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Filipović I, Marshall JM, Rašić G. Finding divergent sequences of homomorphic sex chromosomes via diploidized nanopore-based assembly from a single male. bioRxiv 2024:2024.02.29.582759. [PMID: 38464271 PMCID: PMC10925256 DOI: 10.1101/2024.02.29.582759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Although homomorphic sex chromosomes can have non-recombining regions with elevated sequence divergence between its complements, such divergence signals can be difficult to detect bioinformatically. If found in genomes of e.g. insect pests, these sequences could be targeted by the engineered genetic sexing and control systems. Here, we report an approach that can leverage long-read nanopore sequencing of a single XY male to identify divergent regions of homomorphic sex chromosomes. Long-read data are used for de novo genome assembly that is diploidized in a way that maximizes sex-specific differences between its haploid complements. We show that the correct assembly phasing is supported by the mapping of nanopore reads from the male's haploid Y-bearing sperm cells. The approach revealed a highly divergent region (HDR) near the centromere of the homomorphic sex chromosome of Aedes aegypti, the most important arboviral vector, for which there is a great interest in creating new genetic control tools. HDR is located ~5Mb downstream of the known male-determining locus on chromosome 1 and is significantly enriched for ovary-biased genes. While recombination in HDR ceased relatively recently (~1.4 MYA), HDR gametologs have divergent exons and introns of protein coding genes, and most lncRNA genes became X-specific. Megabases of previously invisible sex-linked sequences provide new putative targets for engineering the genetic systems to control this deadly mosquito. Broadly, our approach expands the toolbox for studying cryptic structure of sex chromosomes.
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Affiliation(s)
- Igor Filipović
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
- The University of Queensland, School of Biological Sciences, St Lucia, QLD, Australia
| | - John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gordana Rašić
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
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Filipović I, Rašić G. De novo circular genome assembly of Elizabethkingia anophelis found in the mosquito Aedes aegypti from an Australian colony. Microbiol Resour Announc 2023; 12:e0031023. [PMID: 37623319 PMCID: PMC10508104 DOI: 10.1128/mra.00310-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
We report the complete circular genome assembly of Elizabethkingia anophelis (Flavobacteriales) generated with the ONT and Illumina sequences from a laboratory-reared Aedes aegypti mosquito. This genome sequence does not belong to the lineage of known isolates from Anopheles mosquitoes, indicating that E. anophelis is genomically diverse across mosquito disease vectors.
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Affiliation(s)
- Igor Filipović
- The University of Queensland, School of Biological Sciences, St. Lucia, Australia
| | - Gordana Rašić
- Population Health, QIMR Berghofer Medical Research Institute, Mosquito Genomics, Herston, Australia
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Filipović I. Genomic resources for population analyses of an invasive insect pest Oryctes rhinoceros. Sci Data 2023; 10:199. [PMID: 37041187 PMCID: PMC10090205 DOI: 10.1038/s41597-023-02109-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Over the last few years, various types of NGS data have been accumulating for the coconut rhinoceros beetle (CRB, Oryctes rhinoceros), reflecting the growing interest in curtailing this invasive pest of palm trees. Whilst reference-free analyses of RNA-seq and RAD-seq datasets have been done for different CRB collections, recent availability of the CRB's genome assembly provides an opportunity to collate diverse data and create a reference-based population dataset. Here, I release such a dataset containing 6,725,935 SNPs and genotypes called across 393 individual samples from 16 populations, using the previously published raw sequences generated in 9 different experiments (RAD-Seq, RNA-Seq, WGS). I also provide reference-based datasets for the CRB's mitochondrial variants and for variants of its viral biocontrol agent Oryctes rhinoceros nudivirus. SNP data provide high resolution for determining the geographic origin of invasive CRB. With these genomic resources, new data can be analysed without re-processing the published samples and then integrated to expand the reference datasets.
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Affiliation(s)
- Igor Filipović
- The University of Queensland, School of Biological Sciences, St. Lucia, Australia.
- QIMR Berghofer Medical Research Institute, Herston, Australia.
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4
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Filipović I, Rašić G, Hereward J, Gharuka M, Devine GJ, Furlong MJ, Etebari K. A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros). BMC Genomics 2022; 23:426. [PMID: 35672676 PMCID: PMC9172067 DOI: 10.1186/s12864-022-08628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle’s mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. Results High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles. Conclusions The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08628-z.
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Affiliation(s)
- Igor Filipović
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia. .,Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James Hereward
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
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Aubry F, Dabo S, Manet C, Filipović I, Rose NH, Miot EF, Martynow D, Baidaliuk A, Merkling SH, Dickson LB, Crist AB, Anyango VO, Romero-Vivas CM, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Lutwama JJ, Kohl A, Duong V, Ponlawat A, Sylla M, Akorli J, Otoo S, Lutomiah J, Sang R, Mutebi JP, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, McBride CS, Montagutelli X, Rašić G, Lambrechts L. Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations. Science 2021; 370:991-996. [PMID: 33214283 DOI: 10.1126/science.abd3663] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
The drivers and patterns of zoonotic virus emergence in the human population are poorly understood. The mosquito Aedes aegypti is a major arbovirus vector native to Africa that invaded most of the world's tropical belt over the past four centuries, after the evolution of a "domestic" form that specialized in biting humans and breeding in water storage containers. Here, we show that human specialization and subsequent spread of A. aegypti out of Africa were accompanied by an increase in its intrinsic ability to acquire and transmit the emerging human pathogen Zika virus. Thus, the recent evolution and global expansion of A. aegypti promoted arbovirus emergence not solely through increased vector-host contact but also as a result of enhanced vector susceptibility.
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Affiliation(s)
- Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Caroline Manet
- Mouse Genetics Laboratory, Institut Pasteur, Paris, France
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Noah H Rose
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Elliott F Miot
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Daria Martynow
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Sarah H Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Laura B Dickson
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Anna B Crist
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Victor O Anyango
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Claudia M Romero-Vivas
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Anubis Vega-Rúa
- Institut Pasteur of Guadeloupe, Laboratory of Vector Control Research, Transmission Reservoir and Pathogens Diversity Unit, Morne Jolivière, Guadeloupe, France
| | - Isabelle Dusfour
- Vector Control and Adaptation, Institut Pasteur de la Guyane, Vectopole Amazonien Emile Abonnenc, Cayenne, French Guiana, France
| | - Davy Jiolle
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Martin N Mayanja
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Alongkot Ponlawat
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Massamba Sylla
- Unité d'Entomologie, de Bactériologie, de Virologie, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Jewelna Akorli
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Otoo
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joel Lutomiah
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rosemary Sang
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John-Paul Mutebi
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cheikh T Diagne
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Oumar Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Ousmane Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Amadou A Sall
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Carolyn S McBride
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
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Filipović I, Hereward JP, Rašić G, Devine GJ, Furlong MJ, Etebari K. The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing. PeerJ 2021; 9:e10552. [PMID: 33520439 PMCID: PMC7811291 DOI: 10.7717/peerj.10552] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/21/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts. METHODS Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes. RESULTS The complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.
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Affiliation(s)
- Igor Filipović
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James P. Hereward
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gregor J. Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
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Filipović I, Hapuarachchi HC, Tien WP, Razak MABA, Lee C, Tan CH, Devine GJ, Rašić G. Using spatial genetics to quantify mosquito dispersal for control programs. BMC Biol 2020; 18:104. [PMID: 32819378 PMCID: PMC7439557 DOI: 10.1186/s12915-020-00841-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background Hundreds of millions of people get a mosquito-borne disease every year and nearly one million die. Transmission of these infections is primarily tackled through the control of mosquito vectors. The accurate quantification of mosquito dispersal is critical for the design and optimization of vector control programs, yet the measurement of dispersal using traditional mark-release-recapture (MRR) methods is logistically challenging and often unrepresentative of an insect’s true behavior. Using Aedes aegypti (a major arboviral vector) as a model and two study sites in Singapore, we show how mosquito dispersal can be characterized by the spatial analyses of genetic relatedness among individuals sampled over a short time span without interruption of their natural behaviors. Results Using simple oviposition traps, we captured adult female Ae. aegypti across high-rise apartment blocks and genotyped them using genome-wide SNP markers. We developed a methodology that produces a dispersal kernel for distance which results from one generation of successful breeding (effective dispersal), using the distance separating full siblings and 2nd- and 3rd-degree relatives (close kin). The estimated dispersal distance kernel was exponential (Laplacian), with a mean dispersal distance (and dispersal kernel spread σ) of 45.2 m (95% CI 39.7–51.3 m), and 10% probability of a dispersal > 100 m (95% CI 92–117 m). Our genetically derived estimates matched the parametrized dispersal kernels from previous MRR experiments. If few close kin are captured, a conventional genetic isolation-by-distance analysis can be used, as it can produce σ estimates congruent with the close-kin method if effective population density is accurately estimated. Genetic patch size, estimated by spatial autocorrelation analysis, reflects the spatial extent of the dispersal kernel “tail” that influences, for example, the critical radii of release zones and the speed of Wolbachia spread in mosquito replacement programs. Conclusions We demonstrate that spatial genetics can provide a robust characterization of mosquito dispersal. With the decreasing cost of next-generation sequencing, the production of spatial genetic data is increasingly accessible. Given the challenges of conventional MRR methods, and the importance of quantified dispersal in operational vector control decisions, we recommend genetic-based dispersal characterization as the more desirable means of parameterization.
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Affiliation(s)
- Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
| | | | - Wei-Ping Tien
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore, 138667, Singapore
| | | | - Caleb Lee
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore, 138667, Singapore
| | - Cheong Huat Tan
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore, 138667, Singapore
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
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8
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Etebari K, Filipović I, Rašić G, Devine GJ, Tsatsia H, Furlong MJ. Complete genome sequence of Oryctes rhinoceros nudivirus isolated from the coconut rhinoceros beetle in Solomon Islands. Virus Res 2020; 278:197864. [PMID: 31945420 DOI: 10.1016/j.virusres.2020.197864] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 11/18/2022]
Abstract
Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, 1.698 bp shorter than the originally-described full genome sequence of Ma07 strain from Malaysia. We found 130 out of 139 previously annotated ORFs (seven contained interrupted/non-coding sequences, two were identified as duplicated versions of the existing genes), as well as a putatively inverted regions containing four genes. These results demonstrate the usefulness of a long-read sequencing technology for resolving potential structural variations when describing new virus isolates. While the Solomon Islands isolate exhibited 99.41 % nucleotide sequence identity with the originally described strain, we found several genes, including a core gene (vlf-1), that contained multiple amino acid insertions and/or deletions as putative polymorphisms of large effect. Our complete annotated genome sequence of a newly found isolate in Solomon Islands provides a valuable resource to help elucidate the mechanisms that compromise the efficacy of OrNV as a biocontrol agent against the coconut rhinoceros beetle.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, Australia.
| | - Igor Filipović
- School of Biological Sciences, The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia.
| | - Gordana Rašić
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia.
| | - Gregor J Devine
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia.
| | - Helen Tsatsia
- Ministry of Agriculture and Livestock, Honiara, Solomon Islands.
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, Australia.
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Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018; 563:501-507. [PMID: 30429615 PMCID: PMC6421076 DOI: 10.1038/s41586-018-0692-z] [Citation(s) in RCA: 305] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/05/2018] [Indexed: 11/10/2022]
Abstract
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.
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Affiliation(s)
- Benjamin J Matthews
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA. .,Kavli Neural Systems Institute, New York, NY, USA.
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - William J Glassford
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
| | - Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Gareth D Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK.,Liverpool John Moores University, Liverpool, UK
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.,Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Sanjit S Batra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Carlos A Brito-Sierra
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Steven D Buckingham
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Corey L Campbell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Saki Chan
- Bionano Genomics, San Diego, CA, USA
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin R Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thanyalak Fansiri
- Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France.,Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), IHU - Méditerranée Infection, Marseille, France
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | | | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Raissa G G Kay
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Gareth J Lycett
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | | | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Vidya Ramasamy
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sourav Roy
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Karla Saavedra-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Shruti Sharan
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Atashi Sharma
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA
| | | | - Joe Turner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Zhilei Zhao
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Omar S Akbari
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA, USA
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alexander S Raikhel
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | | | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria V Sharakhova
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | | | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
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10
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Filipović I, Markov S, Filipović V, Filipović J, Vidaković A, Novković N, Rafajlovska V. Modelling of factors influencing the effect of osmotic solution on reduction of selected microorganisms. J Appl Microbiol 2018; 125:843-852. [PMID: 29791770 DOI: 10.1111/jam.13927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/22/2018] [Accepted: 05/18/2018] [Indexed: 11/29/2022]
Abstract
AIMS The goal of this research is to model the effects of two osmotic solutions factors on the reduction of selected microorganisms, and to assess the application in osmotic dehydration process of animal raw materials from the aspect of microbiological safety. METHODS AND RESULTS Sugar beet molasses and aquatic osmotic solution were prepared and inoculated with Escherichia coli, Listeria monocytogenes and Salmonella spp. Varied factors of osmotic solutions were: time, temperature and concentration of osmotic solutions. Samples of osmotic solutions were subjected to standard and modified microbiological ISO methods. The result showed that increase in factors had a positive effect on the reduction of microbiological load, while the time of the process was the most influential technological parameter. Number of L. monocytogenes was reduced to <10 CFU per g at the end of the process in the highest concentration of sugar beet molasses at all process temperatures. CONCLUSIONS Developed mathematical models of reduction ratios for tested microorganisms were statistically significant, allowing good prediction of reduction ratio values based on applied factors. SIGNIFICANCE AND IMPACT OF THE STUDY Obtained levels of reduction of all tested microorganisms present good base for the production of safe osmotically dehydrated products of animal origin.
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Affiliation(s)
- I Filipović
- Faculty of Technology, University of Novi Sad, Novi Sad, Serbia.,SP Laboratory, Bečej, Serbia
| | - S Markov
- Faculty of Technology, University of Novi Sad, Novi Sad, Serbia
| | - V Filipović
- Faculty of Technology, University of Novi Sad, Novi Sad, Serbia
| | - J Filipović
- Insititute for Food Technology, University of Novi Sad, Novi Sad, Serbia
| | - A Vidaković
- Faculty of Technology, University of Novi Sad, Novi Sad, Serbia
| | - N Novković
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - V Rafajlovska
- Faculty of Technology and Metallurgy, Department of Food Technology and Biotechnology, Ss. Cyril and Methodius University in Skopje, Skopje, FYR Macedonia
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11
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Zakrzewski M, Rašić G, Darbro J, Krause L, Poo YS, Filipović I, Parry R, Asgari S, Devine G, Suhrbier A. Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok. Sci Rep 2018; 8:4690. [PMID: 29549363 PMCID: PMC5856816 DOI: 10.1038/s41598-018-22945-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/02/2018] [Indexed: 12/12/2022] Open
Abstract
Medically important arboviruses such as dengue, Zika, and chikungunya viruses are primarily transmitted by the globally distributed mosquito Aedes aegypti. Increasing evidence suggests that transmission can be influenced by mosquito viromes. Herein RNA-Seq was used to characterize RNA metaviromes of wild-caught Ae. aegypti from Bangkok (Thailand) and from Cairns (Australia). The two mosquito populations showed a high degree of similarity in their viromes. BLAST searches of assembled contigs suggest up to 27 insect-specific viruses may infect Ae. aegypti, with up to 23 of these currently uncharacterized and up to 16 infecting mosquitoes from both Cairns and Bangkok. Three characterized viruses dominated, Phasi Charoen-like virus, Humaita-Tubiacanga virus and Cell fusing agent virus, and comparisons with other available RNA-Seq datasets suggested infection levels with these viruses may vary in laboratory-reared mosquitoes. As expected, mosquitoes from Bangkok showed higher mitochondrial diversity and carried alleles associated with knock-down resistance to pyrethroids. Blood meal reads primarily mapped to human genes, with a small number also showing homology with rat/mouse and dog genes. These results highlight the wide spectrum of data that can be obtained from such RNA-Seq analyses, and suggests differing viromes may need to be considered in arbovirus vector competence studies.
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Affiliation(s)
- Martha Zakrzewski
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia
| | - Gordana Rašić
- Mosquito Control, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia
| | - Jonathan Darbro
- Mosquito Control, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia.,Metro North Public Health Unit, Bryden Street, Windsor, QLD, 4030, Australia
| | - Lutz Krause
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia.,The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Yee S Poo
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia
| | - Igor Filipović
- Mosquito Control, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia
| | - Rhys Parry
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4029, Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4029, Australia
| | - Greg Devine
- Mosquito Control, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld, 4029, Australia.
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12
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Rašić G, Filipović I, Callahan AG, Stanford D, Chan A, Lam-Phua SG, Tan CH, Hoffmann AA. The queenslandensis and the type Form of the Dengue Fever Mosquito (Aedes aegypti L.) Are Genomically Indistinguishable. PLoS Negl Trop Dis 2016; 10:e0005096. [PMID: 27806047 PMCID: PMC5091912 DOI: 10.1371/journal.pntd.0005096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/07/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The mosquito Aedes aegypti (L.) is a major vector of viral diseases like dengue fever, Zika and chikungunya. Aedes aegypti exhibits high morphological and behavioral variation, some of which is thought to be of epidemiological significance. Globally distributed domestic Ae. aegypti have often been grouped into (i) the very pale variety queenslandensis and (ii) the type form. Because the two color forms co-occur across most of their range, there is interest in understanding how freely they interbreed. This knowledge is particularly important for control strategies that rely on mating compatibilities between the release and target mosquitoes, such as Wolbachia releases and SIT. To address this question, we analyzed nuclear and mitochondrial genome-wide variation in the co-occurring pale and type Ae. aegypti from northern Queensland (Australia) and Singapore. METHODS/FINDINGS We typed 74 individuals at a 1170 bp-long mitochondrial sequence and at 16,569 nuclear SNPs using a customized double-digest RAD sequencing. 11/29 genotyped individuals from Singapore and 11/45 from Queensland were identified as var. queenslandensis based on the diagnostic scaling patterns. We found 24 different mitochondrial haplotypes, seven of which were shared between the two forms. Multivariate genetic clustering based on nuclear SNPs corresponded to individuals' geographic location, not their color. Several family groups consisted of both forms and three queenslandensis individuals were Wolbachia infected, indicating previous breeding with the type form which has been used to introduce Wolbachia into Ae. aegypti populations. CONCLUSION Aedes aegypti queenslandensis are genomically indistinguishable from the type form, which points to these forms freely interbreeding at least in Australia and Singapore. Based on our findings, it is unlikely that the presence of very pale Ae. aegypti will affect the success of Aedes control programs based on Wolbachia-infected, sterile or RIDL mosquitoes.
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Affiliation(s)
- Gordana Rašić
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Igor Filipović
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Ashley G. Callahan
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Darren Stanford
- Institute of Vector Borne Disease, Monash University, Clayton, Australia
| | - Abigail Chan
- Environmental Health Institute, National Environment Agency, Environment Building, Singapore
| | - Sai Gek Lam-Phua
- Environmental Health Institute, National Environment Agency, Environment Building, Singapore
| | - Cheong Huat Tan
- Environmental Health Institute, National Environment Agency, Environment Building, Singapore
| | - Ary Anthony Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, Australia
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13
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Rašić G, Endersby-Harshman N, Tantowijoyo W, Goundar A, White V, Yang Q, Filipović I, Johnson P, Hoffmann AA, Arguni E. Aedes aegypti has spatially structured and seasonally stable populations in Yogyakarta, Indonesia. Parasit Vectors 2015; 8:610. [PMID: 26627473 PMCID: PMC4666043 DOI: 10.1186/s13071-015-1230-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dengue fever, the most prevalent global arboviral disease, represents an important public health problem in Indonesia. Control of dengue relies on the control of its main vector, the mosquito Aedes aegypti, yet nothing is known about the population history and genetic structure of this insect in Indonesia. Our aim was to assess the spatio-temporal population genetic structure of Ae. aegypti in Yogyakarta, a densely populated region on Java with common dengue outbreaks. METHODS We used multiple marker systems (microsatellites, nuclear and mitochondrial genome-wide single nucleotide polymorphisms generated via Restriction-site Associated DNA sequencing) to analyze 979 Ae. aegypti individuals collected from the Yogyakarta city and the surrounding hamlets during the wet season in 2011 and the following dry season in 2012. We employed individual- and group-based approaches for inferring genetic structure. RESULTS We found that Ae. aegypti in Yogyakarta has spatially structured and seasonally stable populations. The spatial structuring was significant for the nuclear and mitochondrial markers, while the temporal structuring was non-significant. Nuclear markers identified three main genetic clusters, showing that hamlets have greater genetic isolation from each other and from the inner city sites. However, one hamlet experienced unrestricted mosquito interbreeding with the inner city, forming a single genetic cluster. Genetic distance was poorly correlated with the spatial distance among mosquito samples, suggesting stronger influence of human-assisted gene flow than active mosquito movement on spatial genetic structure. A star-shaped mitochondrial haplotype network and a significant R(2) test statistic (R(2) = 0.0187, P = 0.001) support the hypothesis that Ae. aegypti in Yogyakarta originated from a small or homogeneous source and has undergone a relatively recent demographic expansion. CONCLUSION We report the first insights into the spatio-temporal genetic structure and the underlying processes in the dengue fever mosquito from Yogyakarta, Indonesia. Our results provide valuable information on the effectiveness of local control measures as well as guidelines for the implementation of novel biocontrol strategies such as release of Wolbachia-infected mosquitoes.
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Affiliation(s)
- Gordana Rašić
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Nancy Endersby-Harshman
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Warsito Tantowijoyo
- Eliminate Dengue Project-Yogyakarta, Center for Tropical Medicine, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Anjali Goundar
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Vanessa White
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Qiong Yang
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Igor Filipović
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Petrina Johnson
- Eliminate Dengue Project, School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia.
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Eggi Arguni
- Eliminate Dengue Project-Yogyakarta, Center for Tropical Medicine, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
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14
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Rašić G, Schama R, Powell R, Maciel-de Freitas R, Endersby-Harshman NM, Filipović I, Sylvestre G, Máspero RC, Hoffmann AA. Contrasting genetic structure between mitochondrial and nuclear markers in the dengue fever mosquito from Rio de Janeiro: implications for vector control. Evol Appl 2015; 8:901-15. [PMID: 26495042 PMCID: PMC4610386 DOI: 10.1111/eva.12301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 07/24/2015] [Indexed: 12/16/2022] Open
Abstract
Dengue is the most prevalent global arboviral disease that affects over 300 million people every year. Brazil has the highest number of dengue cases in the world, with the most severe epidemics in the city of Rio de Janeiro (Rio). The effective control of dengue is critically dependent on the knowledge of population genetic structuring in the primary dengue vector, the mosquito Aedes aegypti. We analyzed mitochondrial and nuclear genomewide single nucleotide polymorphism markers generated via Restriction-site Associated DNA sequencing, as well as traditional microsatellite markers in Ae. aegypti from Rio. We found four divergent mitochondrial lineages and a strong spatial structuring of mitochondrial variation, in contrast to the overall nuclear homogeneity across Rio. Despite a low overall differentiation in the nuclear genome, we detected strong spatial structure for variation in over 20 genes that have a significantly altered expression in response to insecticides, xenobiotics, and pathogens, including the novel biocontrol agent Wolbachia. Our results indicate that high genetic diversity, spatially unconstrained admixing likely mediated by male dispersal, along with locally heterogeneous genetic variation that could affect insecticide resistance and mosquito vectorial capacity, set limits to the effectiveness of measures to control dengue fever in Rio.
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Affiliation(s)
- Gordana Rašić
- Pest and Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - Renata Schama
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FiocruzRio de Janeiro, Brazil
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, FiocruzRio de Janeiro, Brazil
| | - Rosanna Powell
- Pest and Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - Rafael Maciel-de Freitas
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, FiocruzRio de Janeiro, Brazil
| | - Nancy M Endersby-Harshman
- Pest and Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - Igor Filipović
- Pest and Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - Gabriel Sylvestre
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, FiocruzRio de Janeiro, Brazil
| | - Renato C Máspero
- Gerencia de Risco Biológico da Coordenação de Vigilância Ambiental em Saude, Superintendência de Vigilânciaem Saude – SMSRio de Janeiro, Brazil
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
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15
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Rašić G, Filipović I, Weeks AR, Hoffmann AA. Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti. BMC Genomics 2014; 15:275. [PMID: 24726019 PMCID: PMC4023594 DOI: 10.1186/1471-2164-15-275] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/02/2014] [Indexed: 11/10/2022] Open
Abstract
Background Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. In particular, the delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). We aimed to characterize the new SNP set and to test the resolution against previously described microsatellite markers in detecting broad and fine-scale genetic patterns in Ae. aegypti. Results We developed bioinformatics tools that support the customization of restriction enzyme-based protocols for SNP discovery. We showed that our approach for RAD library construction achieves unbiased genome representation that reflects true evolutionary processes. In Ae. aegypti samples from three continents we identified more than 18,000 putative SNPs. They were widely distributed across the three Ae. aegypti chromosomes, with 47.9% found in intergenic regions and 17.8% in exons of over 2,300 genes. Pattern of their imputed effects in ORFs and UTRs were consistent with those found in a recent transcriptome study. We demonstrated that individual mosquitoes from Indonesia, Australia, Vietnam and Brazil can be assigned with a very high degree of confidence to their region of origin using a large SNP panel. We also showed that familial relatedness of samples from a 0.4 km2 area could be confidently established with a subset of SNPs. Conclusions Using a cost-effective customized RAD sequencing approach supported by our bioinformatics tools, we characterized over 18,000 SNPs in field samples of the dengue fever mosquito Ae. aegypti. The variants were annotated and positioned onto the three Ae. aegypti chromosomes. The new SNP set provided much greater resolution in detecting population structure and estimating fine-scale relatedness than a set of polymorphic microsatellites. RAD-based markers demonstrate great potential to advance our understanding of mosquito population processes, critical for implementing new control measures against this major disease vector.
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Affiliation(s)
- Gordana Rašić
- Pest and Disease Vector Group, Department of Genetics, The University of Melbourne, Victoria 3010, Australia.
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Filipović I, Hahl Z, Gašparac Z, Klemenčić V. Polarographic Characteristics of +5 Vanadium in Phosphate, Borate and Carbonate Buffers. J Am Chem Soc 2002. [DOI: 10.1021/ja01637a013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kovcić V, Jelić S, Filipović I, Tomasević Z. [Serum haptoglobin and alpha-1 antitrysin levels as biological evolution markers in patients with gastric and colorectal cancer]. SRP ARK CELOK LEK 1994; 122:311-313. [PMID: 17974404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Increased serum levels of acute-phase proteins in cancers are considered to be indicative for the presence of a tumour. Following radical treatment, their serum levels are expected to revert to normal. Haptoglobin and alpha-1 antitrypsin have important serum concentrations which allow precision in the detection of their variations. The aim of the study was to determine wherther serial measurements of haptoglobin and alpha-1-antitrypsin levels could be relevant in postoperative monitoring of patients with gastrointestinal cancer. As a model advanced disease was used. Haptoglobin and alpha-1-antitypsin serum levels were determined in 20 healthy controls, andin 100 camples of sera originating from 61 patients with advanced disease: 21 with 16 gastric carcinoma, 27 with 17 large bowel cancer, and 52 with 28 rectal cancer. Both proteins were determined by radial immunodiffusion M+/-SD in healthy controls, being 2.167 +/- 0.733 g/l for HP and 2.372 +/- 0.481 g/l for alpha-1-antitrypsin. Haptoglobin M+/-SD was 2.256 +/- 1.466 in gastric carcinoma, 3.031 +/- 1.517 in bowel cancer and 2.964 +/- 1.189 in rectal cancer. The difference from healthy controls was significant in bowel cancer (p < 0.05) and rectal cancer (p < 0.01). It was also significant between gastric carcinoma and rectal cancer (p < 0.05). Alpha-1-antitrypsin M+/-SD was 2.557 +/- 1.063 in gastric carcinoma, 2.885 +/- 1.746 in bowel cancer and 3.111 +/- 1.192 in rectal cancer. The difference from healthy subjects was significant only for rectal cancer (p < 0.01). In 28 patients with serial sera samples, the disease progression was associated in 64-68% of them with further increase of haptoglobin and alpha-1-antitrypsin levels. Development of microangiopathic haemolytic anaemia decreased levels of both haptoglobin (1.444 +/- 1.165 vs 2.833 +/- 1.311 in the whole group, (p < 0.05) and alpha-1-antitrypsin (1.405 +/- 0.859 vs. 2.934 +/- 1.252 in the whole group, (p < 0.01). Serial determination of haptoglobin and alpha-1-antitrypsin levels seem to be useful in postoperative monitoring of patients with rectal cancer and possibly bowel cancer. They are of no relevance in monitoring patients with gastric carcinoma. Microangiopathic haemolytic anaemia development is associated with serum depletion of both haptoglobin and alpha-1-antitrypsin.
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Grabarić BS, Tkalčec M, Merzel V, Filipović I. Computerized potentiometric determination of stability constants of metal ion-crown complexes by the method of corresponding solutions. ELECTROANAL 1991. [DOI: 10.1002/elan.1140030709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Matusinović T, Filipović I. Potentiometric determination of stability constants of cyanoacetato complexes of cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II) and lead(II). Talanta 1981; 28:199-200. [PMID: 18962893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/1980] [Accepted: 08/31/1980] [Indexed: 05/27/2023]
Abstract
Stability constants of cyanoacetato complexes of cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II) and lead(II) were determined potentiometrically at 25.0 +/- 0.1 degrees and ionic strength 2M (sodium perchlorate). The stability constants were evaluated by a weighted least-squares method.
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Affiliation(s)
- T Matusinović
- Laboratory of Inorganic Chemistry, Faculty of Technology, University of Zagreb, POB 179, 41000 Zagreb, Croatia, Yugoslavia
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Tkalčec M, Granarić B, Filipović I, Piljac I. Polarographic determination of stability constants and thermodynamic parameters of lead(II) propanoate and 2-hydroxypropanoate complexes with a computer-controlled system. Anal Chim Acta 1980. [DOI: 10.1016/s0003-2670(01)83887-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Buddecke E, Filipović I, Wortberg B, Seher A. Wirkungsmechanismus langkettiger Monoenfettsäuren im Energiestoffwechsel des Herzens. ACTA ACUST UNITED AC 1976. [DOI: 10.1002/lipi.19760780505] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Grabarić B, Tkalčec M, Piljac I, Filipović I, Simeon V. Numerical evaluation of complex stability constants from polarographic data for quasi-reversible processes. Anal Chim Acta 1975. [DOI: 10.1016/s0003-2670(01)82789-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Filipović I, Buddecke E. [Mutual activation and intracellular localization of hyaluronidase (EC 3.2.1.35) cathepsin D (EC 3.4.4.23) from bovine spleen]. Hoppe Seylers Z Physiol Chem 1968; 349:533-43. [PMID: 5697787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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