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Similar ratios of introns to intergenic sequence across animal genomes

View ORCID ProfileWarren R. Francis, View ORCID ProfileGert Wörheide
doi: https://doi.org/10.1101/068627
Warren R. Francis
1Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straβe 10, 80333 Munich, Germany
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Gert Wörheide
1Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straβe 10, 80333 Munich, Germany
2GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
3Bavarian State Collection for Paleontology and Geology, Munich, Germany
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Abstract

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of non-model organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 09, 2017.
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Similar ratios of introns to intergenic sequence across animal genomes
Warren R. Francis, Gert Wörheide
bioRxiv 068627; doi: https://doi.org/10.1101/068627
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Similar ratios of introns to intergenic sequence across animal genomes
Warren R. Francis, Gert Wörheide
bioRxiv 068627; doi: https://doi.org/10.1101/068627

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