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. 2025 May 6;42(5):msaf102. doi: 10.1093/molbev/msaf102

Fig. 4.

Fig. 4.

Tokudaia Y-MRCA-derived region in X chromosome of T. muenninki. a) Overview of the Tokudaia Y-chromosomal most recent common ancestor (Y-MRCA)-derived region identified in the X chromosome of T. muenninki. This region appears in two distinct locations: the Xhet-region and Xq-region2. b) Self-dot-plot alignment of the neo-ancX chromosome of T. muenninki. The central region of neo-ancX consists of a heterochromatic region composed of repetitive elements. c) Enlarged view of the Xhet-region (115.2 to 198.3 Mbp). Genes and BASD are shown as horizontal lines in the genome. Regions of Y-chromosome origin, X-chromosome origin, heterochromatin, and BASD are distinguished by their labels and positions. We identified 52 copies of partial Uba1y (pseudogene) within the heterochromatic region spanning approximately 80 Mbp. On the 3′ side of this region, intact Zfy, pseudogenes of Uba1y and Usp9y, and BASD, are located. The ancX region begins at Zfp300. At the bottom, a dot-plot alignment diagram shows how the highlighted 542 kbp basic repeat unit aligns within the region. The heterochromatic region is composed of irregular repeats of a basic unit that includes partial Uba1y. Genes labeled with “-ps” represent pseudogenes, while intact genes are indicated in bold. d) Enlarged view of the 3′ side of the Xhet-region (195.3 to 199.0 Mbp). This figure shows an enlargement of the area between the heterochromatic region and the start of the ancX region, as shown in b). Within the genomic region depicted by boxed outlines, Uba1y pseudogenes, intact Zfy, BASD, and Usp9y pseudogenes are aligned. Genes labeled with “-ps” represent pseudogenes, while intact genes are indicated in bold. e) Enlarged view of Xq-region2 (344.9 to 346.0 Mbp). Between the X-linked genes Ikbkg and Gab3, a 162 kbp T. muenninki-specific insertion of the Tokudaia Y-MRCA-originated sequence, containing intact Zfy, Tspy, and BASD, was identified (indicated by the lower arrow). This sequence, along with an approximately 300 kbp region containing it (indicated by the upper arrow), has undergone an inverted duplication. Genes labeled with “-ps” represent pseudogenes, while intact genes are indicated in bold.