Data from: Unconstrained evolution in short introns?—An analysis of genome-wide polymorphism and divergence data from Drosophila

 

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Title Short intron sequence alignment of the 2L chromosome arm
Downloaded 21 times
Description We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the six D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.
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Title Short intron sequence alignment of the 2R chromosome arm
Downloaded 14 times
Description We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the six D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.
Download alignment_2R (1.121 Mb)
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Title Short intron sequence alignment of the 3L chromosome arm
Downloaded 13 times
Description We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.
Download alignment_3L (788.9 Kb)
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Title Short intron sequence alignment of the 3R chromosome arm
Downloaded 17 times
Description We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.
Download alignment_3R (1.126 Mb)
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When using this data, please cite the original publication:

Clemente F, Vogl C (2012) Unconstrained evolution in short introns?—An analysis of genome-wide polymorphism and divergence data from Drosophila. Journal of Evolutionary Biology 25(10): 1975-1990. http://dx.doi.org/10.1111/j.1420-9101.2012.02580.x

Additionally, please cite the Dryad data package:

Clemente F, Vogl C (2012) Data from: Unconstrained evolution in short introns?—An analysis of genome-wide polymorphism and divergence data from Drosophila. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t201q
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