Bedrock radioactivity influences the rate and spectrum of mutation - Orthologous genes
Creators
- 1. Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
- 2. LPC, Université Clermont Auvergne, CNRS/IN2P3 UMR6533, Clermont-Ferrand, France
- 3. Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
Description
Alignments of the 2490 orthologous genes used in the article "Natural Bedrock radioactivity influences the rate and spectrum of mutation" to estimate the mutational spectrum and synonymous substitution rate.
To compute accurate synonymous substitution rate, we removed genes with short sequences (<half of the alignment) and genes strongly supporting another phylogeny using ProfileNJ (Noutahi et al. 2016) with a bootstrap threshold of 90%, resulting in a subset of 769 genes listed in the file "List_769_1-to-1_orthologs_EvolutionRate.txt".
Transcriptome paired-end reads used to define these orthologous genes have been deposited to the European Nucleotide Archive and are available under the study ID PRJEB14193.
Sequences were aligned with Prank (Löytynoja & Goldman 2008) using a codon model and sites ambiguously aligned were removed with Gblocks (Castresana 2000).
Files
List_769_1-to-1_orthologs_EvolutionRate.txt
Files
(6.7 MB)
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Additional details
References
- Löytynoja, A. & Goldman, N., 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320(5883), pp.1632–1635.
- Castresana, J., 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution, 17(4), pp.540–552.
- Noutahi, E. et al., 2016. Efficient Gene Tree Correction Guided by Genome Evolution. PloS one, 11(8), p.e0159559.