Fig. 2

The zebra finch germline-restricted chromosome is expressed in male and female gonads. a, b Comparison of coverage and read pileups for DNA-seq data from Spain_1 and Spain_2 testis/muscle, RNA-seq data from Spain_1 and Spain_2 testis, and available ovary RNA-seq data¹⁰. Shown are 100-bp regions within trim71 a and bicc1 b. Colours indicate SNVs deviating from the reference genome taeGut2 (adenine: green; cytosine: blue; guanine: brown; thymine/uracil: red). c Example alignments of proteomics data showing a subset of peptide expression of the respective GRC-linked paralog of ugdh and napa (alternative or ‘alt’ peptide; cf. reference or ‘ref’ peptide). d Proteomic evidence for GRC peptide expression (‘alt’) in comparison to their A-chromosomal paralog (‘ref’) of 5 genes in 7 sampled testes and 2 sampled ovaries. For label-free quantification (LFQ), unique as well as razor (non-unique) peptides were used. Note that unique peptides may occur in several of the 9 samples. e Gene ontology term enrichment analysis of the 115 high-confidence GRC-linked genes (77 mapped gene symbols). Colours indicate the log₁₀ of the false discovery rate-corrected p-value (PANTHER overrepresentation test, with a Fisher exact test for significance and filtering using a false discovery rate of 0.05), circle sizes denote fold enrichment above expected values. f Expression evidence for chicken orthologs of three different sets of zebra finch GRC gene paralogs in testes, ovaries, or other tissues of chicken²³. Randomisation tests show a significant enrichment for germline-expressed genes among the chicken orthologs of 115 high-confidence GRC gene paralogs and all 267 GRC gene paralogs, but not the 38 GRC-amplified gene paralogs.