Casper Breuker
Oxford Brookes University, Faculty of Health and Life Sciences, Department Member
- The model system in my lab is the Speckled wood butterfly, Pararge aegeria, for which we collect data on phenotypic v... moreThe model system in my lab is the Speckled wood butterfly, Pararge aegeria, for which we collect data on phenotypic variation in reproductive success under a range of environmental conditions. In order to understand the genetic variation, and the interaction with environmental factors, underlying such reproductive variation, we investigate the developmental genetic regulation of oogenesis. Such studies are crucial in elucidating, for example, life-history trade-offs, maternal effects of all kinds, setting up offspring body axes, and oocyte pathology. Furthermore, oogenesis is a popular model system for studying epigenetic programming, stem cell behaviour, cell cycle regulation and developmental patterning mechanisms.edit
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This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform... more
This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform a more informative primary annotation of your non-model organism by implementing our multi-BLAST annotation strategy. We also provide a general guide to other essential steps in the next-generation sequencing analysis workflow. Before undertaking these methods, we recommend you familiarize yourself with command line usage and fundamental concepts of database handling. Most of the operations in the primary annotation pipeline can be performed in Galaxy (or equivalent standalone versions of the tools) and through the use of common database operations (e.g. to remove duplicates) but other equivalent programs and/or custom scripts can be implemented for further automation.
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<p>Alignment of the conserved LOTUS domain shared by the TDRD7 and Oskar proteins from <i>Pararge aegeria</i> (<i>Pa</i>), <i>Danaus plexippus</i> (<i>Dp</i>), <i>Bombyx... more
<p>Alignment of the conserved LOTUS domain shared by the TDRD7 and Oskar proteins from <i>Pararge aegeria</i> (<i>Pa</i>), <i>Danaus plexippus</i> (<i>Dp</i>), <i>Bombyx mori</i> (<i>Bm</i>), <i>Drosophila melanogaster</i> (<i>Dm</i>), <i>Nasonia vitripennis</i> (<i>Nv</i>), <i>Apis mellifera</i> (<i>Am</i>), <i>Tribolium castaneum</i> (<i>Tc</i>), <i>Mus musculus</i> (<i>Mm</i>) and <i>Gryllus bimaculatus</i> (<i>Gb</i>). Secondary structure annotation obtained from <i>M</i>. <i>musculus</i> structural data (PDB: 2LH9). Figure generated in ESPript 3.0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144471#pone.0144471.ref057" target="_blank">57</a>]. Columns with residues of similar physico-chemical properties (equivalent residue percentage) over 70% are in red with blue frames, strictly conserved positions highlighted red. The consensus sequence displays strictly conserved residues in uppercase while lowercase symbols indicate columns with a “MultAlin” similarity over 70% (IV / LM / FY / NDQEBZ). Exclamation mark refers to the amino acid I or V, “$”refers to the amino acid L or M, “%”refers to the amino acid F or Y, “#”refers to either the amino acid N, D, Q, E, B, or Z.</p
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<p><i>Pararge aegeria</i> ovaries consist of 8 ovarioles [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144471#pone.0144471.ref006" target="_blank">6</a>]. The... more
<p><i>Pararge aegeria</i> ovaries consist of 8 ovarioles [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144471#pone.0144471.ref006" target="_blank">6</a>]. The diagram illustrates the morphology of a single <i>P</i>. <i>aegeria ovariole</i> annotated with the approximate equivalent <i>Drosophila melanogaster</i> oogenesis stages (i.e. 1 to 14) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144471#pone.0144471.ref056" target="_blank">56</a>] on the basis of relative size, morphological characteristics and position of the nucleus (abbreviations explained in figure). Cellular processes (e.g. meiosis I and II) and ovarian regions (e.g. oviducts) relevant to oogenesis are also annotated. Progression of oocytes beyond the vitellarium is scaled to fit. The nurse cells have fully degenerated and the oocytes in this region will enter the oviducts and be ready for fertilisation and laying, upon which embryogenesis commences.</p
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<p> Agarose gel electrophoresis of RT-PCR products obtained using intron-crossing primers (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004698#pgen.1004698.s010"... more
<p> Agarose gel electrophoresis of RT-PCR products obtained using intron-crossing primers (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004698#pgen.1004698.s010" target="_blank">Figure S10</a>). (B) Schematic overview of serosa formation in <i>P. aegeria</i>. Diagrammatic cross section through a developing embryo and associated extra-embryonic cell layers inside a 10–12 h AEL egg. Chorion (brown), vitelline membrane (violet), extraembryonic region/serosa (red), germ anlage (green) and presumptive amniotic cells (blue) are illustrated during serosal specification, maturation and closure. Top row shows ventral half while bottom row shows dorsal half, anterior is top in both. Embryo-vitelline cavity following germ anlage sinking is shown in the middle panel. Orientation 3D axis indicates anterior (A), left (L) and ventral (V) or dorsal (D). AEL, after egg-laying (hours).</p
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This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform... more
This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform a more informative primary annotation of your non-model organism by implementing our multi-BLAST annotation strategy. We also provide a general guide to other essential steps in the next-generation sequencing analysis workflow. Before undertaking these methods, we recommend you familiarize yourself with command line usage and fundamental concepts of database handling. Most of the operations in the primary annotation pipeline can be performed in Galaxy (or equivalent standalone versions of the tools) and through the use of common database operations (e.g. to remove duplicates) but other equivalent programs and/or custom scripts can be implemented for further automation.
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Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five... more
Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five lepidopteran species (Polygonia c-album, Pararge aegeria, Callimorpha dominula, Cameraria ohridella, Hepialus sylvina) plus a caddisfly outgroup (Glyphotaelius pellucidus) to trace the evolution of the lepidopteran Shx genes. We demonstrate that Shx genes originated by tandem duplication of zen early in the evolution of large clade Ditrysia; Shx are not found in a caddisfly and a member of the basally diverging Hepialidae (swift moths). Four distinct Shx genes were generated early in ditrysian evolution, and were stably retained in all descendent Lepidoptera except the silkmoth which has additional duplications. Despite extensive sequence divergence, molecular modelling indicates that all four Shx genes have the potential to encode stable homeodomains. The f...
Research Interests: Evolutionary Biology, Genetics, Developmental Biology, Evolutionary Developmental Biology, Phylogenetics, and 15 moreBiology, Evolution, Medicine, Oogenesis, Lepidoptera, Biological Sciences, Butterflies, Phylogeny, Animals, Hox Genes, Genome, Gene, Gene Duplication, Gene Regulatory Networks, and PLoS Genetics
Research Interests: Zoology, Morphometrics, Biology, Medicine, Energy Metabolism, and 8 moreTerritoriality, Aggression, Animals, Male, Odonata, Aspect Ratio, Damselfly, and Wing
Sub-lethal impacts are known to affect the insect-host relationship and have an important role in describing host dynamics. The impact of sub-lethal infections of pathogens on life history traits of affected hosts has been understudied in... more
Sub-lethal impacts are known to affect the insect-host relationship and have an important role in describing host dynamics. The impact of sub-lethal infections of pathogens on life history traits of affected hosts has been understudied in natural or semi-natural systems. ...
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In aerial animals, flight morphology needs to be designed to allow daily behavioural activities. Within species differences in behaviour can therefore be expected to relate to differences in flight morphology, not only between males and... more
In aerial animals, flight morphology needs to be designed to allow daily behavioural activities. Within species differences in behaviour can therefore be expected to relate to differences in flight morphology, not only between males and females but also between same-sex members when they use different behavioural strategies. In female polymorphic damselflies, one female morph is considered a male mimic that resembles the male’s body colour and behaviour (andromorph), whereas the other is dissimilar (gynomorph). Here, we questioned whether males, andromorphs, and gynomorphs of the damselfly Enallagma cyathigerum (Charpentier, 1840) differ in flight morphology, with andromorphs being more similar to males than gynomorphs. In addition, we evaluated whether differences in flight morphology are consistent or whether some morphs are more plastic in response to seasonal environmental fluctuations. Most morphometrics showed similar seasonal plasticity for males and both female morphs, which...
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BackgroundButterflies are popular model organisms to study physiological mechanisms underlying variability in oogenesis and egg provisioning in response to environmental conditions. Nothing is known, however, about; the developmental... more
BackgroundButterflies are popular model organisms to study physiological mechanisms underlying variability in oogenesis and egg provisioning in response to environmental conditions. Nothing is known, however, about; the developmental mechanisms governing butterfly oogenesis, how polarity in the oocyte is established, or which particular maternal effect genes regulate early embryogenesis. To gain insights into these developmental mechanisms and to identify the conserved and divergent aspects of butterfly oogenesis, we analysed ade novoovarian transcriptome of the Speckled Wood butterflyPararge aegeria(L.), and compared the results with known model organisms such asDrosophila melanogasterandBombyx mori.ResultsA total of 17306 contigs were annotated, with 30% possibly novel or highly divergent sequences observed.Pararge aegeriafemales expressed 74.5% of the genes that are known to be essential forD. melanogasteroogenesis. We discuss the genes involved in all aspects of oogenesis, inclu...
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microRNAs (miRNAs) are important regulators of animal development and other processes, and impart robustness to living systems through post-transcriptional regulation of specific mRNA transcripts. It is postulated that newly emergent... more
microRNAs (miRNAs) are important regulators of animal development and other processes, and impart robustness to living systems through post-transcriptional regulation of specific mRNA transcripts. It is postulated that newly emergent miRNAs are generally expressed at low levels and with spatiotemporally restricted expression domains, thus minimising effects of spurious targeting on animal transcriptomes. Here we present ovarian miRNA transcriptome data for two geographically distinct populations of the Speckled Wood butterfly (Pararge aegeria). A total of 74 miRNAs were identified, including 11 newly discovered and evolutionarily-young miRNAs, bringing the total of miRNA genes known from P. aegeria up to 150. We find a positive correlation between miRNA age and expression level. A common set of 55 miRNAs are expressed in both populations. From this set, we identify seven that are consistently either ovary-specific or highly upregulated in ovaries relative to other tissues. This ‘ovary set’ includes miRNAs with known contributions to ovarian function in other insect species with similar ovaries and mode of oogenesis, including miR-989 and miR-2763, plus new candidates for ovarian function. We also note that conserved miRNAs are overrepresented in the ovary relative to the whole body.
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The maternal effect genes responsible for patterning the embryo along the antero-posterior (AP) axis are broadly conserved in insects. The precise function of these maternal effect genes is the result of the localisation of their mRNA in... more
The maternal effect genes responsible for patterning the embryo along the antero-posterior (AP) axis are broadly conserved in insects. The precise function of these maternal effect genes is the result of the localisation of their mRNA in the oocyte. The main developmental mechanisms involved have been elucidated in Drosophila melanogaster, but recent studies have shown that other insect orders often diverge in RNA localisation patterns. A recent study has shown that in the butterfly Pararge aegeria the distinction between blastodermal embryonic (i.e. germ band) and extra-embryonic tissue (i.e. serosa) is already specified in the oocyte during oogenesis in the ovariole, long before blastoderm cellularisation. To examine the extent by which a female butterfly specifies and patterns the AP axis within the region fated to be the germ band, and whether she specifies a germ plasm, we performed in situ hybridisation experiments on oocytes in P. aegeria ovarioles and on early embryos. RNA localisation of the following key maternal effect genes were investigated: caudal (cad), orthodenticle (otd), hunchback (hb) and four nanos (nos) paralogs, as well as TDRD7 a gene containing a key functional domain (OST-HTH/LOTUS) shared with oskar. TDRD7 was mainly confined to the follicle cells, whilst hb was exclusively zygotically transcribed. RNA of some of the nos paralogs, otd and cad revealed complex localisation patterns within the cortical region prefiguring the germ band (i.e. germ cortex). Rather interestingly, otd was localised within and outside the anterior of the germ cortex. Transcripts of nos-O formed a distinct granular ring in the middle of the germ cortex possibly prefiguring the region where germline stem cells form. These butterfly RNA localisation patterns are highly divergent with respect to other insects, highlighting the diverse ways in which different insect orders maternally regulate early embryogenesis of their offspring.
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A so-called R-gene renders the yellow-striped flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae: Alticinae) resistant to the defenses of the yellow rocket Barbarea vulgaris R.Br. (Brassicacea) and enables it to use it as a... more
A so-called R-gene renders the yellow-striped flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae: Alticinae) resistant to the defenses of the yellow rocket Barbarea vulgaris R.Br. (Brassicacea) and enables it to use it as a host plant in Denmark. In this study, genetic markers for an autosomal R-gene, inherited as a single, dominant locus in flea beetles from the Danish locality "Kvaerkeby" are described, and a genetic linkage map around this particular R-gene is constructed, using the technique of AFLP (Amplified Fragment Length Polymorphism).
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The eyespots on the ventral wings of Bicyclus anynana butterflies are exposed when at rest and interact with predators. Those on the dorsal surface are not exposed in this way, and may be involved in courtship and mate choice. In this... more
The eyespots on the ventral wings of Bicyclus anynana butterflies are exposed when at rest and interact with predators. Those on the dorsal surface are not exposed in this way, and may be involved in courtship and mate choice. In this study, we examined whether the size and fluctuating asymmetry (FA) of dorsal eyespots are reliable signals of male quality. High developmental stability is considered to result in low FA, and to be associated with high quality. Individuals of high quality are predicted to produce sexually selected traits that are large and symmetrical, at a relatively low cost. In this study, we manipulated eyespot development to uncouple eyespot size and FA in order to examine their independent roles in signalling to the female. Individual females in cages were given the choice between two or three males differing in eyespot traits. The results indicate that although size per se of the eyespots is used as a signal, FA and wing size are not. We discuss the use of FA in studies of sexual selection and aspects of sexual selection on dorsal eyespot size.
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... An analysis of covariance (ancova) was used to test the effects of mother&amp;amp;amp;#x27;s treatment (forced flight versus control ... could also result from a decline in maternal physiological condition as a result ofsenescence... more
... An analysis of covariance (ancova) was used to test the effects of mother&amp;amp;amp;#x27;s treatment (forced flight versus control ... could also result from a decline in maternal physiological condition as a result ofsenescence (Kern et ... Crabtree, B. &amp;amp;amp;amp; Newsholme, EA (1975) Comparative aspects of ...
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... 1): cold shock, resistant; Dashed line (=2): cold shock, non-resistant; Dotted line (=3): non-cold shock, resistant; Dash-Dotted line (=4): non ... This was in agreement with previous experiments carried out with P. nemorum beetles... more
... 1): cold shock, resistant; Dashed line (=2): cold shock, non-resistant; Dotted line (=3): non-cold shock, resistant; Dash-Dotted line (=4): non ... This was in agreement with previous experiments carried out with P. nemorum beetles from both Ejby as well as Kvær-keby (De Jong et al. ...
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Fluctuating asymmetry (FA) is considered to provide a means of evaluating developmental stability and to reflect an individual&#39;s quality or the stress experienced during development. Stress is predicted to increase the phenotypic... more
Fluctuating asymmetry (FA) is considered to provide a means of evaluating developmental stability and to reflect an individual&#39;s quality or the stress experienced during development. Stress is predicted to increase the phenotypic variation of both FA and trait size. In this study we examined the effect of a particular heat shock on both FA and size of eyespots in the butterfly, Bicyclus anynana. We also examined whether those eyespots thought to be involved in partner choice and sexual selection were particularly sensitive to stress. We applied a heat shock of 39.5 degrees C for 3 h before, during, and after a sensitive period in eyespot development. We examined the FA, variation in FA, size, and variation in size of five eyespots, two on the dorsal forewing (sexually selected traits), two on the ventral forewing, and one on the ventral hindwing (nonsexually selected traits). For each sex and treatment, the heat shock did not result in significant changes in mean trait size and FA nor in the variation of size and FA. There were no differences in the response to the heat shock between sexually and nonsexually selected traits. We discuss how the increased production of heat shock proteins, including HSP60, may have stabilized development and how this might explain the results.
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... plant. The individual plants were placed into separate 0.5 m 3 netted cages in abutterfly house. More details on maintenance of the larval rearing plants can be found in Gibbs et al. (2004). Table 1. Experimental design. Mean ...
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During offspring growth, reduction in resource availability through competitive interactions will restrict how large individuals can become. Given that selection to mature at a large size will be greater for the sex in which large size... more
During offspring growth, reduction in resource availability through competitive interactions will restrict how large individuals can become. Given that selection to mature at a large size will be greater for the sex in which large size provides the highest fitness return, sex-specific differences in response to a decrease in resource availability may be expected. Using Nicrophorus vespilloides Herbst (Coleoptera: Silphidae) we examined the sex-specific response of offspring to resource availability through sibling competition. We found that males and females were affected similarly by an increase in the level of sibling competition as brood size increased. Interestingly, although male N. vespilloides were consistently heavier than females, over a range of brood sizes, they were only significantly heavier than females at intermediate brood sizes. At present, the causes behind this finding remain unclear.