, Lobo NF, Fitzpatrick MC, Kern M, Grushko O, Thaner DV, Traoré SF, Collins FH, Besansky NJ. Segmental duplication implicated in the genesis of inversion 2Rj of Anopheles gambiae. PLoS One 2007; 2:e849. [PMID: 17786220 PMCID: PMC1952172 DOI: 10.1371/journal.pone.0000849] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 08/15/2007] [Indexed: 01/26/2023] Open
Abstract
The malaria vector Anopheles gambiae maintains high levels of inversion polymorphism that facilitate its exploitation of diverse ecological settings across tropical Africa. Molecular characterization of inversion breakpoints is a first step toward understanding the processes that generate and maintain inversions. Here we focused on inversion 2Rj because of its association with the assortatively mating Bamako chromosomal form of An. gambiae, whose distinctive breeding sites are rock pools beside the Niger River in Mali and Guinea. Sequence and computational analysis of 2Rj revealed the same 14.6 kb insertion between both breakpoints, which occurred near but not within predicted genes. Each insertion consists of 5.3 kb terminal inverted repeat arms separated by a 4 kb spacer. The insertions lack coding capacity, and are comprised of degraded remnants of repetitive sequences including class I and II transposable elements. Because of their large size and patchwork composition, and as no other instances of these insertions were identified in the An. gambiae genome, they do not appear to be transposable elements. The 14.6 kb modules inserted at both 2Rj breakpoint junctions represent low copy repeats (LCRs, also called segmental duplications) that are strongly implicated in the recent (∼0.4Ne generations) origin of 2Rj. The LCRs contribute to further genome instability, as demonstrated by an imprecise excision event at the proximal breakpoint of 2Rj in field isolates.
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Affiliation(s)
- Mamadou B. Coulibaly
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Neil F. Lobo
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Meagan C. Fitzpatrick
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Marcia Kern
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Olga Grushko
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Daniel V. Thaner
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sékou F. Traoré
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Frank H. Collins
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Nora J. Besansky
- Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- * To whom correspondence should be addressed. E-mail:
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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: 90] [Impact Index Per Article: 5.3] [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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Wang Z, Miyake T, Edwards SV, Amemiya CT. Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family. J Hered 2006; 97:541-8. [PMID: 17135461 DOI: 10.1093/jhered/esl040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.
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Affiliation(s)
- Zhenshan Wang
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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Wang W, Xu HL, Lin LP, Su B, Wang YQ. Construction of a BAC library for Chinese amphioxus Branchiostoma belcheri and identification of clones containing Amphi-Pax genes. Genes Genet Syst 2006; 80:233-6. [PMID: 16172535 DOI: 10.1266/ggs.80.233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.
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Affiliation(s)
- Wei Wang
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, China
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13
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Topalis P, Koutsos A, Dialynas E, Kiamos C, Hope LK, Strode C, Hemingway J, Louis C. AnoBase: a genetic and biological database of anophelines. INSECT MOLECULAR BIOLOGY 2005; 14:591-7. [PMID: 16313559 DOI: 10.1111/j.1365-2583.2005.00596.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
AnoBase (http://www.anobase.org) is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.
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Affiliation(s)
- P Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Vassilika Vouton, Heraklion, Crete, Greece
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14
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Lumjuan N, McCarroll L, Prapanthadara LA, Hemingway J, Ranson H. Elevated activity of an Epsilon class glutathione transferase confers DDT resistance in the dengue vector, Aedes aegypti. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2005; 35:861-71. [PMID: 15944082 DOI: 10.1016/j.ibmb.2005.03.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 03/18/2005] [Accepted: 03/21/2005] [Indexed: 05/02/2023]
Abstract
Glutathione transferases (GSTs) play a central role in the detoxification of xenobiotics such as insecticides and elevated GST expression is an important mechanism of insecticide resistance. In the mosquito, Anopheles gambiae, increased expression of an Epsilon class GST, GSTE2, confers resistance to DDT. We have identified eight GST genes in the dengue vector, Aedes aegypti. Four of these belong to the insect specific GST classes Delta and Epsilon and three are from the more ubiquitously distributed Theta and Sigma classes. The expression levels of the two Epsilon genes, a Theta GST and a previously identified Ae. aegypti GST [Grant and Hammock, 1992. Molecular and General Genetics 234, 169-176] were established for an insecticide susceptible and a resistant strain. We show that the putative ortholog of GSTe2 in Ae. aegypti (AaGSTe2) is over expressed in mosquitoes that are resistant to the insecticides DDT and permethrin. Characterisation of recombinant AaGSTE2-2 confirmed the role of this enzyme in DDT metabolism. In addition, unlike its Anopheles ortholog, AaGSTE2-2 also exhibited glutathione peroxidase activity.
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Affiliation(s)
- Nongkran Lumjuan
- Vector Research Group, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
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15
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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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16
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Hill CA, Wikel SK. The Ixodes scapularis Genome Project: an opportunity for advancing tick research. Trends Parasitol 2005; 21:151-3. [PMID: 15780833 DOI: 10.1016/j.pt.2005.02.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The Ixodes scapularis Genome Project (IGP), the first to sequence a tick genome, will provide an unparalleled resource for studying tick biology and tick-host-pathogen relationships, and identifying novel targets for tick and tick-borne disease control. The IGP will be the first genomic analysis of a member of the subphylum Chelicerata and will accelerate the pace of tick research. The challenge for scientists is to translate IGP data into public health benefits.
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Affiliation(s)
- Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
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17
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Adam-Blondon AF, Bernole A, Faes G, Lamoureux D, Pateyron S, Grando MS, Caboche M, Velasco R, Chalhoub B. Construction and characterization of BAC libraries from major grapevine cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:1363-71. [PMID: 15834699 DOI: 10.1007/s00122-005-1924-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 01/05/2005] [Indexed: 05/20/2023]
Abstract
Genome projects were initiated on grapevine (Vitis vinifera L., 2n=38, genome size 475 Mb) through the successful construction of four bacterial artificial chromosome (BAC) libraries from three major cultivars, Cabernet Sauvignon (Cabernet S), Syrah and two different clones of Pinot Noir (Pinot N). Depending on the library, the genome coverage represented 4.5-14.8 genome equivalents with clones having a mean insert size of 93-158 kb. BAC pools suitable for PCR screening were constructed for two of these BAC libraries [Cabernet S and Pinot N clone (cl) 115] and subsequently used to confirm the genome coverage of both libraries by PCR anchoring of 74 genetic markers sampled from the 19 linkage groups. For ten of these markers, two bands on separate BAC pools were differentiated that could correspond either to different alleles or to a duplication of the locus being studied. Finally, a preliminary assessment of the correspondence between genetic and physical distances was made through the anchoring of all the markers mapped along linkage group 1 of the V. vinifera genetic map. A pair of markers, 2.1 cM apart, anchored the same BAC clones, which allowed us to estimate that 1 cM corresponded in this particular region to a maximum length of 130 kb.
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Affiliation(s)
- A-F Adam-Blondon
- Unité Mixte de Recherches sur les Génomes des Végétaux, INRA, 2 rue Gaston Crémieux, 5708 91 057, Evry Cedex, France.
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18
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Krzywinski J, Nusskern DR, Kern MK, Besansky NJ. Isolation and characterization of Y chromosome sequences from the African malaria mosquito Anopheles gambiae. Genetics 2004; 166:1291-302. [PMID: 15082548 PMCID: PMC1470776 DOI: 10.1534/genetics.166.3.1291] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The karyotype of the African malaria mosquito Anopheles gambiae contains two pairs of autosomes and a pair of sex chromosomes. The Y chromosome, constituting approximately 10% of the genome, remains virtually unexplored, despite the recent completion of the A. gambiae genome project. Here we report the identification and characterization of Y chromosome sequences of total length approaching 150 kb. We developed 11 Y-specific PCR markers that consistently yielded male-specific products in specimens from both laboratory colony and natural populations. The markers are characterized by low sequence polymorphism in samples collected across Africa and by presence in more than one copy on the Y. Screening of the A. gambiae BAC library using these markers allowed detection of 90 Y-linked BAC clones. Analysis of the BAC sequences and other Y-derived fragments showed massive accumulation of a few transposable elements. Nevertheless, more complex sequences are apparently present on the Y; these include portions of an approximately 48-kb-long unmapped AAAB01008227 scaffold from the whole genome shotgun assembly. Anopheles Y appears not to harbor any of the genes identified in Drosophila Y. However, experiments suggest that one of the ORFs from the AAAB01008227 scaffold represents a fragment of a gene with male-specific expression.
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Affiliation(s)
- Jaroslaw Krzywinski
- Center for Tropical Disease Research and Training, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
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19
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Pitts RJ, Fox AN, Zwiebel LJ. A highly conserved candidate chemoreceptor expressed in both olfactory and gustatory tissues in the malaria vector Anopheles gambiae. Proc Natl Acad Sci U S A 2004; 101:5058-63. [PMID: 15037749 PMCID: PMC387373 DOI: 10.1073/pnas.0308146101] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Indexed: 11/18/2022] Open
Abstract
Anopheles gambiae is a highly anthropophilic mosquito responsible for the majority of malaria transmission in Africa. The biting and host preference behavior of this disease vector is largely influenced by its sense of smell, which is presumably facilitated by G protein-coupled receptor signaling [Takken, W. & Knols, B. (1999) Annu. Rev. Entomol. 44, 131-157]. Because of the importance of host preference to the mosquitoes' ability to transmit disease, we have initiated studies intended to elucidate the molecular mechanisms underlying olfaction in An. gambiae. In the course of these studies, we have identified a number of genes potentially involved in signal transduction, including a family of candidate odorant receptors. One of these receptors, encoded by GPRor7 (hereafter referred to as AgOr7), is remarkably similar to an odorant receptor that is expressed broadly in olfactory tissues and has been identified in Drosophila melanogaster and other insects [Krieger, J., Klink, O., Mohl, C., Raming, K. & Breer, H. (2003) J. Comp. Physiol. A 189, 519-526; Vosshall, L. B., Amrein, H., Morozov, P. S., Rzhetsky, A. & Axel, R. (1999) Cell 96, 725-736]. We have observed AgOr7 expression in olfactory and gustatory tissues in adult An. gambiae and during several stages of the mosquitoes' development. Within the female adult peripheral chemosensory system, antiserum against the AgOR7 polypeptide labels most sensilla of the antenna and maxillary palp as well as a subset of proboscis sensilla. Furthermore, AgOR7 antiserum labeling is observed within the larval antenna and maxillary palpus. These results are consistent with a role for AgOr7 in both olfaction and gustation in An. gambiae and raise the possibility that AgOr7 orthologs may also be of general importance to both modalities of chemosensation in other insects.
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Affiliation(s)
- R Jason Pitts
- Department of Biological Sciences, Center for Molecular Neuroscience and Program in Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
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20
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Jiménez LV, Kang BK, deBruyn B, Lovin DD, Severson DW. Characterization of an Aedes aegypti bacterial artificial chromosome (BAC) library and chromosomal assignment of BAC clones for physical mapping quantitative trait loci that influence Plasmodium susceptibility. INSECT MOLECULAR BIOLOGY 2004; 13:37-44. [PMID: 14728665 DOI: 10.1046/j.0962-1075.2004.00456.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Previous studies have confirmed a genetic basis for susceptibility of mosquitoes to Plasmodium parasites. Here we describe our efforts to characterize a bacterial artificial chromosome genomic library for the yellow fever mosquito, Aedes aegypti, and to identify BAC clones containing genetic markers that define quantitative trait loci (QTL) for Plasmodium gallinaceum susceptibility. This library (NDL) was prepared from the Ae. aegypti Liverpool strain and consists of 50 304 clones arrayed in 384-well microplates. We used PCR analysis with oligonucleotide primer pairs specific to 106 genetic markers (as sequence-tagged sites or STS) to screen the NDL library. Each STS identified between one and thirteen independent clones with an average of 3.3 clones. The average insert size was 122 kb and therefore the NDL library provides approximately 7.87-fold genome coverage. The availability of the NDL library should greatly facilitate physical mapping efforts, including positional cloning of QTL for traits of interest such as Plasmodium susceptibility and for whole genome sequence determination and assembly.
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Affiliation(s)
- L V Jiménez
- Center for Tropical Disease Research and Training, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556-5645, USA.
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21
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003; 4. [PMCID: PMC2447311 DOI: 10.1002/cfg.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Li L, Lu S, O'Halloran DM, Garvin DF, Vrebalov J. High-resolution genetic and physical mapping of the cauliflower high-beta-carotene gene Or ( Orange). Mol Genet Genomics 2003; 270:132-8. [PMID: 12908106 DOI: 10.1007/s00438-003-0904-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2003] [Accepted: 07/17/2003] [Indexed: 11/25/2022]
Abstract
Mutation in the cauliflower gene Or causes high levels of beta-carotene to accumulate in various tissues of the plant that are normally devoid of carotenoids. To decipher the molecular basis by which Or regulates carotenoid accumulation, we have undertaken the isolation of Or by a map-based cloning strategy. Two previously isolated, locus-specific, sequence-characterized amplified region (SCAR) markers that flank Or were employed for the analysis of a large segregating population consisting of 1632 F(2) individuals, and a high-resolution genetic linkage map of the Or locus region was developed. To facilitate positional cloning, we constructed a cauliflower genomic library in a bacterial artificial chromosome (BAC) vector, using high molecular weight DNA from Or homozygotes. The BAC library comprises 60,288 clones with an average insert size of 110 kb, and represents an estimated 10-fold coverage of the genome. A BAC contig encompassing the Or locus was established by screening the library with a marker that is closely linked to Or and by identifying overlapping BAC clones by chromosome walking. Physical mapping delimited the Or locus to a 50-kb DNA fragment within a single BAC clone, which corresponds to a genetic interval of 0.3 cM.
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Affiliation(s)
- L Li
- USDA-ARS, Plant, Soil and Nutrition Laboratory, Cornell University, Ithaca, NY 14853, USA.
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23
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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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