A sampling strategy for genome sequencing the British terrestrial arthropod fauna

Crowley, Liam M.; Allen, Heather; Barnes, Ian; Holland, Peter W.H.; Broad, Gavin R.; Fletcher, Chris; Holland, Peter; Januszczak, Inez; Lawniczak, Mara; Lewis, Owen T.; Macadam, Craig R.; Mulhair, Peter O.; Conceicoa, Lyndall Pereira da; Price, Benjamin W.; Raper, Chris; Sivell, Olga; Sivess, Laura

doi:10.12688/wellcomeopenres.18925.1

Cited by 151 publications

(2 citation statements)

References 12 publications

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“…Thus, both changes in coding regions and CREs are key to explain the wide range of insect (and animal) morphologies. Comparative genomics projects (Crowley et al 2023; Formenti et al 2022; Molik 2022) promoted a better understanding of changes in trans elements, due to their higher degree of conservation between species. By contrast, CREs are more difficult to identify by homology, since they are usually less pleiotropic and for this, they tend to accumulate more changes in their sequences that impede their proper characterisation by sequence similarity.…”

Section: Introductionmentioning

confidence: 99%

Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum

Pallarès-Albanell,

Ortega-Flores,

Senar-Serra

et al. 2024

Preprint

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The evolution of insects has been marked by the appearance of key body plan innovations and novel organs that promoted the outstanding ability of this lineage to adapt to new habitats, boosting the most successful radiation in animals. To understand the origin and evolution of these new structures, it is essential to investigate which are the genes and gene regulatory networks participating during the embryonic development of insects. Great efforts have been made to fully understand, from a gene expression and gene regulation point of view, the development of holometabolous insects, in particular Drosophila melanogaster, with the generation of numerous functional genomics resources and databases. Conversely, how hemimetabolous insects develop, and which are the dynamics of gene expression and gene regulation that control their embryogenesis, are still poorly characterized. Therefore, to provide a new platform to study gene regulation in insects, we generated ATAC-seq (Assay for transposase-Accessible Chromatin using sequencing) for the first time during the development of the mayfly Cloeon dipterum. This new available resource will allow to better understand the dynamics of gene regulation during hemimetabolan embryogenesis, since C. dipterum belongs to the paleopteran order of Ephemeroptera, the sister group to all other winged insects. These new datasets include six different time points of its embryonic development and identify accessible chromatin regions corresponding to both general and stage-specific promoters and enhancers. With these comprehensive datasets, we characterised pronounced changes in accessible chromatin between stages 8 and 10 of embryonic development, which correspond to the transition from the last stages of segmentation to organogenesis and appendage differentiation. The application of ATAC-seq in mayflies has contributed to identify the epigenetic mechanisms responsible for embryonic development in hemimetabolous insects and it will provide a fundamental resource to understand the evolution of gene regulation in winged insects.

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Section: Introductionmentioning

confidence: 99%

Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum

Pallarès-Albanell,

Ortega-Flores,

Senar-Serra

et al. 2024

Preprint

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“…The recent advent of long-read DNA sequencing, coupled with Hi-C sequencing, has enabled the rapid generation of very high quality genome assemblies. The Darwin Tree of Life (DToL) is one of several projects exploiting these technologies to sequence and assemble high-quality genomes from large numbers of species (Crowley et al, 2023; The Darwin Tree of Life Project Consortium, 2022; Wright et al 2023). Here we interrogate 150 newly generated insect genome assemblies to investigate GC sequence heterogeneity across Lepidoptera, Diptera, Hymenoptera, and Coleoptera.…”

Section: Introductionmentioning

confidence: 99%

GC content across insect genomes: phylogenetic patterns, causes and consequences

Kyriacou,

Mulhair,

Holland

2023

Preprint

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The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Hymenoptera, Coleoptera and, most strikingly, Lepidoptera. Two species of Diptera,Bombylius majorandB. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Hymenoptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

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GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences

Kyriacou,

Mulhair,

Holland

2024

J Mol Evol

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The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

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A sampling strategy for genome sequencing the British terrestrial arthropod fauna

Cited by 151 publications

References 12 publications

Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum

Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum

GC content across insect genomes: phylogenetic patterns, causes and consequences

GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences

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