Supplementary Material for: Genomic Structures of the kW1 Loci on the Z and W Chromosomes in Ratite Birds: Structural Changes at an Early Stage of W Chromosome Differentiation Ishijima J. Uno Y. Nishida C. Matsuda Y. 10.6084/m9.figshare.5126467.v1 https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Genomic_Structures_of_the_kW1_Loci_on_the_Z_and_W_Chromosomes_in_Ratite_Birds_Structural_Changes_at_an_Early_Stage_of_W_Chromosome_Differentiation/5126467 The W chromosome of ratite birds shows minimal morphological differentiation and retains homology of genetic linkage and gene order with a substantial stretch of the Z chromosome; however, the molecular structure in the differentiated region is still not well known. The kW1 sequence was isolated from the kiwi as a W-specific DNA marker for PCR-based molecular sexing of ratite birds. In ratite W chromosomes, this sequence commonly contains a ∼200-bp deletion. To characterize the very early event of avian sex chromosome differentiation, we performed molecular cytogenetic analyses of kW1 and its flanking sequences in paleognathous and neognathous birds and reptiles. Female-specific repeats were found in the kW1-flanking sequence of the cassowary <i>(Casuarius casuarius)</i>, and the repeats have been amplified in the pericentromeric region of the W chromosomes of ratites, which may have resulted from the cessation of meiotic recombination between the Z and W chromosomes at an early stage of sex chromosome differentiation. The presence of the kW1 sequence in neognathous birds and a crocodilian species suggests that the kW1 sequence was present in the ancestral genome of Archosauria; however, it disappeared in other reptilian taxa and several lineages of neognathous birds. 2014-05-08 00:00:00 kW1 sequence Neognathous birds Paleognathous birds Ratite Repetitive sequence Reptiles Sex chromosome differentiation