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Byrne S, Schughart M, Carolan JC, Gaffney M, Thorpe P, Malloch G, Wilkinson T, McNamara L. Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola. G3 Genes|Genomes|Genetics 2022; 12:6456306. [PMID: 34878113 PMCID: PMC9210274 DOI: 10.1093/g3journal/jkab418] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022]
Abstract
The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of barley yellow dwarf virus leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high-quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.
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Affiliation(s)
- Stephen Byrne
- Teagasc, Crop Science Department, Carlow R93 XE12, Ireland
| | - Maximilian Schughart
- Teagasc, Crop Science Department, Carlow R93 XE12, Ireland
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, W23 F2H6, Ireland
| | | | - Peter Thorpe
- School of Medicine, University of St Andrews, North Haugh, KY16 9TF St Andrews, UK
| | - Gaynor Malloch
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Tom Wilkinson
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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Lazarova SS, Brown DJ, Oliveira CMG, Fenton B, MacKenzie K, Wright F, Malloch G, Neilson R. Diversity of endosymbiont bacteria associated with a non-filarial nematode group. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
There is a significant knowledge gap with regard to non-filarial nematodes and their relationships, if any, with intracellular bacteria, with only sporadic reports in the literature. An intracellular bacteriaXiphinematobacter, belonging to subdivision 2 of the Verrucomicrobia, was previously reported in the ovaries of three species of the non-filarialXiphinema americanum-group of nematodes. We explored the diversity ofXiphinematobacterin 22 populations ofX. americanumsourced from six continents and conservatively have identified nine phylotypes, six of which have not previously been reported. A geographic basis to the phylotypes was noted with phylotypes A and B only found in Europe, whereas phylotypes F, G, H and I were mainly found in North America. Phylotypes C, D and E showed greater geographical variation. Sequences ofXiphinematobacterfrom this study help to inform the taxonomy of Verrucomicrobia such that the status and composition of Verrucomicrobia subdivision 2 potentially requires reflection.
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Affiliation(s)
- Stela S. Lazarova
- Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Derek J.F. Brown
- Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | | | - Brian Fenton
- Scotland’s Rural College (SRUC), Peter Wilson Building, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, Scotland, UK
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland, Dundee DD2 5DA, Scotland, UK
| | - Frank Wright
- Biomathematics and Statistics Scotland, Dundee DD2 5DA, Scotland, UK
| | - Gaynor Malloch
- The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Roy Neilson
- The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
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Fenton B, Salter WT, Malloch G, Begg G, Anderson E. Stopped in its tracks: how λ-cyhalothrin can break the aphid transmission of a potato potyvirus. Pest Manag Sci 2015; 71:1611-1616. [PMID: 25523839 DOI: 10.1002/ps.3967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Pyrethroids are one of the most widespread and commonly used classes of insecticide and are used in multiple roles, including protecting potato crops from virus vector aphids. Resistance in some genotypes of a few species is now widespread, but most species remain susceptible. The rate of virus transmission by two genotypes of the peach potato aphid, Myzus persicae, fed on potato virus Y (PVY)-infected leaves of potato treated with the pyrethroid λ-cyhalothrin was evaluated. RESULTS The susceptible genotype, type J, was significantly inhibited from transmitting virus to uninfected seedlings. A genotype containing the M918L super knockdown resistance mutation conferring resistance to pyrethroids, type O, showed no inhibition of transmission. However, when survival of the aphids after exposure was compared, the pyrethroid had not killed the type J aphids. CONCLUSIONS λ-Cyhalothrin in a commercial formulation disrupts PVY transmission by disorienting aphid vectors for a sufficient time for the virus to lose its transmissibility. However, M. persicae genotypes carrying the M918L mutation are not prevented from transmitting.
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Affiliation(s)
- Brian Fenton
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - William T Salter
- The James Hutton Institute, Invergowrie, Dundee, UK
- University of Sydney, NSW, Australia
| | | | - Graham Begg
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Eric Anderson
- The James Hutton Institute, Invergowrie, Dundee, UK
- Scottish Agronomy, Arlary Farm, Kinross, UK
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Wilson AC, Fenton B, Malloch G, Boag B, Hubbard S, Begg GS. Coexisting small mammals display contrasting strategies for tolerating instability in arable habitat. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0852-x] [Citation(s) in RCA: 5] [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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Fenton B, Kasprowicz L, Malloch G, Pickup J. Reproductive performance of asexual clones of the peach-potato aphid, ( Myzus persicae, Homoptera: Aphididae), colonising Scotland in relation to host plant and field ecology. Bull Entomol Res 2010; 100:451-60. [PMID: 19941675 DOI: 10.1017/s0007485309990447] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The population of peach-potato aphid, Myzus persicae (Sulzer), in Scotland comprises large numbers of a few superclones with much smaller numbers of other clones, and the reason for their differential success has yet to be elucidated. In the current study, the reproduction of lineages derived from these clones was measured by counting the numbers of offspring produced by a one-day-old nymph after 15 days. This was measured on four plant species, including local agricultural hosts and at two different temperatures (14 and 18 degrees C). There were significant differences in clonal lineage reproduction on different hosts and at different temperatures and amongst clonal lineages on the same hosts at the same temperature. Lineages of local insecticide sensitive clones did not have the best reproductive potential; instead, a recently introduced clonal lineage carrying MACE insecticide resistance was the best reproducer. The clonal lineage with the lowest reproductive potential also carried insecticide resistance, but this was kdr. A lineage from a local insecticide-sensitive clone was the least affected by reduced temperature. There was evidence of host plant specialisation in some of the clonal lineages.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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Kasprowicz L, Malloch G, Foster S, Pickup J, Zhan J, Fenton B. Clonal turnover of MACE-carrying peach-potato aphids (Myzus persicae (Sulzer), Homoptera: Aphididae) colonizing Scotland. Bull Entomol Res 2008; 98:115-124. [PMID: 18076780 DOI: 10.1017/s0007485307005445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Peach-potato aphids, Myzus persicae (Sulzer), collected in Scotland in the years 1995 and 2002-2004 were characterized using four microsatellite loci and three insecticide resistance mechanisms. From 868 samples, 14 multilocus genotypes were defined (designated clones A-N). Five of these (denoted A, B, H, M and N) carried modified acetylcholinesterase (MACE) resistance, the most recent resistance mechanism to have evolved in M. persicae. The current paper shows that the continued presence of MACE aphids is due to turnover, as clones A and B were replaced in field samples by clones H, M and N in later seasons. Thus, insecticide-resistant populations in Scotland can be attributed to multiple waves of rapid clone colonisations and not to the continued presence of stable resistant clones or mutation or sexual recombination in local populations. The MACE clones carried varying levels of the other insecticide resistance mechanisms, kdr and esterase. The presence of these mechanisms could alter the clones success in the field depending on insecticide spraying (positive selection) and resistance fitness costs (negative selection).
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Affiliation(s)
- L Kasprowicz
- Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Ramsey JS, Wilson ACC, de Vos M, Sun Q, Tamborindeguy C, Winfield A, Malloch G, Smith DM, Fenton B, Gray SM, Jander G. Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design. BMC Genomics 2007; 8:423. [PMID: 18021414 PMCID: PMC2213679 DOI: 10.1186/1471-2164-8-423] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [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: 06/11/2007] [Accepted: 11/16/2007] [Indexed: 01/05/2023] Open
Abstract
Background The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. Results Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. Conclusion New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible interactions with its host plants, complementing ongoing work illuminating plant molecular responses to phloem-feeding insects.
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Affiliation(s)
- John S Ramsey
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA.
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Lazarova SS, Malloch G, Oliveira CMG, Hübschen J, Neilson R. Ribosomal and Mitochondrial DNA Analyses of Xiphinema americanum-Group Populations. J Nematol 2006; 38:404-410. [PMID: 19259456 PMCID: PMC2586466] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Indexed: 05/27/2023] Open
Abstract
The 18S ribosomal DNA (rDNA) and cytochrome oxidase I region of mitochondrial DNA (mtDNA) were sequenced for 24 Xiphinema americanum-group populations sourced from a number of geographically disparate locations. Sequences were subjected to phylogenetic analysis and compared. 18S rDNA strongly suggested that only X. pachtaicum, X. simile (two populations) and a X. americanum s.l. population from Portugal were different from the other 20 populations studied, whereas mtDNA indicated some heterogeneity between populations. Phylogenetically, based on mtDNA, an apparent dichotomy existed amongst X. americanum-group populations from North America and those from Asia, South America and Oceania. Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the X. americanum-group.
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Affiliation(s)
- Stela S Lazarova
- Central Laboratory of General Ecology, 2 Gargarin Street, 1113 Sofia, Bulgaria Scottish Crop Research Institute, Dundee, DD2 5DA, Scotland, UK Instituto Biológico, P.O. Box 70, 13001-970, Campinas, SP, Brazil Laboratoire National de Santé, 20A, rue Auguste Lumière, L-1950, Luxembourg
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Malloch G, Highet F, Kasprowicz L, Pickup J, Neilson R, Fenton B. Microsatellite marker analysis of peach-potato aphids (Myzus persicae, Homoptera: Aphididae) from Scottish suction traps. Bull Entomol Res 2006; 96:573-82. [PMID: 17201975 DOI: 10.1017/ber2006459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The peach-potato aphid Myzus persicae (Sulzer) is an important vector of plant viruses. A network of suction traps collects aerial samples of this aphid in order to monitor and help predict its spatial distribution and likely impact on virus transmission in crops. A suction trap catch is thought to be a good representation of the total aphid pool. Sensitive molecular markers have been developed that determine the genetic composition of the M. persicae population. In Scotland, UK, these were applied to field collections revealing a limited number of clones. Molecular markers are less successful when applied to specimens that have been preserved in an ethanol-based trap fluid designed to preserve morphology. An assessment of different DNA extraction and PCR techniques is presented and the most efficient are used to analyse M. persicae specimens caught in the Dundee suction trap in 2001, a year when exceptionally high numbers were caught. The results reveal that the majority of the M. persicae caught belonged to two highly insecticide resistant clones. In addition, it was possible to compare the relative frequencies of genotypes caught in the trap with those collected at insecticide treated and untreated field sites in the vicinity. These results indicate that, in addition to suction trap data, the ability to sample field sites provides valuable early warning data which have implications for pest control and virus management strategies.
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Affiliation(s)
- G Malloch
- Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Fenton B, Malloch G, Woodford JAT, Foster SP, Anstead J, Denholm I, King L, Pickup J. The attack of the clones: tracking the movement of insecticide-resistant peach-potato aphids Myzus persicae (Hemiptera: Aphididae). Bull Entomol Res 2005; 95:483-94. [PMID: 16197569 DOI: 10.1079/ber2005380] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Myzus persicae (Sulzer) collected in Scotland were characterized for four microsatellite loci, intergenic spacer fingerprints and the resistance mechanisms modified acetylcholinesterase (MACE), overproduced carboxylesterase and knockdown resistance (kdr). Microsatellite polymorphisms were used to define a limited number of clones that were either fully susceptible to insecticides or possessed characteristic combinations of resistance mechanisms. Within these clones, intergenic spacer fingerprints could either be very consistent or variable, with the latter indicating ongoing evolution within lineages, most likely derived from the same zygote. Two clones (termed A and B) possessed all three resistance mechanisms and predominated at sites treated with insecticides. Their appearance on seed potatoes and oilseed rape in Scotland in 2001 coincided with extensive insecticide use and severe control failures. Clones C, I and J, with no or fewer resistance mechanisms, were found in samples from 1995 and were dominant at untreated sites in 2001. A comparison of Scottish collections with those from other UK and non-UK sites provides insight into the likely origins, distribution and dynamics of M. persicae clones in a region where asexual (anholocyclic) reproduction predominates, but is vulnerable to migration by novel genotypes from areas of Europe where sexual (holocyclic) reproduction occurs.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
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Abstract
Wolbachia are maternally inherited bacteria responsible for altering host reproduction. The two main groups found in insects, A and B, are based on molecular characterization using ribosomal, ftsZ, wsp (Wolbachia surface protein) or groE genes. We have used the wsp and ftsZ genes to study Wolbachia in byturid beetles. Byturus affinis contained a single copy of the ftsZ gene which grouped with A ftsZ sequences and a single copy of the wsp gene which grouped with B wsp sequences. This suggests that genetic exchange between A and B groups has occurred in the Wolbachia of this beetle. FtsZ and wsp sequences that were identical or nearly identical to those of B. affinis were found in B. tomentosus, suggesting that it also contains the same recombinant Wolbachia genotype. Most other byturids had more than one wsp sequence with at least one from the A and B groups, suggesting multiple copies of bacterial genes or multiple infections. B. ochraceus and B. unicolor both had four distinct wsp gene sequences. All the byturids had a closely related A wsp sequence and most a closely related B wsp sequence. Therefore, there appears to be an association between specific A and B wsp types.
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Affiliation(s)
- G Malloch
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK.
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Ritchie A, Blackwell A, Malloch G, Fenton B. Heterogeneity of ITS1 sequences in the biting midge Culicoides impunctatus (Goetghebuer) suggests a population in Argyll, Scotland, may be genetically distinct. Genome 2004; 47:546-58. [PMID: 15190372 DOI: 10.1139/g04-003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, variation in ITS1 from eight Culicoides species was analysed by PCR, DNA restriction analysis, cloning, and sequencing. ITS1 variants were essentially homogenized within a species, as sequences were identical or closely related. However, Culicoides impunctatus ITS1 sequences derived from one (Argyll) of five populations contained considerable genomic diversity. The secondary structure of each ITS1 was computed. The structure aided the production of an accurate alignment and the identification of a large indel. A phylogenetic analysis was performed. Some of the sequences from the diverse Argyll C. impunctatus population were more related to Culicoides imicola, a vector of animal pathogens in the Old World, than they were to the other C. impunctatus sequences. Thus, the rDNA ITS1 regions of individuals in the Argyll C. impunctatus population were not conforming to the general theory of rDNA homogenization through molecular drive.Key words: Culicoides, ITS1, phylogeny, rDNA, secondary structure.
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Affiliation(s)
- Allyson Ritchie
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, UK
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Fenton B, Oliveira C, Monteiro A, Malloch G, Neilson R, Ferraz L. Molecular and morphometric analyses of Xiphidorus species (Nematoda: Longidoridae). NEMATOLOGY 2004. [DOI: 10.1163/1568541042843487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AbstractXiphidorus nematodes are indigenous to Latin America and have a restricted geographical distribution compared to Xiphinema. A principal component analysis (PCA) based on eight morphometric characters from 39 South American populations clearly separated populations previously identified as X. achalae, X. amazonensis, X. minor, X. saladillensis and X. uruguayensis and three undescribed Xiphidorus species. However, populations identified as X. balcarceanus, X. parthenus and X. yepesara did not form similar discrete groupings and exhibited either considerable morphological variability or were incorrectly identified. Maximum likelihood phylogenetic trees derived from both 18S rDNA and ITS-1 sequences discriminated six Xiphidorus species (X. balcarceanus, X. minor, X. parthenus, X. yepesara, and two undescribed Xiphidorus species) from Brazil. Also, restriction analysis of PCR products derived from the ITS-1 region using three restriction enzymes (Taq I, Rsa I and Hin f I) yielded repeatable patterns that clearly discriminated these six Xiphidorus species. Sequence divergence was noted between X. parthenus and X. yepesara. Our morphometric and molecular data suggests that X. parthenus and X. yepesara are distinct species contrary to their previous subspecific status.
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Abstract
Nuclear ribosomal ITS2 and mitochondrial cytochrome oxidase DNA sequences were analysed from the Byturidae (Coleoptera), which includes the raspberry beetles. The secondary structure of ITS2 was plotted and interspecific changes analysed. Evidence for selection on simple sequence repeats within the ITS2 was found. Phylogenetic trees based on the mitochondrial and ribosomal sequences were compared. They were in parity, indicating they reflect the true evolutionary histories of these insects. There was no evidence for hybridization in the populations surveyed, but there was evidence that the American raspberry beetle, Byturus unicolor, is divided into at least three distinct groupings. Despite sharing a related host, the raspberry pests from America were not the most related to the European raspberry beetle. Instead, links between Byturus affinis from Japan and the American raspberry beetle suggest that this lineage originated in Asia and colonized the Western USA.
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Affiliation(s)
- G Malloch
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, UK.
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Abstract
Wolbachia, a group of maternally inherited intracellular parasitic bacteria, alter host reproduction, including the induction of thelytokous parthenogenesis, feminization of genetic males, son killing and, most commonly, the induction of cytoplasmic incompatibility (CI), in a diverse array of arthropods. CI can result in infertility and has attracted attention because of its potential in biological control and as an agent in speciation. Although there has been some analysis of overall infection rates in arthropods and within individual insect orders, there has been little exploration of within-species variation. In this study, primers specific for the ftsZ gene of Wolbachia were used to amplify it from different geographical samples of the European raspberry beetle (Byturus tomentosus), confirming the presence of Wolbachia. More than 99% of UK individuals were found to be infected with Wolbachia and 97% of these B. tomentosus beetles harboured multiple infections. Preliminary analysis of B. tomentosus beetles from continental European populations revealed a lower level of infection (24%) than those from the UK. Phylogenetic analysis using the ftsZ DNA sequences places Wolbachia from B. tomentosus into a new clade (Abt) within the A division, with some revisions to the existing Wolbachia phylogeny.
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Affiliation(s)
- G Malloch
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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Fenton B, Birch AN, Malloch G, Lanham PG, Brennan RM. Gall mite molecular phylogeny and its relationship to the evolution of plant host specificity. Exp Appl Acarol 2000; 24:831-861. [PMID: 11345319 DOI: 10.1023/a:1006488120364] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The phylogenetic relationships of all seven known species of Cecidophyopsis mites (Acari: Eriophyidae) with Ribes hosts have been inferred from ribosomal DNA sequences. This analysis found groups of closely related mites. The five gall-forming species, four of which are monophagous and one which has two hosts, were found in two groups. Another group consisted of the two non gall-forming species, one of which has two hosts, while the other is monophagous. The molecular phylogeny of their known Ribes host plants was calculated using the equivalent ribosomal regions as the mites. The structure of the two trees (mites vs hosts) was clearly different, implying that mite speciation did not closely follow speciation events in the plant hosts. Instead, the three groups of Ribes-infesting Cecidophyopsis mites have derived from a common galling ancestor millions of years ago. Each mite group has recently diversified onto different primary hosts. One group of mites has also lost the galling habit. The results have implications for host range changes and the durability of mite-resistance genes in cultivated Ribes.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Dundee, Tayside, United Kingdom.
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Fenton B, Woodford JA, Malloch G. Analysis of clonal diversity of the peach-potato aphid, Myzus persicae (Sulzer), in Scotland, UK and evidence for the existence of a predominant clone. Mol Ecol 1998; 7:1475-87. [PMID: 9819902 DOI: 10.1046/j.1365-294x.1998.00479.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Clones of the peach-potato aphid, Myzus persicae (Sulzer), mostly from Scotland, UK were examined using an rDNA fingerprinting technique. Eighty patterns (genotypes) were found amongst the 276 clones. A large number of clones (30%) from all sample areas in Scotland exhibited the same simple pattern, suggesting the presence of a single M. persicae clone. There was no difference in genotype distributions between M. persicae collected from brassica or potato crops, suggesting that host-adapted genotypes have no advantage in the field. Different fingerprints were randomly distributed in the environment, although clones taken from the same leaf were more often the same fingerprint. Highly distinctive fingerprints, which were more widely distributed, suggest that this technique could be used to follow individual clones. In addition to the common clonal type, multiple fingerprint bands were found over successive years, implying that, in Scotland, local overwintering asexual populations are the most common source of M. persicae in the following year.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Invergowrie, Dundee, UK.
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Fenton B, Malloch G, Germa F. A study of variation in rDNA ITS regions shows that two haplotypes coexist within a single aphid genome. Genome 1998. [DOI: 10.1139/g98-030] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report variation in the rDNA internal transcribed spacers (ITSs) of aphid species, the first for these insects. Variation at 6 sites within ITS1 sequences of the green peach aphid, Myzus persicae, identified two haplotypes coexisting within the same individuals, indicating that molecular drive has not homogenised different copies of rDNA. During this study, we found that PCR can cause a precise 58-bp loss in the amplified copies of an ITS haplotype (type 1). This occurs in all detectable copies under routine PCR conditions, at different annealing temperatures and with Pfu and Taq polymerases. In addition, "hot-start" PCR exclusively copied a different, rare haplotype (type 2). These observations have important considerations for using PCR, as large deletions in PCR products may not reflect real deletions in the genome, and changes in PCR conditions may be needed to copy cryptic haplotypes.Key words: PCR, aphid, ITS, variation, selection.
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Blok VC, Malloch G, Harrower B, Phillips MS, Vrain TC. Intraspecific Variation in Ribosomal DNA in Populations of the Potato Cyst Nematode Globodera pallida. J Nematol 1998; 30:262-274. [PMID: 19274220 PMCID: PMC2620292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The relationships among a number of populations of Globodera pallida from Britian, the Netherlands, Germany, Switzerland, and South America were examined using PCR amplification of the ribosomal cistron between the 18S and 28S genes that include the two intergenic spacer regions (ITS1 and ITS2) and the 5.8S gene. Amplifications produced a similar-sized product of 1150 bp from all populations. Digestion of the amplified fragment with a number of restriction enzymes showed differences among the populations. The restriction enzyme RsaI distinguished the most populations. The RFLP patterns revealed by this enzyme were complex and could have arisen from heterogeneity between individuals within populations and from differences between the repeats of an individual. Sequence analysis from six of the populations, together with RFLP analysis of PCR products, shows that there is intraspecific variation in the rDNA of G. pallida.
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Fenton B, Malloch G, Germa F. A study of variation in rDNA ITS regions shows that two haplotypes coexist within a single aphid genome. Genome 1998; 41:337-45. [PMID: 9729768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report variation in the rDNA internal transcribed spacers (ITSs) of aphid species, the first for these insects. Variation at 6 sites within ITS1 sequences of the green peach aphid, Myzus persicae, identified two haplotypes coexisting within the same individuals, indicating that molecular drive has not homogenised different copies of rDNA. During this study, we found that PCR can cause a precise 58-bp loss in the amplified copies of an ITS haplotype (type 1). This occurs in all detectable copies under routine PCR conditions, at different annealing temperatures and with Pfu and Taq polymerases. In addition, "hot-start" PCR exclusively copied a different, rare haplotype (type 2). These observations have important considerations for using PCR, as large deletions in PCR products may not reflect real deletions in the genome, and changes in PCR conditions may be needed to copy cryptic haplotypes.
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Affiliation(s)
- B Fenton
- Pests and Diseases Unit, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, U.K.
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Fenton B, Malloch G, Moxey E. Analysis of eriophyid mite rDNA internal transcribed spacer sequences reveals variable simple sequence repeats. Insect Mol Biol 1997; 6:23-32. [PMID: 9013252 DOI: 10.1046/j.1365-2583.1997.00152.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ribosomal DNA internal transcribed spacers of the eriophyid mites Cecidophyopsis ribis, C. selachodon, C. spicata, C. alpina, C. aurea, C. grossulariae and Phylocoptes gracillis were amplified using PCR, cloned and sequenced. Sequences for the ITS1 of Cecidophyopsids were 92-99% homologous. Cecidophyopsis inter-specific differences were found in seventeen simple sequence repeats (vSSRs), fourteen point mutations and two indels. No intra-specific variation in vSSRs was detected. A hypothetical structure for ITS1 was obtained and vSSRs were mapped onto this. Changes in vSSRs were compensated for by changes in complementary vSSRs or through multiple point mutations. A comparison with vSSRs of other arthropods suggested that the levels of intra-specific variation in Cecidophyopsis mites was less than in organisms which do not use arrhentoky for male determination.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland
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Fenton B, Malloch G, Jones AT, Amrine JW, Gordon SC, A'Hara S, McGavin WJ, Birch AN. Species identification of Cecidophyopsis mites (Acari: Eriophyidae) from different Ribes species and countries using molecular genetics. Mol Ecol 1995; 4:383-7. [PMID: 7663755 DOI: 10.1111/j.1365-294x.1995.tb00231.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cecidophyopsis mites were studied by PCR amplification of parts of their ribosomal DNA, followed by restriction enzyme analysis. Mite specimens on Ribes nigrum (black currant) from six countries gave the same digestion pattern, which was distinct from the pattern for mites found on R. rubrum from Poland and Finland and for R. grossularia from the USA. This suggests that each Ribes species is host to a different mite species: C. ribis, C. selachodon and C. grossulariae, respectively. Two other mite samples from R. alpinum and R. aureum were identical but were distinct from each of the other species.
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Affiliation(s)
- B Fenton
- Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Birch AN, Fenton B, Malloch G, Jones AT, Phillips MS, Harrower BE, Woodford JA, Catley MA. Ribosomal spacer length variability in the large raspberry aphid, Amphorophora idaei (Aphidinae: macrosiphini). Insect Mol Biol 1994; 3:239-245. [PMID: 7704307 DOI: 10.1111/j.1365-2583.1994.tb00172.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The large raspberry aphid, Amphorophora idaei, has several biotypes described by their abilities to overcome plant resistance genes. Bioassays of field populations showed a strong shift towards A1 resistance-breaking biotypes since the 1960s. RFLP analysis of the rDNA cistron was used to study variation found within and between standard clones of three A. idaei biotypes and twenty-nine field populations collected over 3 years. Probing genomic DNA with the ribosomal DNA probe pBG 35 produced consistent differences in RFLPs between standard clones of biotypes. However, analysis of field populations gave more complex RFLP patterns that were not biotype-specific, unlike characteristic intergenic spacer (IGS) patterns reported for Schizaphis graminum biotypes. All but one sample collected from separate fields showed considerable genetic diversity within populations, attributed to alate migrations of parthenogenetic females in summer and males in autumn.
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Affiliation(s)
- A N Birch
- Scottish Crop Research Institute, Invergowrie, Dundee
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Fenton B, Birch AN, Malloch G, Woodford JA, Gonzalez C. Molecular analysis of ribosomal DNA from the aphid Amphorophora idaei and an associated fungal organism. Insect Mol Biol 1994; 3:183-189. [PMID: 7894750 DOI: 10.1111/j.1365-2583.1994.tb00165.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The ribosomal DNA cistron from the large raspberry aphid, Amphorophora idaei (Hemiptera: Aphididae), has been mapped by restriction analysis. The results showed that the map of A. idaei was similar to those of the previously characterized aphids Schizaphis graminum and Acyrthosiphon pisum. An extra Bgl II site was found in some of the ribosomal DNA intergenic spacer repeats in A. idaei. Using in-situ hybridization to aphid mitotic chromosomes it was demonstrated that probes derived from this region mapped to the pair of X chromosomes and it was therefore aphid in origin. Polymerase chain reaction using conserved rDNA primers also detected significant amounts of a fungal genome in the DNA samples. Microscopic investigation showed that the external surface of A. idaei harboured fungal propagules, hyphae and yeast-like organisms.
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Affiliation(s)
- B Fenton
- Zoology Department, Scottish Crop Research Institute, Invergowrie, Dundee, Tayside
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Fenton B, Malloch G, Brennan R, Jones A, Gordon S, McGavin W, Birch A. TAXONOMIC EVALUATION OF THREE REPUTED SPECIES OF CECIDOPHYOPSIS MITE ON RIBES. ACTA ACUST UNITED AC 1993. [DOI: 10.17660/actahortic.1993.352.78] [Citation(s) in RCA: 7] [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: 11/17/2022]
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Abstract
The utilization of lactate, glucose, 3-hydroxybutyrate, and glutamine has been studied in isolated brain cells from early newborn rats. Isolated brain cells actively utilized these substrates, showing saturation at concentrations near physiological levels during the perinatal period. The rate of lactate utilization was 2.5-fold greater than that observed for glucose, 3-hydroxybutyrate, or glutamine, suggesting that lactate is the main metabolic substrate for the brain immediately after birth. The apparent Km for glucose utilization suggested that this process is limited by the activity of hexokinase. However, lactate, 3-hydroxybutyrate, and glutamine utilization seems to be limited by their transport through the plasma membrane. The presence of fatty acid-free bovine serum albumin (BSA) in the incubation medium significantly increased the rate of lipogenesis from lactate or 3-hydroxybutyrate, although this was balanced by the decrease in their rates of oxidation in the same circumstances. BSA did not affect the rate of glucose utilization. The effect of BSA was due not to the removal of free fatty acid, but possibly to the binding of long-chain acyl-CoA, resulting in the disinhibition of acetyl-CoA carboxylase and citrate carrier.
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Affiliation(s)
- C Vicario
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Salamanca, Spain
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Wilson J, Cholewinski A, Malloch G, Joiner M, Burnet F. Acquisition of glial fibrillary acidic protein-containing fibres by astroglial cells in primary culture is orchestrated by a communicable factor. Brain Res 1985; 347:196-9. [PMID: 4052803 DOI: 10.1016/0006-8993(85)90913-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In a previous study we discovered that primary cultures initiated from the whole brain of 21-day foetal rats contained astroblasts that concertedly acquired glial fibrillary acidic protein (GFAP) fibres. The mechanism of this burst of cytoskeletal differentiation could not be investigated in these cultures because it occurred too quickly (completed within 2 h). We report that cultures initiated from the region of the third ventricle display an extended burst of GFAP acquisition whose rate could be markedly reduced by medium changing. Temporary medium deprivation or the addition of cytosine arabinoside to the growth medium had no effect. Our findings suggest that an as yet uncharacterised communicable factor is involved in the orchestration of cytoskeletal differentiation in culture. This factor may be responsible for synchronising the appearance of GFAP-positive cells in the periventricular regions of the foetal brain.
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Wilson J, Malloch G, Joiner M, Burnet F. Concerted and predictable acquisition of glial fibrillary acidic protein filaments by a cohort of astroblasts in culture. Brain Res 1985; 339:158-60. [PMID: 3896400 DOI: 10.1016/0006-8993(85)90637-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Primary cultures of the 21 day foetal rat brain contain a cohort of astroblasts that concertedly acquire glial fibrillary acidic protein (GFAP) filaments between the 16th and 18th hour after plating. This burst of cytoskeletal differentiation is not observed in cultures initiated from the 18 day foetal brain and is not effected by the addition of cytosine arabinoside, an inhibitor of glial cell proliferation.
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