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Thomas R Buckley - One of the best experts on this subject based on the ideXlab platform.
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Assembling large Genomes: analysis of the stick Insect (Clitarchus hookeri) Genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Background Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. Results The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria , the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
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assembling large Genomes analysis of the stick Insect clitarchus hookeri Genome reveals a high repeat content and sex biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria, the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
Victoria G Twort - One of the best experts on this subject based on the ideXlab platform.
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Assembling large Genomes: analysis of the stick Insect (Clitarchus hookeri) Genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Background Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. Results The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria , the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
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assembling large Genomes analysis of the stick Insect clitarchus hookeri Genome reveals a high repeat content and sex biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria, the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
Richard D. Newcomb - One of the best experts on this subject based on the ideXlab platform.
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Assembling large Genomes: analysis of the stick Insect (Clitarchus hookeri) Genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Background Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. Results The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria , the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
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assembling large Genomes analysis of the stick Insect clitarchus hookeri Genome reveals a high repeat content and sex biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria, the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
Ross N Crowhurst - One of the best experts on this subject based on the ideXlab platform.
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Assembling large Genomes: analysis of the stick Insect (Clitarchus hookeri) Genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Background Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. Results The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria , the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
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assembling large Genomes analysis of the stick Insect clitarchus hookeri Genome reveals a high repeat content and sex biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Ross N Crowhurst, Victoria G Twort, Richard D. Newcomb, Thomas R BuckleyAbstract:Stick Insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the Genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick Insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo Genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large Genome size in stick Insects. The C. hookeri Genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest Insect Genome sequenced and assembled to date. Like the large Genome of Locusta migratoria, the Genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced Insect Genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae Genome, is the most abundant repeat type in the C. hookeri Genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the Genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large Insect Genomes such as L. migratoria and C. hookeri Genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri Genome size yet are surprisingly absent from the T. cristinae Genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick Insects.
Cornelis J P Grimmelikhuijzen - One of the best experts on this subject based on the ideXlab platform.
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invertebrate neurohormone gpcrs
Reference Module in Neuroscience and Biobehavioral Psychology#R##N#Encyclopedia of Neuroscience, 2009Co-Authors: Cornelis J P Grimmelikhuijzen, Giuseppe Cazzamali, Michael Williamson, Martina Schneider, Frank HauserAbstract:Neurohormones (biogenic amines, neuropeptides, and protein hormones) and their G-protein-coupled receptors (GPCRs) occupy a high hierarchic position in the physiology of invertebrates because they steer important processes such as development, growth, reproduction, feeding, homeostasis, and behavior. In this article, we focus on the neurohormone GPCRs from Insects (which comprise 75% of all animal species) and complement them with further examples from other invertebrates. The presence of 24 Insect Genome projects has greatly facilitated the identification of Insect neurohormone GPCRs and has enabled us to draw important conclusions on the evolution and co-evolution of Insect neurohormone GPCRs and their ligands.
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a Genome wide inventory of neurohormone gpcrs in the red flour beetle tribolium castaneum
Frontiers in Neuroendocrinology, 2008Co-Authors: Giuseppe Cazzamali, Reinhard Predel, Susanne Neupert, Michael Williamson, Peter Verleyen, Joachim Schachtner, Yoonseong Park, Cornelis J P GrimmelikhuijzenAbstract:Insect neurohormones (biogenic amines, neuropeptides, and protein hormones) and their G protein-coupled receptors (GPCRs) play a central role in the control of behavior, reproduction, development, feeding and many other physiological processes. The recent completion of several Insect Genome projects has enabled us to obtain a complete inventory of neurohormone GPCRs in these Insects and, by a comparative genomics approach, to analyze the evolution of these proteins. The red flour beetle Tribolium castaneum is the latest addition to the list of Insects with a sequenced Genome and the first coleopteran (beetle) to be sequenced. Coleoptera is the largest Insect order and about 30% of all animal species living on earth are coleopterans. Some coleopterans are severe agricultural pests, which is also true for T. castaneum, a global pest for stored grain and other dried commodities for human consumption. In addition, T. castaneum is a model for Insect development. Here, we have investigated the presence of neurohormone GPCRs in Tribolium and compared them with those from the fruit fly Drosophila melanogaster (Diptera) and the honey bee Apis mellifera (Hymenoptera). We found 20 biogenic amine GPCRs in Tribolium (21 in Drosophila; 19 in the honey bee), 48 neuropeptide GPCRs (45 in Drosophila; 35 in the honey bee), and 4 protein hormone GPCRs (4 in Drosophila; 2 in the honey bee). Furthermore, we identified the likely ligands for 45 of these 72 Tribolium GPCRs. A highly interesting finding in Tribolium was the occurrence of a vasopressin GPCR and a vasopressin peptide. So far, the vasopressin/GPCR couple has not been detected in any other Insect with a sequenced Genome (D. melanogaster and six other Drosophila species, Anopheles gambiae, Aedes aegypti, Bombyx mori, and A. mellifera). Tribolium lives in very dry environments. Vasopressin in mammals is the major neurohormone steering water reabsorption in the kidneys. Its presence in Tribolium, therefore, might be related to the animal's need to effectively control water reabsorption. Other striking differences between Tribolium and the other two Insects are the absence of the allatostatin-A, kinin, and corazonin neuropeptide/receptor couples and the duplications of other hormonal systems. Our survey of 340 million years of Insect neurohormone GPCR evolution shows that neuropeptide/receptor couples can easily duplicate or disappear during Insect evolution. It also shows that Drosophila is not a good representative of all Insects, because several of the hormonal systems that we now find in Tribolium do not exist in Drosophila.