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Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 2019; 7:e7724. [PMID: 31616583 PMCID: PMC6791345 DOI: 10.7717/peerj.7724] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 11/24/2022] Open
Abstract
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
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Affiliation(s)
- Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Peter A. Scott
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Nicholas Troendle
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Natural, Health, and Mathematical Sciences, MidAmerica Nazarene University, Olathe, KS, United States of America
| | - Pindaro Diaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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Moolhuijzen PM, Lew-Tabor AE, Morgan JAT, Valle MR, Peterson DG, Dowd SE, Guerrero FD, Bellgard MI, Appels R. The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones. BMC Res Notes 2011; 4:254. [PMID: 21777481 PMCID: PMC3160391 DOI: 10.1186/1756-0500-4-254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 07/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhipicephalus (Boophilus) microplus (Rmi) a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the de-novo assembly of two R. microplus BAC sequences from the understudied R microplus genome. Based on available R. microplus sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction. RESULTS In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs). Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA) encoding gene sequence (rDNA), related internal transcribed spacer and complex intergenic region.In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb papilin gene was a helicase gene. This helicase overlapped in two exonic regions with the papilin. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence differences were also determined for the papilin gene and the protein binding sites of the 18S subunit in a comparison to Bos taurus. CONCLUSION In the absence of a sequenced reference genome we have assembled two complex BAC sequences, characterised novel gene structure that was confirmed by gene expression and sequencing analyses. This is the first report to provide evidence for 2 eukaryotic genes with exon regions that overlap on the same strand, the first to describe Rhipicephalinae papilin, and the first to report the complete ribosomal DNA repeated unit sequence structure for ticks. The Cot data estimation of genome wide sequence frequency means this research will underpin future efforts for genome sequencing and assembly of the R. microplus genome.
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Affiliation(s)
- Paula M Moolhuijzen
- Centre for Comparative Genomics, Murdoch University, South St,, Perth, Western Australia, 6150, Australia.
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3
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Socolovschi C, Mediannikov O, Raoult D, Parola P. The relationship between spotted fever group Rickettsiae and ixodid ticks. Vet Res 2009; 40:34. [PMID: 19358804 PMCID: PMC2695030 DOI: 10.1051/vetres/2009017] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Accepted: 04/09/2009] [Indexed: 11/14/2022] Open
Abstract
Spotted fever group Rickettsiae are predominantly transmitted by ticks. Rickettsiae have developed many strategies to adapt to different environmental conditions, including those within their arthropod vectors and vertebrate hosts. The tick-Rickettsiae relationship has been a point of interest for many researchers, with most studies concentrating on the role of ticks as vectors. Unfortunately, less attention has been directed towards the relationship of Rickettsiae with tick cells, tissues, and organs. This review summarizes our current understanding of the mechanisms involved in the relationship between ticks and Rickettsiae and provides an update on the recent methodological improvements that have allowed for comprehensive studies at the molecular level.
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Affiliation(s)
| | | | | | - Philippe Parola
- Unité de Recherche en Maladies Infectieuses et Tropicales Émergentes (URMITE), UMR CNRS-IRD 6236, WHO Collaborative Center for Rickettsial diseases and other arthropod-borne bacterial diseases, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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4
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Hill CA, Guerrero FD, Van Zee JP, Geraci NS, Walling JG, Stuart JJ. The position of repetitive DNA sequence in the southern cattle tick genome permits chromosome identification. Chromosome Res 2009; 17:77-89. [PMID: 19221885 DOI: 10.1007/s10577-008-9003-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 10/24/2008] [Accepted: 10/24/2008] [Indexed: 11/28/2022]
Abstract
Fluorescent in-situ hybridization (FISH) using meiotic chromosome preparations and highly repetitive DNA from the southern cattle tick, Rhipicephalus microplus, was undertaken to investigate genome organization. Several classes of highly repetitive DNA elements were identified by screening a R. microplus bacterial artificial chromosome (BAC) library. A repeat unit of approximately 149 bp, RMR-1 was localized to the subtelomeric regions of R. microplus autosomes 1-6 and 8-10. A second repeat unit, RMR-2 was localized to the subtelomeric regions of all autosomes and the X chromosome. RMR-2 was composed of three distinct repeat populations, RMR-2a, RMR-2b and RMR-2c of 178, 177 and 216 bp in length, respectively. Localization of an rDNA probe identified a single nucleolar organizing region on one autosome. Using a combination of labeled probes, we developed a preliminary karyotype for R. microplus. We present evidence that R. microplus has holocentric chromosomes and explore the implications of these findings for tick chromosome biology and genomic research.
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Affiliation(s)
- Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
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Sunter JD, Patel SP, Skilton RA, Githaka N, Knowles DP, Scoles GA, Nene V, de Villiers E, Bishop RP. A novel SINE family occurs frequently in both genomic DNA and transcribed sequences in ixodid ticks of the arthropod sub-phylum Chelicerata. Gene 2008; 415:13-22. [PMID: 18394826 DOI: 10.1016/j.gene.2008.01.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 01/14/2008] [Accepted: 01/30/2008] [Indexed: 11/18/2022]
Abstract
Reassociation kinetics and flow cytometry data indicate that ixodid tick genomes are large, relative to most arthropods, containing>or=10(9) base pairs. The molecular basis for this is unknown. We have identified a novel small interspersed element with features of a tRNA-derived SINE, designated Ruka, in genomic sequences of Rhipicephalus appendiculatus and Boophilus (Rhipicephalus) microplus ticks. The SINE was also identified in expressed sequence tag (EST) databases derived from several tissues in four species of ixodid ticks, namely R. appendiculatus, B. (R.) microplus, Amblyomma variegatum and also the more distantly related Ixodes scapularis. Secondary structure predictions indicated that Ruka could adopt a tRNA structure that was, atypically, most similar to a serine tRNA. By extrapolation the frequency of occurrence in the randomly selected BAC clone sequences is consistent with approximately 65,000 copies of Ruka in the R. appendiculatus genome. Real time PCR analyses on genomic DNA indicate copy numbers for specific Ruka subsets between 5800 and 38,000. Several putative conserved Ruka insertion sites were identified in EST sequences of three ixodid tick species based on the flanking sequences associated with the SINEs, indicating that some Ruka transpositions probably occurred prior to speciation within the metastriate division of the Ixodidae. The data strongly suggest that Class I transposable elements form a significant component of tick genomes and may partially account for the large genome sizes observed.
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Affiliation(s)
- Jack D Sunter
- The International Livestock Research Institute (ILRI), PO Box 30709, Nairobi, Kenya
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6
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Couvreur B, Beaufays J, Charon C, Lahaye K, Gensale F, Denis V, Charloteaux B, Decrem Y, Prévôt PP, Brossard M, Vanhamme L, Godfroid E. Variability and action mechanism of a family of anticomplement proteins in Ixodes ricinus. PLoS One 2008; 3:e1400. [PMID: 18167559 PMCID: PMC2151134 DOI: 10.1371/journal.pone.0001400] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 12/11/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ticks are blood feeding arachnids that characteristically take a long blood meal. They must therefore counteract host defence mechanisms such as hemostasis, inflammation and the immune response. This is achieved by expressing batteries of salivary proteins coded by multigene families. METHODOLOGY/PRINCIPAL FINDINGS We report the in-depth analysis of a tick multigene family and describe five new anticomplement proteins in Ixodes ricinus. Compared to previously described Ixodes anticomplement proteins, these segregated into a new phylogenetic group or subfamily. These proteins have a novel action mechanism as they specifically bind to properdin, leading to the inhibition of C3 convertase and the alternative complement pathway. An excess of non-synonymous over synonymous changes indicated that coding sequences had undergone diversifying selection. Diversification was not associated with structural, biochemical or functional diversity, adaptation to host species or stage specificity but rather to differences in antigenicity. CONCLUSIONS/SIGNIFICANCE Anticomplement proteins from I. ricinus are the first inhibitors that specifically target a positive regulator of complement, properdin. They may provide new tools for the investigation of role of properdin in physiological and pathophysiological mechanisms. They may also be useful in disorders affecting the alternative complement pathway. Looking for and detecting the different selection pressures involved will help in understanding the evolution of multigene families and hematophagy in arthropods.
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Affiliation(s)
- Bernard Couvreur
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Jérôme Beaufays
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Cédric Charon
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Kathia Lahaye
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - François Gensale
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Valérie Denis
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Benoît Charloteaux
- Centre de Biophysique Moléculaire Numérique, Gembloux Agricultural University, Gembloux, Belgium
| | - Yves Decrem
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Pierre-Paul Prévôt
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Michel Brossard
- Institute of Zoology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Luc Vanhamme
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
- Laboratory of Molecular Parasitology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Edmond Godfroid
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
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7
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Pagel Van Zee J, Geraci NS, Guerrero FD, Wikel SK, Stuart JJ, Nene VM, Hill CA. Tick genomics: The Ixodes genome project and beyond. Int J Parasitol 2007; 37:1297-305. [PMID: 17624352 DOI: 10.1016/j.ijpara.2007.05.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 05/18/2007] [Accepted: 05/21/2007] [Indexed: 11/25/2022]
Abstract
Ticks and mites (subphylum Chelicerata; subclass Acari) include important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a blood-feeding tick vector of human disease and a member of the subphylum Chelicerata. Genome projects for other species of Acari are forthcoming and their genome sequences will likely feature significantly in the future of tick research. Parasitologists interested in advancing the field of tick genomics research will be faced with specific challenges. The development of genetic tools and resources, and the size and repetitive nature of tick genomes are important considerations. Innovative approaches may be required to sequence, assemble, annotate and analyse tick genomes. Overcoming these challenges will enable scientists to investigate the genes and genome organisation of this important group of arthropods and may ultimately lead to new solutions for control of ticks and tick-borne diseases.
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Affiliation(s)
- J Pagel Van Zee
- Purdue University, 901 West State Street, West Lafayette, IN 47907, USA
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8
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Jongejan F, Nene V, de la Fuente J, Pain A, Willadsen P. Advances in the genomics of ticks and tick-borne pathogens. Trends Parasitol 2007; 23:391-6. [PMID: 17656151 DOI: 10.1016/j.pt.2007.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 05/23/2007] [Accepted: 07/05/2007] [Indexed: 11/18/2022]
Abstract
Ticks and the diseases for which they are vectors engage in complex interactions with their mammalian hosts. These interactions involve the developmental processes of tick and pathogen, and interplay between the defensive responses and counter responses of host, tick and pathogen. Understanding these interactions has long been an intractable problem, but progress is now being made thanks to the flood of genomic information on host, tick and pathogen, and the attendant, novel experimental tools that have been generated. Each advance reveals new levels of complexity, but there are encouraging signs that genomics is leading to novel means of parasite control.
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9
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Abstract
Ectoparasites of livestock are of great economic and social importance but their effective control remains difficult. The feasibility of vaccination as a novel control measure was established over a decade ago with the commercial release of a recombinant vaccine against the cattle tick Boophilus microplus. Since then, research has continued on ticks and other ectoparasites. While some ectoparasite species will undoubtedly be refractory to immunological control, for others there has been a steady accumulation of knowledge of partially protective antigens, now accelerating through the application of genomic technologies. Nevertheless, progress towards usable, commercially available vaccines has been limited by a number of factors. The number of highly effective antigens is still very small. Although some classes of antigen have been investigated in more detail than others, we have no systematic knowledge of what distinguishes an effective antigen. Much hope has been placed on the potential of multi-antigen mixtures to deliver the efficacy required of a successful vaccine but with little experimental evidence. The application of current knowledge across parasite and host species needs to be explored but little has been done. In most cases, the path to commercial delivery is uncertain. Although many constraints and challenges remain, the need for vaccines and our capacity to develop them can only increase.
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Affiliation(s)
- P Willadsen
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia QLD 4067 Australia.
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10
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Guerrero FD, Nene VM, George JE, Barker SC, Willadsen P. Sequencing a new target genome: the Boophilus microplus (Acari: Ixodidae) genome project. JOURNAL OF MEDICAL ENTOMOLOGY 2006; 43:9-16. [PMID: 16506442 DOI: 10.1603/0022-2585(2006)043[0009:santgt]2.0.co;2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The southern cattle tick, Boophilus microplus (Canestrini), causes annual economic losses in the hundreds of millions of dollars to cattle producers throughout the world, and ranks as the most economically important tick from a global perspective. Control failures attributable to the development of pesticide resistance have become commonplace, and novel control technologies are needed. The availability of the genome sequence will facilitate the development of these new technologies, and we are proposing sequencing to a 4-6X draft coverage. Many existing biological resources are available to facilitate a genome sequencing project, including several inbred laboratory tick strains, a database of approximately 45,000 expressed sequence tags compiled into a B. microplus Gene Index, a bacterial artificial chromosome (BAC) library, an established B. microplus cell line, and genomic DNA suitable for library synthesis. Collaborative projects are underway to map BACs and cDNAs to specific chromosomes and to sequence selected BAC clones. When completed, the genome sequences from the cow, B. microplus, and the B. microplus-borne pathogens Babesia bovis and Anaplasma marginale will enhance studies of host-vector-pathogen systems. Genes involved in the regeneration of amputated tick limbs and transitions through developmental stages are largely unknown. Studies of these and other interesting biological questions will be advanced by tick genome sequence data. Comparative genomics offers the prospect of new insight into many, perhaps all, aspects of the biology of ticks and the pathogens they transmit to farm animals and people. The B. microplus genome sequence will fill a major gap in comparative genomics: a sequence from the Metastriata lineage of ticks. The purpose of the article is to synergize interest in and provide rationales for sequencing the genome of B. microplus and for publicizing currently available genomic resources for this tick.
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Affiliation(s)
- Felix D Guerrero
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory, Kerrville, TX 78028, USA
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11
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Bunikis J, Barbour AG. Ticks have R2 retrotransposons but not the consensus transposon target site of other arthropods. INSECT MOLECULAR BIOLOGY 2005; 14:465-74. [PMID: 16164602 DOI: 10.1111/j.1365-2583.2005.00577.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: 05/04/2023]
Abstract
Some copies of the large subunit rRNA genes (LSU rDNA) of most arthropods studied to date are inactivated by R-element retrotransposons at a specific target region that is highly conserved in sequence across all kingdoms of organisms. Here we report finding R2 elements in low copy numbers in the LSU rDNA of hard and soft ticks. Although the elements were inserted at the same LSU rDNA location as in insects, there were substitutions in the consensus R2 endonuclease cleavage site in the ticks and some other parasitiform mites. The substituted region comprises a critical contact point with small subunit rRNA, but in vitro structure probing analysis revealed novel, presumably stabilizing base-pairing.
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Affiliation(s)
- J Bunikis
- Department of Microbiology, University of California Irvine, Irvine, CA 92697-4025, USA.
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12
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Jasinskas A, Barbour AG. The Fc fragment mediates the uptake of immunoglobulin C from the midgut to hemolymph in the ixodid tick Amblyomma americanum (Acari: Ixodidae). JOURNAL OF MEDICAL ENTOMOLOGY 2005; 42:359-66. [PMID: 15962788 DOI: 10.1093/jmedent/42.3.359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The phenomenon of immunoglobulin uptake from the midgut into the hemolymph has been observed in both argasid and ixodid ticks, but the mechanism of the uptake is not known. Using capillary feeding of adult Amblyomma americanum (L.) female ticks, we investigated the role of immunoglobulin G Fc and Fab fragments in the uptake process. Intact IgG and fragments labeled with 125I were introduced alone or as a mixture with a 10-fold molar excess of unlabeled compounds into ticks, and then the concentration of the compounds after 3 and 6 h of continuous feeding was assessed in the hemolymph. Our results showed that the uptake of Fc fragments was approximately 4 times higher than Fab fragments at 6 h of the feeding and that Fc but not Fab fragments competed with uptake of intact IgG. Glycosylation of the immunoglobulins did not seem to be required for uptake. There was not a statistically significant difference between the uptake of untreated IgG and IgG treated either with periodate or N-glycanase, and untreated Fc fragments or deglycosylated Fc fragments had equal activity in competition experiments with IgG. The uptake into hemolymph of IgG and Fc fragments, but not Fab fragments, was dependent on the pH of the feeding solution and showed a maximum at approximately pH 7.0. In addition, tick midgut cells bound Fc fragments with high affinity, estimated at 21 nM; the interaction with Fab fragments seemed nonspecific. Our results suggest that Fc fragments are the major determinant for the specific uptake of immunoglobulin G into tick hemolymph.
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Affiliation(s)
- Algis Jasinskas
- Departments of Microbiology and Molecular Genetics and Medicine, University of California, Irvine, Irvine, CA 92697, USA
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13
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Ullmann AJ, Lima CMR, Guerrero FD, Piesman J, Black WC. Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus. INSECT MOLECULAR BIOLOGY 2005; 14:217-222. [PMID: 15796755 DOI: 10.1111/j.1365-2583.2005.00551.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genome sizes and the organization of repetitive DNA were determined in the hard ticks Ixodes scapularis and Boophilus microplus using reassociation kinetics. The I. scapularis genome contains approximately 2.15 pg (2.1x10(3) Mbp) of DNA and consists of no foldback (FB), 27% highly repetitive (HR), 39% moderately repetitive (MR), and 34% unique DNA. The B. microplus genome contains 7.5 pg (7.1x10(3) Mbp) DNA, and consists of 0.82% FB, 31% HR, 38% MR, and 30% unique DNA. In both species, repetitive sequences occur in a mixture of long and short period interspersion but most (65-80%) of the DNA follows a pattern of short period interspersion. Genome size and organization in the three tick species so far examined are distinct from other arthropods in having a greater proportion of MR, a lower proportion of unique and HR DNA of very low sequence complexity.
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Affiliation(s)
- A J Ullmann
- Division of Vector-Borne Infectious Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80522, USA.
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14
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Mans BJ, Neitz AWH. Adaptation of ticks to a blood-feeding environment: evolution from a functional perspective. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 34:1-17. [PMID: 14723893 DOI: 10.1016/j.ibmb.2003.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Ticks had to adapt to an existing and complex vertebrate hemostatic system from being free-living scavengers. A large array of anti-hemostatic mechanisms evolved during this process and includes blood coagulation as well as platelet aggregation inhibitors. Several questions regarding tick evolution exist. What was the nature of the ancestral tick? When did ticks evolve blood-feeding capabilities? How did these capabilities evolve? Did host specificity influence the adaptation of ticks to a blood-feeding environment? What are the implications of tick evolution for future research into tick biology and vaccine development? We investigate these questions in the light of recent research into protein superfamilies from tick saliva. Our conclusions are that the main tick families adapted independently to a blood-feeding environment. This is supported by major differences observed in all processes involved with blood-feeding for hard and soft ticks. Gene duplication events played a major role in the evolution of novel protein functions involved in tick-host interactions. This occurred during the late Cretaceous and was stimulated by the radiation of birds and placental mammals, which provided numerous new niches for ticks to adapt to a new lifestyle. Independent adaptation of the main tick families to a blood-feeding environment has several implications for future tick research in terms of tick genome projects and vaccine development.
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Affiliation(s)
- Ben J Mans
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa.
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Ullmann AJ, Piesman J, Dolan MC, Iv WCB. A preliminary linkage map of the hard tick, Ixodes scapularis. INSECT MOLECULAR BIOLOGY 2003; 12:201-210. [PMID: 12653942 DOI: 10.1046/j.1365-2583.2003.00402.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: 05/24/2023]
Abstract
A linkage map of the Ixodes scapularis genome was constructed, based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F1 intercross progeny from a single, field-collected P1 female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of approximately 109 bp, the relationship of physical to genetic distance was found to be approximately 300 kb/cM in the I. scapularis genome.
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Affiliation(s)
- A J Ullmann
- Division of Vector-Borne Infectious Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado 80522, USA.
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Hill CA, Gutierrez JA. Analysis of the expressed genome of the lone star tick, Amblyomma americanum (Acari: Ixodidae) using an expressed sequence tag approach. MICROBIAL & COMPARATIVE GENOMICS 2001; 5:89-101. [PMID: 11087176 DOI: 10.1089/10906590050179774] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An expressed sequence tag (EST) approach was used to study the genome of two developmental stages of the lone star tick, Amblyomma americanum. cDNA libraries were constructed from the larval and adult stages of A. americanum. In total, 1942 ESTs were sequenced (1462 adult ESTs and 480 larval ESTs) and analyzed using bioinformatic programs. Contig assembly using the CAPII program revealed 11% and 15% redundancy of sequences in the larval and adult ESTs, respectively. Of the 1942 ESTs, 1738 sequences were considered quality sequences and of these, 771 or approximately 44.4% of the sequences were putatively identified based on amino acid identity using the protein Basic Local Alignment Search Tool (BLAST) algorithm. Putatively identified sequences were classified according to their predicted gene function. In total, 967 sequences, or 55.6% of the quality sequences, had limited or no protein similarity to previously identified gene products. Sequences lacking protein homology were analyzed using an automated sequence annotation system for predicted protein characteristics such as open reading frames, signal peptides, protein motifs, and transmembrane regions. In this paper we describe the sequencing of the largest number of ESTs obtained from an arachnid species to date and the subsequent detailed analysis of these sequences.
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Affiliation(s)
- C A Hill
- Elanco Animal Health, A Division of Eli Lilly and Company, Greenfield, Indiana 46140, USA.
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