Data from: Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura

Chang C, Larracuente AM

Date Published: March 13, 2017

DOI: http://dx.doi.org/10.5061/dryad.rp949

 

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Title dpse_falcon assembly
Downloaded 3 times
Description We downloaded raw PacBio reads from ftp://ftp.hgsc.bcm.edu/Dpseudoobscura/Towards_finishing_the_D.pseudoobscura_genome/PacBio_Data/FastQ_files/ (these reads was generously granted by Drs. Stephen Schaeffer and Stephen Richards). We used the Falcon assembler v0.3.0 (https://github.com/PacificBiosciences/FALCON-integrate) to filter, correct and assemble reads. Then we polished the assembly using Quiver (SMRT Analysis v2.3.0)
Download dpse_falcon.quiver.fasta (158.4 Mb)
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Title dpse_falcon gtf
Downloaded 2 times
Description We identified exon-introns junctions by mapping annotated transcripts (r3.03; Flybase) and transcripts of Y-linked genes from NCBI (gi|295126506|gb|GU937420.1|, gi|255764727|gb|EU595397.2|, gi|295126512|gb|GU937423.1|) to our assembly using exonerate 2.4.0. To complement these data, we mapped RNA-seq reads to our assembly using Tophat v2.0.13. We annotated transcripts, eliminated small redundant isoforms with cufflinks v2.2.2 .
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Title dpse expression and annotation
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Description We mapped RNA-seq reads to our assembly using Tophat v2.0.13 and estimated expression level with cufflinks v2.2.2. We then searched for homologous genes using the predicted transcripts as BLAST queries to all D. melanogaster translations and transposon sequences (r6.07) with NCBIblast.
Download expression and annotation.xlsx (6.902 Mb)
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When using this data, please cite the original publication:

Chang C, Larracuente AM (2017) Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Evolution 71(5): 1285-1296. http://dx.doi.org/10.1111/evo.13229

Additionally, please cite the Dryad data package:

Chang C, Larracuente AM (2017) Data from: Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rp949
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