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Haber DA, Arien Y, Lamdan LB, Alcalay Y, Zecharia C, Krsticevic F, Yonah ES, Avraham RD, Krzywinska E, Krzywinski J, Marois E, Windbichler N, Papathanos PA. Targeting mosquito X-chromosomes reveals complex transmission dynamics of sex ratio distorting gene drives. Nat Commun 2024; 15:4983. [PMID: 38862555 PMCID: PMC11166636 DOI: 10.1038/s41467-024-49387-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Engineered sex ratio distorters (SRDs) have been proposed as a powerful component of genetic control strategies designed to suppress harmful insect pests. Two types of CRISPR-based SRD mechanisms have been proposed: X-shredding, which eliminates X-bearing sperm, and X-poisoning, which eliminates females inheriting disrupted X-chromosomes. These differences can have a profound impact on the population dynamics of SRDs when linked to the Y-chromosome: an X-shredder is invasive, constituting a classical meiotic Y-drive, whereas X-poisoning is self-limiting, unable to invade but also insulated from selection. Here, we establish X-poisoning strains in the malaria vector Anopheles gambiae targeting three X-linked genes during spermatogenesis, resulting in male bias. We find that sex distortion is primarily driven by a loss of X-bearing sperm, with limited evidence for postzygotic lethality of female progeny. By leveraging a Drosophila melanogaster model, we show unambiguously that engineered SRD traits can operate differently in these two insects. Unlike X-shredding, X-poisoning could theoretically operate at early stages of spermatogenesis. We therefore explore premeiotic Cas9 expression to target the mosquito X-chromosome. We find that, by pre-empting the onset of meiotic sex chromosome inactivation, this approach may enable the development of Y-linked SRDs if mutagenesis of spermatogenesis-essential genes is functionally balanced.
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Affiliation(s)
- Daniella An Haber
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yael Arien
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Lee Benjamin Lamdan
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yehonathan Alcalay
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Chen Zecharia
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Flavia Krsticevic
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Elad Shmuel Yonah
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Rotem Daniel Avraham
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Elzbieta Krzywinska
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, UK
| | - Jaroslaw Krzywinski
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
- Genetics and Ecology Research Centre, Polo d'Innovazione di Genomica Genetica e Biologia, Via Mazzieri, 05100, Terni, Italy
| | - Eric Marois
- Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, INSERM, CNRS, Strasbourg, France
| | | | - Philippos Aris Papathanos
- Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
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Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, Sharakhova MV. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes. BMC Biol 2024; 22:16. [PMID: 38273363 PMCID: PMC10809549 DOI: 10.1186/s12915-024-01825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. METHODS In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. RESULTS We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. CONCLUSION The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
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Affiliation(s)
- Sergei S Ryazansky
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Molecular Genetics of Cell, NRC "Kurchatov Institute", Moscow, Russia
| | - Chujia Chen
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Group of Genomic Mechanisms of Development, Institute of Cytology and Genetics, Novosibirsk, Russia
- Laboratory of Structural and Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Vitor L Dos Anjos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Rong Guo
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Theresa Menna
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily Ferrill
- County of San Diego Vector Control Program, San Diego, CA, USA
| | - Karen E Schultz
- Mosquito and Vector Management District of Santa Barbara County, Santa Barbara, CA, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | | | | | - Chunhong Mao
- Biocomplexity Institute & Initiative University of Virginia, Charlottesville, VA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, the University of Tennessee, Knoxville, TN, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Zhijian Tu
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia.
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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Alfieri JM, Jonika MM, Dulin JN, Blackmon H. Tempo and Mode of Genome Structure Evolution in Insects. Genes (Basel) 2023; 14:336. [PMID: 36833264 PMCID: PMC9957073 DOI: 10.3390/genes14020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists' early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects. In this article, we synthesize data from thousands of species and use biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. Our results show that orders vary dramatically in the overall rate of chromosome number evolution (a proxy of genome structural stability) and the pattern of evolution (e.g., the balance between fusions and fissions). These findings have important implications for our understanding of likely modes of speciation and offer insight into the most informative clades for future genome sequencing.
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Affiliation(s)
- James M. Alfieri
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
| | - Michelle M. Jonika
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Jennifer N. Dulin
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
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4
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Frankham R. Effects of genomic homozygosity on total fitness in an invertebrate: lethal equivalent estimates for Drosophila melanogaster. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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5
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Anderson N, Jaron KS, Hodson CN, Couger MB, Ševčík J, Weinstein B, Pirro S, Ross L, Roy SW. Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems. Proc Natl Acad Sci U S A 2022; 119:e2122580119. [PMID: 35653559 PMCID: PMC9191650 DOI: 10.1073/pnas.2122580119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/08/2022] [Indexed: 11/18/2022] Open
Abstract
Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species’ genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These empirical results substantiate longstanding proposals for a role for intragenomic conflict in the evolution of genetic systems such as HD/PGE.
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Affiliation(s)
- Noelle Anderson
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343
| | - Kamil S. Jaron
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Christina N. Hodson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Matthew B. Couger
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA 02115
| | - Jan Ševčík
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Brooke Weinstein
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343
| | | | - Laura Ross
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Scott William Roy
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Department of Biology, San Francisco State University, San Francisco, CA 94132
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Gouvi G, Gariou-Papalexiou A, Augustinos AA, Drosopoulou E, Tsiamis G, Bourtzis K, Zacharopoulou A. The Chromosomes of Zeugodacus tau and Zeugodacus cucurbitae: A Comparative Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.854723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Availability of polytene chromosomes and development of polytene chromosome maps have greatly facilitated genetic analysis in Diptera and understanding of chromosomal organization. In tephritids, following the first polytene chromosome maps constructed for the Mediterranean fruit fly, Ceratitis capitata, additional maps have been developed for only few species belonging to the main genera of agricultural importance that are Anastrepha, Bactrocera, Ceratitis, Dacus, Rhagoletis, and Zeugodacus. Comparison of the polytene chromosomes of these species has pointed to the presence of chromosomal rearrangements that can, at least partially, shed light to the chromosomal evolution in this family. Up to now, polytene chromosome maps are available only for one Zeugodacus species, that is Zeugodacus cucurbitae. Here we report the cytogenetic analysis of the mitotic and polytene chromosomes of the pumpkin fly, Zeugodacus tau, along with a comparative analysis with polytene chromosomes of Zeugodacus cucurbitae as well as other tephritids. In situ hybridization experiments resulting to chromosomal localization of selected genes in both species are also presented. The genes used as markers are hsp70, hsp83, scarlet and white pupae. The established homologies presented in this study verify that the two Zeugodacus species are genetically close and support the current taxonomic placement of the Zeugodacus genus. The differences in polytene chromosome level, in combination with results of in situ hybridization experiments, reveal the presence of chromosomal rearrangements, mainly inversions, to both closely and distantly related species, which could potentially be a useful diagnostic tool.
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7
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Morelli MW, Blackmon H, Hjelmen CE. Diptera and Drosophila Karyotype Databases: A Useful Dataset to Guide Evolutionary and Genomic Studies. Front Ecol Evol 2022; 10. [PMID: 36238425 PMCID: PMC9555809 DOI: 10.3389/fevo.2022.832378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Karyotypes and chromosome data have been widely used in many subfields of biology over the last century. Unfortunately, this data is largely scattered among hundreds of articles, books, and theses, many of which are only available behind paywalls. This creates a barrier to new researchers wishing to use this data, especially those from smaller institutions or in countries lacking institutional access to much of the scientific literature. We solved this problem by building two datasets for true flies (Order: Diptera and one specific to Drosophila), These datasets are available via a public interactive database that allows users to explore, visualize and download all data. The Diptera karyotype databases currently contain a total of 3,474 karyotype records from 538 publications. Synthesizing this data, we show several groups are of particular interest for future investigations by whole genome sequencing.
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Affiliation(s)
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Carl E. Hjelmen
- Department of Biology, Utah Valley University, Orem, UT, United States
- Correspondence: Carl E. Hjelmen,
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8
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Mathers TC, Wouters RHM, Mugford ST, Swarbreck D, van Oosterhout C, Hogenhout SA. Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome. Mol Biol Evol 2021; 38:856-875. [PMID: 32966576 PMCID: PMC7947777 DOI: 10.1093/molbev/msaa246] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera and Lepidoptera have conserved genome structure at the scale of whole chromosomes or chromosome arms. Whether this reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids-an important group of hemipteran plant pests-using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganization over the last 30 My, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (Myzus persicae and Acyrthosiphon pisum) and Aphidini (Rhopalosiphum maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression, and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies with chromosome-scale assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Roland H M Wouters
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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9
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Choo A, Fung E, Chen IY, Saint R, Crisp P, Baxter SW. Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni. BMC Genet 2020; 21:127. [PMID: 33339510 PMCID: PMC7747451 DOI: 10.1186/s12863-020-00934-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not required for SIT and their removal or separation from males prior to release remains challenging. In order to develop genetic sexing strains (GSS), conditional traits such as temperature sensitive lethality are required. Results Here we introduce a known Drosophila melanogaster temperature sensitive embryonic lethal mutation into Bactrocera tryoni, a serious horticultural pest in Australia. A non-synonymous point mutation in the D. melanogaster gene shibire causes embryonic lethality at 29 °C and we successfully used CRISPR/Cas9 technology to recreate the orthologous shibire temperature sensitive-1 (shits1) mutation in B. tryoni. Genotypic analyses over three generations revealed that a high fitness cost was associated with the shits1 mutant allele and shits1 homozygotes were not viable at 21 °C, which is a more severe phenotype than that documented in D. melanogaster. Conclusions We have demonstrated the first successful use of CRISPR/Cas9 to introduce precise single base substitutions in an endogenous gene via homology-directed repair in an agricultural pest insect and this technology can be used to trial other conditional mutations for the ultimate aim of generating genetic sexing strains for SIT. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00934-3.
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Affiliation(s)
- Amanda Choo
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
| | - Elisabeth Fung
- South Australian Research and Development Institute (SARDI), Adelaide, SA, Australia
| | - Isabel Y Chen
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Peter Crisp
- South Australian Research and Development Institute (SARDI), Adelaide, SA, Australia.,School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Simon W Baxter
- School of BioSciences, University of Melbourne, Melbourne, Australia
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10
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Yeap HL, Lee SF, Robinson F, Mourant RG, Sved JA, Frommer M, Papanicolaou A, Edwards OR, Oakeshott JG. Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysis. BMC Genet 2020; 21:132. [PMID: 33339498 PMCID: PMC7747370 DOI: 10.1186/s12863-020-00936-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Bactrocera tryoni and Bactrocera neohumeralis mate asynchronously; the former mates exclusively around dusk while the latter mates during the day. The two species also differ in the colour of the post-pronotal lobe (callus), which is predominantly yellow in B. tryoni and brown in B. neohumeralis. We have examined the genetic relationship between the two characters in hybrids, backcrosses and multigeneration hybrid progeny. Results Our analysis of the mating time of the parental species revealed that while B. tryoni mate exclusively at dusk, B. neohumeralis females pair with B. neohumeralis males during the day and with B. tryoni males at dusk. We found considerable variance in mating time and callus colour among hybrid backcross individuals of both sexes but there was a strong although not invariant trend for callus colour to co-segregate with mating time in both sexes. To genetically separate these two phenotypes we allowed the interspecific F1 hybrids to propagate for 25 generations (F25) without selection for mating time or callus colour, finding that the advanced hybrid population had moved towards B. tryoni phenotypes for both traits. Selection for day mating in replicate lines at F25 resulted in significant phenotypic shifts in both traits towards B. neohumeralis phenotypes in F26. However, we were unable to completely recover the mating time profile of B. neohumeralis and relaxation of selection for day mating led to a shift back towards dusk mating, but not yellow callus colour, by F35. Conclusion We conclude that the inheritance of the two major species-defining traits is separable but tightly linked and involves more than one gene in each case. It also appears that laboratory conditions select for the B. tryoni phenotypes for mating time. We discuss our findings in relation to speciation theory and the likely effects of domestication during the generation of mass release strains for sterile insect control programmes.
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Affiliation(s)
- Heng Lin Yeap
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia.
| | - Siu Fai Lee
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia.,Applied BioSciences, Macquarie University, Macquarie Park, Sydney, NSW, 2109, Australia
| | - Freya Robinson
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia
| | - Roslyn G Mourant
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia
| | - John A Sved
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Marianne Frommer
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Sydney, NSW, 2753, Australia
| | - Owain R Edwards
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia.,Applied BioSciences, Macquarie University, Macquarie Park, Sydney, NSW, 2109, Australia
| | - John G Oakeshott
- CSIRO Land and Water, Black Mountain, Canberra, ACT, 2601, Australia.,Applied BioSciences, Macquarie University, Macquarie Park, Sydney, NSW, 2109, Australia
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11
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Sylvester T, Hjelmen CE, Hanrahan SJ, Lenhart PA, Johnston JS, Blackmon H. Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects. Proc Biol Sci 2020; 287:20201388. [PMID: 32993470 PMCID: PMC7542826 DOI: 10.1098/rspb.2020.1388] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/03/2020] [Indexed: 11/13/2022] Open
Abstract
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalizations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed these data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes, and that orders exhibit striking differences in rates of fusions, fissions and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.
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Affiliation(s)
- Terrence Sylvester
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Carl E. Hjelmen
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Shawn J. Hanrahan
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Paul A. Lenhart
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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12
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Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Sex chromosome evolution in parasitic nematodes of humans. Nat Commun 2020; 11:1964. [PMID: 32327641 PMCID: PMC7181701 DOI: 10.1038/s41467-020-15654-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/20/2020] [Indexed: 11/09/2022] Open
Abstract
Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.
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Affiliation(s)
- Jeremy M Foster
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - John Mattick
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Matthew Chung
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Yichao Li
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Silvia Libro
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Michelle L Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Matthew B Rogers
- Department of Surgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Laura Teigen
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Alan Twaddle
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julie C Dunning Hotopp
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Global Public Health, New York University, New York, NY, 10003, USA.
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13
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Abstract
Sex chromosomes and sex determining genes can evolve fast, with the sex-linked chromosomes often differing between closely related species. Population genetics theory has been developed and tested to explain the rapid evolution of sex chromosomes and sex determination. However, we do not know why the sex chromosomes are divergent in some taxa and conserved in others. Addressing this question requires comparing closely related taxa with conserved and divergent sex chromosomes to identify biological features that could explain these differences. Cytological karyotypes suggest that muscid flies (e.g., house fly) and blow flies are such a taxonomic pair. The sex chromosomes appear to differ across muscid species, whereas they are conserved across blow flies. Despite the cytological evidence, we do not know the extent to which muscid sex chromosomes are independently derived along different evolutionary lineages. To address that question, we used genomic and transcriptomic sequence data to identify young sex chromosomes in two closely related muscid species, horn fly (Haematobia irritans) and stable fly (Stomoxys calcitrans). We provide evidence that the nascent sex chromosomes of horn fly and stable fly were derived independently from each other and from the young sex chromosomes of the closely related house fly (Musca domestica). We present three different scenarios that could have given rise to the sex chromosomes of horn fly and stable fly, and we describe how the scenarios could be distinguished. Distinguishing between these scenarios in future work could identify features of muscid genomes that promote sex chromosome divergence.
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14
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Choo A, Nguyen TNM, Ward CM, Chen IY, Sved J, Shearman D, Gilchrist AS, Crisp P, Baxter SW. Identification of Y-chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species. INSECT MOLECULAR BIOLOGY 2019; 28:873-886. [PMID: 31150140 DOI: 10.1111/imb.12602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex-determining Y-chromosome thought to be gene poor and repetitive. Here, we report 39 Y-chromosome scaffolds (~700 kb) from B. tryoni identified using genotype-by-sequencing data and whole-genome resequencing. Male diagnostic PCR assays validated eight Y-scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y-gene, referred to as typo-gyf, is a truncated Y-chromosome paralogue of X-chromosome gene gyf (1773 aa). The Y-chromosome contained ~41 copies of typo-gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo-gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo-gyf evolved within the past 8.02 million years (95% highest posterior density 10.56-5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y-sequences may provide useful sites for future transgene insertions, and typo-gyf could act as a Y-chromosome diagnostic marker for many Bactrocera species, although its function is unknown.
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Affiliation(s)
- Amanda Choo
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Thu N M Nguyen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher M Ward
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Isabel Y Chen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - John Sved
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Deborah Shearman
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony S Gilchrist
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter Crisp
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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15
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The chromosomes of Drosophila suzukii (Diptera: Drosophilidae): detailed photographic polytene chromosomal maps and in situ hybridization data. Mol Genet Genomics 2019; 294:1535-1546. [PMID: 31346719 DOI: 10.1007/s00438-019-01595-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The spotted wing drosophila, D. suzukii, is a serious agricultural pest attacking a variety of soft fruits and vegetables. Although originating from East Asia it has recently invaded America and Europe raising major concern about its expansion potential and the consequent economic losses. Since cytogenetic information on the species is scarce, we report here the mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of D. suzukii. The mitotic metaphase complement contains three pairs of autosomes, one of which is dot-like, and one pair of heteromorphic (XX/XY) sex chromosomes. The salivary gland polytene complement consists of five long polytene arms, representing the two metacentric autosomes and the acrocentric X chromosome, and one very short polytene element, which corresponds to the dot-like autosome. Banding pattern as well as the most characteristic features and prominent landmarks of each polytene chromosome arm are presented and discussed. Furthermore, twelve gene markers have been mapped on the polytene chromosomes of D. suzukii by in situ hybridization. Their distribution pattern was found quite similar to that of D. melanogaster revealing conservation of synteny although the relative position within each chromosome arm for most of the genes differed significantly between D. suzukii and D. melanogaster. The chromosome information presented here is suitable for comparative cytogenetic studies and phylogenetic exploration, while it could also facilitate the assembly of the genome sequence and support the development of genetic tools for species-specific and environment-friendly biological control applications such as the sterile insect technique.
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16
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Perkins RD, Gamboa JR, Jonika MM, Lo J, Shum A, Adams RH, Blackmon H. A database of amphibian karyotypes. Chromosome Res 2019; 27:313-319. [DOI: 10.1007/s10577-019-09613-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/26/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
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17
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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18
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Riddle NC, Elgin SCR. The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. Genetics 2018; 210:757-772. [PMID: 30401762 PMCID: PMC6218221 DOI: 10.1534/genetics.118.301146] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Alabama 35294
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Missouri 63130
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19
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Meisel RP, Scott JG. Using genomic data to study insecticide resistance in the house fly, Musca domestica. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 151:76-81. [PMID: 30704717 DOI: 10.1016/j.pestbp.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/04/2018] [Accepted: 01/08/2018] [Indexed: 06/09/2023]
Abstract
The house fly, Musca domestica, is a major pest at livestock facilities throughout the world. Insecticides have been the most common control strategy for flies, but many populations have evolved resistance. The speed by which we are able to identify the mutations responsible for resistance has been a major challenge for the development of high throughput resistance monitoring assays as new insecticides are introduced for control. This is particularly true for mutations that cause trans regulation of a gene, which then results in resistance. In this paper we take advantage of the conserved homology of dipteran chromosomes to assign 3069 genes to chromosomes. Of these, 234 were of toxicological interest (CYPs, esterases/hydrolases, glutathione S-transferases (GSTs) and target sites). The chromosomal location of genes known from linkage analysis studies matched the location predicted by homology mapping in ten out of ten cases, indicating a high reliability of our approach. The CYPs, esterases/hydrolases and GSTs were not randomly distributed throughout the genome. They clustered on chromosomes, but the pattern was different between the CYPs, esterases/hydrolases and GSTs. Examples are provided for how the availability of the house fly genome, combined with an ability to assign genes to chromosomes, will help to accelerate research in house flies.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Jeffrey G Scott
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA.
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20
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A New Diagnostic Resource for Ceratitis capitata Strain Identification Based on QTL Mapping. G3-GENES GENOMES GENETICS 2017; 7:3637-3647. [PMID: 28889103 PMCID: PMC5677166 DOI: 10.1534/g3.117.300169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Mediterranean fruit fly Ceratitis capitata (Wiedemann) is a destructive agricultural pest and the subject of exclusion efforts in many countries. Suppression and eradication of invasive populations to prevent its establishment is facilitated by the release of sterile males using the sterile insect technique (SIT). In SIT release areas, it is critical to accurately discriminate between released sterile males and wild individuals to detect extremely rare invasive individuals in areas inundated with millions of sterile male flies. Current methods for discrimination exist but are not always definitive, and a more reliable method is necessary. To address this, we developed a genotyping assay that can be used to discriminate between sterile males from the SIT strain and wild individuals. This was achieved by identifying single nucleotide polymorphisms (SNPs) linked to the maintained traits that facilitate male-only releases, white pupae (wp) and temperature-sensitive lethal (tsl), via QTL mapping. This resulted in the identification of one SNP that was in near-perfect linkage disequilibrium between genotype at this locus and the pupal color phenotype. Medfly from many SIT colonies and wild individuals from across its geographic range were genotyped for this locus, and results show its consistency in identifying SIT flies. In addition, linkage and QTL mapping of wp and tsl have larger impacts as they can serve as foundational tools to identify the genetic basis of traits that facilitate the separation of males from female flies, which can be used to develop SIT programs in related species.
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21
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Mandrioli M, Zambonini G, Manicardi GC. Comparative Gene Mapping as a Tool to Understand the Evolution of Pest Crop Insect Chromosomes. Int J Mol Sci 2017; 18:ijms18091919. [PMID: 28880213 PMCID: PMC5618568 DOI: 10.3390/ijms18091919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/22/2022] Open
Abstract
The extent of the conservation of synteny and gene order in aphids has been previously investigated only by comparing a small subset of linkage groups between the pea aphid Acyrthosiphon pisum and a few other aphid species. Here we compared the localization of eight A. pisum scaffolds (covering more than 5 Mb and 83 genes) in respect to the Drosophila melanogaster Muller elements identifying orthologous loci spanning all the four A. pisum chromosomes. Comparison of the genetic maps revealed a conserved synteny across different loci suggesting that the study of the fruit fly Muller elements could favour the identification of chromosomal markers useful for the study of chromosomal rearrangements in aphids. A. pisum is the first aphid species to have its genome sequenced and the finding that there are several chromosomal regions in synteny between Diptera and Hemiptera indicates that the genomic tools developed in A. pisum will be broadly useful not only for the study of other aphids but also for other insect species.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Giada Zambonini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Gian Carlo Manicardi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
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22
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Drosopoulou E, Pantelidou C, Gariou-Papalexiou A, Augustinos AA, Chartomatsidou T, Kyritsis GA, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A. The chromosomes and the mitogenome of Ceratitis fasciventris (Diptera: Tephritidae): two genetic approaches towards the Ceratitis FAR species complex resolution. Sci Rep 2017; 7:4877. [PMID: 28687799 PMCID: PMC5501848 DOI: 10.1038/s41598-017-05132-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/25/2017] [Indexed: 11/29/2022] Open
Abstract
Ceratitis fasciventris is a serious agricultural pest of the Tephritidae family that belongs to the African Ceratitis FAR species complex. Species limits within the FAR complex are obscure and multidisciplinary approaches have attempted to resolve phylogenetic relationships among its members. These studies support the existence of at least three additional species in the complex, C. anonnae, C. rosa and C. quilicii, while they indicate the presence of two structured populations (F1 and F2) within the C. fasciventris species. In the present study we present the mitotic karyotype, polytene chromosome maps, in situ hybridization data and the complete mitochondrial genome sequence of an F2 population of C. fasciventris. This is the first polytene chromosome map and complete mitogenome of a member of the FAR complex and only the second reported for the Ceratitis genus. Both polytene chromosomes and mitochondrial sequence could provide valuable information and be used as reference for comparative analysis among the members of the complex towards the clarification of their phylogenetic relationships.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Christina Pantelidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Antonios A Augustinos
- Department of Biology, University of Patras, Patras, Greece.,Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Tatiana Chartomatsidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios A Kyritsis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Penelope Mavragani-Tsipidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae. G3-GENES GENOMES GENETICS 2017; 7:1927-1940. [PMID: 28450369 PMCID: PMC5473769 DOI: 10.1534/g3.117.040170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genetic sexing strains (GSS) used in sterile insect technique (SIT) programs are textbook examples of how classical Mendelian genetics can be directly implemented in the management of agricultural insect pests. Although the foundation of traditionally developed GSS are single locus, autosomal recessive traits, their genetic basis are largely unknown. With the advent of modern genomic techniques, the genetic basis of sexing traits in GSS can now be further investigated. This study is the first of its kind to integrate traditional genetic techniques with emerging genomics to characterize a GSS using the tephritid fruit fly pest Bactrocera cucurbitae as a model. These techniques include whole-genome sequencing, the development of a mapping population and linkage map, and quantitative trait analysis. The experiment designed to map the genetic sexing trait in B. cucurbitae, white pupae (wp), also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. Quantitative trait loci analysis revealed SNP loci near position 42 MB on chromosome 3 to be tightly linked to wp Gene annotation and synteny analysis show a near perfect relationship between chromosomes in B. cucurbitae and Muller elements A-E in Drosophila melanogaster This chromosome-scale genome assembly is complete, has high contiguity, was generated using a minimal input DNA, and will be used to further characterize the genetic mechanisms underlying wp Knowledge of the genetic basis of genetic sexing traits can be used to improve SIT in this species and expand it to other economically important Diptera.
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24
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Gariou-Papalexiou A, Giardini MC, Augustinos AA, Drosopoulou E, Lanzavecchia SB, Cladera JL, Caceres C, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A. Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member. PLoS One 2016; 11:e0157192. [PMID: 27362546 PMCID: PMC4928812 DOI: 10.1371/journal.pone.0157192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/25/2016] [Indexed: 01/28/2023] Open
Abstract
Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications.
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Affiliation(s)
| | - María Cecilia Giardini
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Antonios A. Augustinos
- Biology Department, University of Patras, Patras, Greece
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Silvia B. Lanzavecchia
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Jorge L. Cladera
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Carlos Caceres
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Penelope Mavragani-Tsipidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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