Abstract
<b><i>Introduction:</i></b> X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA <i>Xist</i> is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus <i>Tokudaia</i> includes three rodent species endemic to Japan. <i>Tokudaia osimensis</i> and <i>Tokudaia tokunoshimensis</i> lost the Y chromosome (XO/XO), while <i>Tokudaia muenninki</i> (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among <i>Tokudaia</i> species. <b><i>Methods:</i></b> Gene structure of nine genes in Xic was predicted, and the gene location and genome sequences of Xic were compared between mouse and <i>Tokudaia</i> species. The expression level of the gene was confirmed by transcripts per million calculation using RNA-seq data. <b><i>Results:</i></b> Compared to mouse, the Xic gene order and location were conserved in <i>Tokudaia</i> species. However, remarkable structure changes were observed in lncRNA genes, <i>Xist</i> and <i>Tsix</i>, in the XO/XO species. In <i>Xist,</i> important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of <i>Xist</i> and <i>Tsix</i> were confirmed in TMU, however, not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between <i>Jpx</i> and <i>Ftx</i> in the XO/XO species. <b><i>Conclusion:</i></b> Our findings indicate that even if the <i>Xist</i> and <i>Tsix</i> lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in the intergenic region of <i>Jpx</i>-<i>Ftx</i> resulted in the inability to perform the XCI, and, as a result, a lack of <i>Xist</i> expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome as a consequence of the degradation of the XCI system.