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Additional file 2:Figure S1. Ovarian section in paraffin, negative control without primary antibody, showing no specific staining by the secondary antibody. DNA is stained with Hoescht 33342 (blue). Bar = 20 µm.

Additional file 3:Figure S2. Oocyte whole mount, negative control without primary antibody, showing no specific staining by the secondary antibody. DNA is stained with Hoescht 33342 (blue) and actin with Acti-stain 555 phalloidin (red). Bar = 20 µm (same magnification was used for swine and bovine).

Additional file 5: Fig. S1. Rangifer tarandus scaffold mis-assembly revealed by comparison with Bos taurus chromosomes. (a) Scaffold 1 mapped to bovine chromosomes 12 and 5; (b) Scaffold 2 mapped to bovine chromosomes 8 and 6; (c) Scaffold 12 mapped to bovine chromosomes 11 and 4; (d) Scaffold 20 mapped to bovine chromosomes 3 and 1; (e) Rearranged scaffold 21 mapped to bovine chromosome 9; (f) Scaffold 25 mapped to bovine chromosomes 13 and 7. Exact breakpoints are listed in Table S1. Green rectangles represent centromere positions.

Additional file 4:Stage and diameter of the follicles used in this study and the corresponding chromatin stage and transcription activity reported in the literature[65-68].

Additional file 8: Table S1. Breakage positions in the mis-assembled scaffolds.

Additional file 1:Table S1. Description of the antibodies used for immunofluorescence in this study.

Additional file 5: Figure S3. Automatic oligo-banding pattern analysis of the rcp(3;6). The “Analyze” tool of the Oligo-Banding plugin [39] analyzes the fluorophore signals of each traced chromosome and generates an output containing ROI manager tracing ID (ROI column), detected fluorophore banding patterns (Signature column), associated chromosome based on pattern identity (Ref column), the number of differences between the detected pattern and the expected one (Err column) and the reference banding pattern of the associated chromosome (Sequence column) (a). The tool also generates plots for each traced chromosome in order to visualize and confirm detected patterns. For instance, the der(3) and der(6) plots of the rcp(3;6) boar are shown in b and c. Based on outputted results table and signal plots, real chromosomal abnormalities and signal detection errors can be distinguished. d After chromosomal abnormality confirmation, images can be generated using basic ImageJ tools. More details on the plugin are available on the associated GitHub page [39].

Additional file 7: Fig. S3. Mapping of chromosomes 27 and 34 as assembled in this study on bovine chromosome 1 . Chromosomal fission led to the formation of the two R. tarandus chromosomes. The distal portion of the larger chromosome subsequently underwent translocation and inversion, the latter rearrangement creating the submetacentric character of R. tarandus chromosome 34. Green rectangles represent centromere positions.

Additional file 6: Fig. S2. Scaffolds 18, 14 and 68 (top to bottom order) forming R. tarandus chromosome 6 and corresponding to split bovine chromosomes 26 and 28. The fission that led to the new chromosomes has been carried in scaffold 14. The centromere of R. tarandus chromosome 6 apparently has been conserved in bovine chromosome 28 based on genome mapping. Green rectangles represent centromere positions.