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Anstead CA, Perry T, Richards S, Korhonen PK, Young ND, Bowles VM, Batterham P, Gasser RB. The Battle Against Flystrike - Past Research and New Prospects Through Genomics. ADVANCES IN PARASITOLOGY 2017; 98:227-281. [PMID: 28942770 DOI: 10.1016/bs.apar.2017.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Flystrike, or cutaneous myiasis, is caused by blow fly larvae of the genus Lucilia. This disease is a major problem in countries with large sheep populations. In Australia, Lucilia cuprina (Wiedemann, 1830) is the principal fly involved in flystrike. While much research has been conducted on L. cuprina, including physical, chemical, immunological, genetic and biological investigations, the molecular biology of this fly is still poorly understood. The recent sequencing, assembly and annotation of the draft genome and analyses of selected transcriptomes of L. cuprina have given a first global glimpse of its molecular biology and insights into host-fly interactions, insecticide resistance genes and intervention targets. The present article introduces L. cuprina, flystrike and associated issues, details past control efforts and research foci, reviews salient aspects of the L. cuprina genome project and discusses how the new genomic and transcriptomic resources for this fly might accelerate fundamental molecular research of L. cuprina towards developing new methods for the treatment and control of flystrike.
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Affiliation(s)
| | - Trent Perry
- The University of Melbourne, Parkville, VIC, Australia
| | | | | | - Neil D Young
- The University of Melbourne, Parkville, VIC, Australia
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Anstead CA, Batterham P, Korhonen PK, Young ND, Hall RS, Bowles VM, Richards S, Scott MJ, Gasser RB. A blow to the fly — Lucilia cuprina draft genome and transcriptome to support advances in biology and biotechnology. Biotechnol Adv 2016; 34:605-620. [DOI: 10.1016/j.biotechadv.2016.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/08/2016] [Accepted: 02/20/2016] [Indexed: 02/07/2023]
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Balakirev ES, Anisimova M, Pavlyuchkov VA, Ayala FJ. DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea). BMC Genet 2016; 17:66. [PMID: 27176219 PMCID: PMC4866015 DOI: 10.1186/s12863-016-0374-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The sperm gene bindin encodes a gamete recognition protein, which plays an important role in conspecific fertilization and reproductive isolation of sea urchins. Molecular evolution of the gene has been extensively investigated with the attention focused on the protein coding regions. Intron evolution has been investigated to a much lesser extent. We have studied nucleotide variability in the complete bindin locus, including two exons and one intron, in the sea urchin Strongylocentrotus intermedius represented by two morphological forms. We have also analyzed all available bindin sequences for two other sea urchin species, S. pallidus and S. droebachiensis. RESULTS The results show that the bindin sequences from the two forms of S. intermedius are intermingled with no evidence of genetic divergence; however, the forms exhibit slightly different patterns in bindin variability. The level of the bindin nucleotide diversity is close for S. intermedius and S. droebachiensis, but noticeably higher for S. pallidus. The distribution of variability is non-uniform along the gene; however there are striking similarities among the species, indicating similar evolutionary trends in this gene engaged in reproductive function. The patterns of nucleotide variability and divergence are radically different in the bindin coding and intron regions. Positive selection is detected in the bindin coding region. The neutrality tests as well as the maximum likelihood approaches suggest the action of diversifying selection in the bindin intron. CONCLUSIONS Significant deviation from neutrality has been detected in the bindin coding region and suggested in the intron, indicating the possible functional importance of the bindin intron variability. To clarify the question concerning possible involvement of diversifying selection in the bindin intron evolution more data combining population genetic and functional approaches are necessary.
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Affiliation(s)
- Evgeniy S Balakirev
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Science, Vladivostok, 690041, Russia.
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA.
- Far Eastern Federal University, Vladivostok, 690950, Russia.
| | - Maria Anisimova
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, 8820, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | | | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
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Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions. Nat Commun 2015; 6:7344. [PMID: 26108605 PMCID: PMC4491171 DOI: 10.1038/ncomms8344] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/29/2015] [Indexed: 01/20/2023] Open
Abstract
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
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Dimitrieva S, Anisimova M. Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. PLoS One 2014; 9:e95034. [PMID: 24896293 PMCID: PMC4045579 DOI: 10.1371/journal.pone.0095034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 03/23/2014] [Indexed: 12/26/2022] Open
Abstract
In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To evaluate the extent and the nature of site-specific selection on synonymous codons, we computed the site-to-site synonymous rate variation (SRV) and identified gene properties that make SRV more likely in a large database of protein-coding gene families and protein domains. To our knowledge, this is the first study that explores the determinants and patterns of the SRV in real data. We show that the SRV is widespread in the evolution of protein-coding sequences, putting in doubt the validity of the synonymous rate as a standard neutral proxy. While protein domains rarely undergo adaptive evolution, the SRV appears to play important role in optimizing the domain function at the level of DNA. In contrast, protein families are more likely to evolve by positive selection, but are less likely to exhibit SRV. Stronger SRV was detected in genes with stronger codon bias and tRNA reusage, those coding for proteins with larger number of interactions or forming larger number of structures, located in intracellular components and those involved in typically conserved complex processes and functions. Genes with extreme SRV show higher expression levels in nearly all tissues. This indicates that codon bias in a gene, which often correlates with gene expression, may often be a site-specific phenomenon regulating the speed of translation along the sequence, consistent with the co-translational folding hypothesis. Strikingly, genes with SRV were strongly overrepresented for metabolic pathways and those associated with several genetic diseases, particularly cancers and diabetes.
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Affiliation(s)
- Slavica Dimitrieva
- Swiss Institute for Experimental Cancer Research (ISREC) and Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Department of Computer Science, ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Maria Anisimova
- Department of Computer Science, ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail:
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Gil M, Zanetti MS, Zoller S, Anisimova M. CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol 2013; 30:1270-80. [PMID: 23436912 PMCID: PMC3649670 DOI: 10.1093/molbev/mst034] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, phylogenetic inference is expected to be more accurate under codon models. So far, phylogeny reconstruction under codon models has been elusive due to computational difficulties of dealing with high dimension matrices. Here, we present a fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated and real data and is shown to offer excellent speed and convergence properties. In addition, CodonPhyML includes most recent fast methods for estimating phylogenetic branch supports and provides an integral framework for models selection, including amino acid and DNA models.
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Affiliation(s)
- Manuel Gil
- Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland.
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Abstract
Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.
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Affiliation(s)
- Claus O Wilke
- Institute of Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America.
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