Supplementary Material for: Toward a Comprehensive Overview of Cytogenomics in the Galliformes: a Focus on Western Capercaillie and Hazel Grouse Karyotypes

Introduction: The Phasianidae family belongs to Galliformes, which is basal to other Neognathae. Despite the availability of chromosome-level genome assemblies for many Phasianidae species, the karyotypes for some species remain poorly investigated.
Methods: In this study, we described karyotypes using classical, differential, and molecular cytogenetic (BAC-FISH) methods. To compare chromosome-level genomes of 10 Galliformes species dot-plot analysis was performed.
Results: We provide the first comprehensive description of the karyotype of two Tetraonini species: the western capercaillie (Tetrao urogallus, 2n=78) and the hazel grouse (Tetrastes bonasia, 2n=80). We mapped chicken BAC clones (CHORI-261) with known coordinates to the chromosomes of the western capercaillie and Japanese quail (Coturnix japonica, 2n=78) to anchor physical chromosomes to chromosome-level assemblies. Finally, we performed dot-plot comparisons of ten available chromosome-level genome assemblies to identify inter- and intrachromosomal rearrangements in Galliformes.
Conclusion: We show that the centromeric fusion of orthologs of GGA6 and GGA8 is shared by all analyzed species in the tetraonid clade: T. urogallus, T. bonasia, and Lagopus muta. We identified linage-specific intrachromosomal rearrangements on chromosomes orthologs to chicken Z (Phasianinae and Tetraoninae), 7 and 12 (Phasianinae and Tetraoninae), 5 and 13 (Perdicinae), 22 (Alectoris). Our study shows that analysis of the genomes of several closely related species allows us to identify chromosomal rearrangements characteristic of individual evolutionary lines.