Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".

Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species”.

BreakpointsData.tar.xz contains:

• Pairwise genome alignment files for Oikopleura, Ciona, Caenorhabditis, insects and muntjaks in GFF format in `inst/extdata/`.
• dN / dS computation results in `inst/extdata/dNdS/`.
• Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.
• OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,
• N3 the tunicates and N20 the _Ciona_ clade.
• `BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.
• The files needed to build the `BreakpointsData` package.

Oidioi_pairwise_v3.tar.gz contains:

• The pairwise alignment files between genomes, in MAF format.
• A copy of the Nextflow pipeline used to generate them.

oist-assembler.tar.gz contains:

• A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.
• A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.
• A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.

Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.

Oidioi_genomes.tar.gz contains:

• For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.
• For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.

OrthoFinderRun.tar.xz contains:

• A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.

Supplemental_Code.tar.gz contains:

• A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.

AugustusAnnotation.tar.gz (added July 26th 2024) contains:

• AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.