Genome breakdown

This data set is part of the Polistes dominula genome project, and describes the protocol used for computing a breakdown of the genome into various categories and comparison to related species, as described in (Standage et al., Molecular Ecology, 2016). Included in this data set are instructions for collecting and preprocessing the comparative genomics data, the scripts used for calculating the breakdown, and the code for plotting the breakdown.

Procedure

Annotated genomes for for 20 Hymenopteran species were collected from NCBI and various other sources using GenHub version 0.3.8.

time genhub-build.py --cfgdir=cfg --batch=hymhub \
                     --workdir=species --numprocs=16 --format='HymHubv0.3.0-{}ILC-%05lu' \
                     download format prepare stats cluster

The download step retrieves genome sequences, protein sequences, and annotations from primary sources; the format step pre-processes these data into a consistent format; the prepare step computes iLoci and performs various other processing tasks; the stats step calculates statistics for a variety of data types (iLoci, mRNAs, exons, etc); and the cluster step determines homologous iLoci via clustering of protein products from the various species.

Next, the conserved.py script determines which hiLoci are conserved as single-copy orthologs amongst 7 representative species.

python conserved.py -v 0.3.0 GenHub.hiloci.tsv > HymHub.hicons.tsv

Then, the breakdown.py script calculates the proportion of each genome occupied by conserved genes (conserved in all 7 representative species), matched genes (conserved in at least two of the 20 species), intergenic regions, and so on.

python breakdown.py --counts \
                    <(cat species/*/*.iloci.tsv) \
                    GenHub.hiloci.tsv \
                    HymHub.hicons.tsv \
    > hymhub-breakdown-counts.tsv
python breakdown.py <(cat species/*/*.iloci.tsv) \
                    GenHub.hiloci.tsv \
                    HymHub.hicons.tsv \
    > hymhub-breakdown-bp.tsv

Finally, the breakdowns of genome content are plotted as bar plots as shown in the attached Jupyter notebook.

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