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

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.

平胸总目鸟类（ratite birds）的W染色体仅存在极微弱的形态分化，且其与Z染色体的大片段区段仍保持遗传连锁关系与基因排布序列的同源性；但目前学界对其分化区域的分子结构仍知之甚少。研究人员从几维鸟中分离得到kW1序列，将其作为可用于平胸总目鸟类基于聚合酶链式反应（Polymerase Chain Reaction, PCR）的分子性别鉴定的W染色体特异性DNA标记。在平胸总目鸟类的W染色体中，该序列通常存在一段约200碱基对（base pair, bp）的缺失片段。为解析鸟类性染色体分化的早期发生事件，研究人员对古颚总目鸟类（paleognathous birds）、今颚总目鸟类（neognathous birds）及爬行类动物中的kW1序列及其侧翼序列开展了分子细胞遗传学分析。研究人员在鹤鸵（*Casuarius casuarius*）的kW1侧翼序列中发现了雌性特异性重复序列；这类重复序列在平胸总目鸟类W染色体的着丝粒周边区域（pericentromeric region）发生了扩增，这一现象可能源于性染色体分化早期阶段Z与W染色体之间减数分裂重组的终止。kW1序列在今颚总目鸟类与一种鳄类物种中的存在，表明该序列曾存在于主龙类（Archosauria）的祖先基因组中；但该序列在其他爬行类类群以及今颚总目鸟类的多个演化支中发生了丢失。