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Cited by 22Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

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

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Kyriacou, Riccardo G., Mulhair, Peter O., Holland, Peter W. H.·2024·Journal of Molecular Evolution
DOI 10.1007/s00239-024-10160-5PMC PMC10978632

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Abstract

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. discolo r, 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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  • The level of significance (the size of a P-value) will depend on the size of the effect and the number of data points, tested against a null hypothesis of exactly zero difference, or exactly zero correlation.

    “Usually, the level of significance (the size of a P-value) will depend on the size of the effect and the number of data points, tested against a null hypothesis of exactly zero difference, or exactly zero correlation119–121.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [120]

    The Methods section, “Relation Between GC Content and Chromosome Size” (page unavailable), describes a comparison with a model that forces correlation to zero; the Results section reports significant Pearson correlations using P < 0.05 (page unavailable). The paper does not state that P-value size depends on effect size and the number of data points, and its explicit zero-correlation model is compared using Bayes factors, not P-values. (LLM, conf=0.78)

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Cited by

Sorted by citations

Authors
Kyriacou, R. G., Mulhair, P. O., & Holland, P. W. H.
Affiliations
University of Oxford (GB)
Corresponding author
Holland, Peter W. H.
ORCID
Venue
Journal of Molecular Evolution
Publisher
Springer Science and Business Media LLC
Published
2024-03-15
Volume
92
Issue
2
Pages
138-152
ISSN
  • 0022-2844 (ISSN-L)
  • 1432-1432
DOI
10.1007/s00239-024-10160-5
PMC
PMC10978632
OpenAlex
W4392856765
Cited by
22
References
2
Citations by year
2026: 6 · 2025: 7 · 2024: 9
FWCI
4.82
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Molecular Evolution (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
Funders
Wellcome Trust (218328, 226458)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
GC content, insect genomes, GC-biased gene conversion, codon usage bias, AT bias, subtelomeric regions, chromosome length, Lepidoptera, Diptera, Coleoptera, Hymenoptera, protein-coding genes, phylogenetic patterns, Darwin Tree of Life
MeSH terms
Animals, Base Composition, Codon, Insecta, Phylogeny, Evolution, Molecular, Genome, Insect

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