Data from: Tempo and mode of genome evolution in a 50,000-generation experiment

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE

Date Published: August 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.6226d

 

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Title REL606, ancestral genome
Downloaded 36 times
Description This files contains the ancestral genome in gff3 format
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Title REL606 non covered regions
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Description This file contains the positons in the ancestral genome that are not covered by the short read sequencing technology used due to repeats.
Download REL606.L20.G15.P0.M35.mask.gd (15.37 Kb)
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Title LTEE mutator status file
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Description This files provides information about the point mutator status of each clone. Clones that have an increased point mutation rate have a value of 1 in column 5.
Download LTEE_Mutator_info.txt (11.28 Kb)
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Title LTEE mutation file
Downloaded 29 times
Description This file stores all mutations that were identified in the sequenced genomes of the LTEE, expect the ones in masked regions or in the neighbourhood of IS elements. It is used to compute most mutation analysis.
Download oli.LTEE.final_masked.no_IS_adjacent.tab (13.76 Mb)
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Title MAE mutation file
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Description This file stores all mutations that were identified in the sequenced genomes of the MAE (Mutation Accumulation Experiment), expect the ones in masked regions or in the neighbourhood of IS elements.
Download oli.MAE.final_masked.no_IS_adjacent.tab (20.56 Kb)
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Title MAE fitness
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Description This files contains the fitness estimates of the MAE clones sequenced.
Download MAE_fitness.csv (791 bytes)
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Title LTEE spectrum counts
Downloaded 15 times
Description This file describes the spectrum of mutations that have accumulated through time in each population of the LTEE
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Title LTEE mutation counts (1)
Downloaded 17 times
Description This file describes, for each sequenced clone of the LTEE, the counts of each mutation types recovered. It is used for the genome size figure.
Download count.LTEE.final_masked.csv (156.2 Kb)
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Title LTEE mutation counts (2)
Downloaded 17 times
Description This file describes, for each sequenced clone of the LTEE, the counts of each mutation types recovered. It is produced by the program ComputeMutationThroughTimeDryad.pl and is used to produce most figures.
Download MutationTypesThroughTime.txt (32.48 Kb)
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Title MAE mutation counts
Downloaded 12 times
Description This file describes, for each sequenced clone of the MAE, the counts of each mutation types recovered. It is produced by the program ComputeMutationThroughTimeDryad.pl and is used to produce figures using the MAE as a reference.
Download MutationTypesThroughTimeMAE.txt (1.426 Kb)
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Title LTEE point mutation matrix for phylogeny
Downloaded 47 times
Description This file contains an array in which the presence and absence of point mutations recovered in the LTEE sequenced clones is stored as 0 or 1 respectively for each clone. It is produced by ComputeMutationThroughTimeDryad.pl and is used to produce figure 2.
Download MutRArray.txt (7.869 Mb)
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Title REL606 ancestral genome composition
Downloaded 17 times
Description This file, produced by GenomeCompositionComputer.pl, reports the composition of the ancestral genome (synonymous, nonsynonymous, intergenic) for each type of point mutations (AT to CG, AT to GC ...). It is used to compute the expected number of nonsynonymous mutations based on the observed number of synonymous.
Download GenomeComposition.txt (268 bytes)
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Title ComputeMutation command file LTEE
Downloaded 15 times
Description This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking for all mutations of the LTEE to be reported.
Download CmdfileLTEE.txt (435 bytes)
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Title ComputeMutation command file MAE
Downloaded 13 times
Description This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking for all mutations of the MAE to be reported.
Download CmdfileMAE.txt (432 bytes)
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Title ComputeMutation command file LTEE mutator
Downloaded 15 times
Description This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking to report only mutations occurring in point mutator clones of the LTEE
Download CmdfileLTEE_Mutator.txt (438 bytes)
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Title ComputeMutation command file LTEE non mutator
Downloaded 9 times
Description This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking to report only mutations occurring in non point mutator clones of the LTEE
Download CmdfileLTEE_nonMutator.txt (436 bytes)
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Title Compute genome composition perl script
Downloaded 17 times
Description This perl script computes the GenomeComposition.txt file that reports the number of synonymous, nonsynonymous and intergenic mutations for each of the 6 types of possible point mutations. See ReadMe.pdf for usage.
Download GenomeCompositionComputer.pl (24.75 Kb)
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Title Figures R script
Downloaded 17 times
Description This R script is used to create all figures and extended data figures. See ReadMe.pdf for usage.
Download ScriptFiguresDryad.r (70.08 Kb)
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Title Gstat perl script
Downloaded 11 times
Description This perl script computes the G stastics of convergence and the randomisation of point mutations used to estimate the p-value of the G estimated. See ReadMe.pdf for usage.
Download ConvergenceGstatDryad.pl (27.40 Kb)
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Title MAE mutator status file
Downloaded 7 times
Description This files provides information about the point mutator status of each clone of the MAE. Clones that have an increased point mutation rate have a value of 1 in column 5.
Download MAE_Mutator_info.txt (486 bytes)
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Title Compute mutation through time perl script
Downloaded 16 times
Description This perl script computes the spectrum of mutations found in each clone as well as the matrix used for the phylogeny. See ReadMe.pdf for usage.
Download ComputeMutationThroughTimeDryad.pl (29.78 Kb)
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Title ReadMe file
Downloaded 34 times
Description This file explains how to use the 4 scripts in order to produce all figures and G scores of the article
Download ReadMe.pdf (93.60 Kb)
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When using this data, please cite the original publication:

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE (2016) Tempo and mode of genome evolution in a 50,000-generation experiment. Nature 536(7615): 165-170. http://dx.doi.org/10.1038/nature18959

Additionally, please cite the Dryad data package:

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE (2016) Data from: Tempo and mode of genome evolution in a 50,000-generation experiment. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6226d
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