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 (Casuarius casuarius), 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.

平胸鸟类（ratite birds）的W染色体形态分化程度极低，且其大片段区域与Z染色体在遗传连锁与基因顺序上保持同源性；但目前学界对其分化区域的分子结构仍不甚明晰。kW1序列是从几维鸟中分离得到的W染色体特异性DNA标记，用于平胸鸟类基于聚合酶链式反应（PCR）的分子性别鉴定。在平胸鸟类的W染色体中，该序列通常带有一段约200 bp的缺失片段。为了阐明鸟类性染色体分化的早期关键事件，本研究对古颚总目鸟类（paleognathous birds）、今颚总目鸟类（neognathous birds）以及爬行动物中的kW1序列及其侧翼序列开展了分子细胞遗传学分析。研究在双垂鹤鸵（Casuarius casuarius）的kW1侧翼序列中发现了雌性特异性重复序列，且该重复序列在平胸鸟类W染色体的着丝粒周缘区域发生了扩增；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及一种鳄目物种中的存在，表明该序列曾存在于主龙类（Archosauria）的祖先基因组中，但在其他爬行动物类群以及多个今颚总目鸟类进化支中发生了丢失。