Larracuente_Supplementary_file2

Maximum likelihood tree with bootstrap support of Rsp and Rsp-like repeats used in Figure 3

dpse_falcon assembly

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

dpse expression and annotation

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

dpse_falcon gtf

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