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Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

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...

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Autores principales: Francis, Warren R., Wörheide, Gert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534336/
https://www.ncbi.nlm.nih.gov/pubmed/28633296
http://dx.doi.org/10.1093/gbe/evx103
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author Francis, Warren R.
Wörheide, Gert
author_facet Francis, Warren R.
Wörheide, Gert
author_sort Francis, Warren R.
collection PubMed
description 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 nonmodel 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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spelling pubmed-55343362017-07-31 Similar Ratios of Introns to Intergenic Sequence across Animal Genomes Francis, Warren R. Wörheide, Gert Genome Biol Evol Research Article 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 nonmodel 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. Oxford University Press 2017-06-13 /pmc/articles/PMC5534336/ /pubmed/28633296 http://dx.doi.org/10.1093/gbe/evx103 Text en © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Francis, Warren R.
Wörheide, Gert
Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title_full Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title_fullStr Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title_full_unstemmed Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title_short Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
title_sort similar ratios of introns to intergenic sequence across animal genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534336/
https://www.ncbi.nlm.nih.gov/pubmed/28633296
http://dx.doi.org/10.1093/gbe/evx103
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