title: Ancestral Y-linked genes were maintained by translocation to the X and Y chromosomes fused to an autosomal pair in the Okinawa spiny rat Tokudaia muenninki.
abstract: Two species of the genus Tokudaia lack the Y chromosome and SRY, but several Y-linked genes have been rescued by translocation or transposition to other chromosomes. Tokudaia muenninki is the only species in the genus that maintains the Y owing to sex chromosome-autosome fusions. According to previous studies, many SRY pseudocopies and other Y-linked genes have evolved by excess duplication in this species. Using RNA-seq and RT-PCR, we found that ZFY, EIF2S3Y, TSPY, UTY, DDX3Y, USP9Y, and RBMY, but not UBA1Y, had high deduced amino acid sequence similarity and similar expression patterns with other rodents, suggesting that these genes were functional. Based on FISH and quantitative real-time PCR, all of the genes except for UTY and DDX3Y were amplified on the X and Y chromosomes with approximately 10-66 copies in the male genome. In a comparative analysis of the 372.4-kb BAC sequence and Y-linked gene transcripts from T. muenninki with the mouse Y genomic sequence, we observed that multiple-copy genes in the ancestral Y genome were nonfunctional, indicating that the gene functions were assumed by amplified copies. We also found a LTR sequence at the distal end of a SRY duplication unit, suggesting that unequal sister chromatid exchange mediated by retrotransposable elements could have been involved in SRY amplification. Our results revealed that the Y-linked genes were rescued from degeneration via translocations to other sex chromosomal regions and amplification events in T. muenninki.
authors.affiliation: Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.
authors.forename: Chie
authors.initials: C
authors.lastname: Murata
authors.affiliation: RIKEN, Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.|Division of Pediatric Disease Genomics, Department of Genome Medicine, National Research Institute for Child Health and Development, 2-10-1, Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.affiliation: Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.
authors.forename: Issei
authors.initials: I
authors.lastname: Imoto
authors.affiliation: Laboratory of Animal Cytogenetics, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. asatok@sci.hokudai.ac.jp.
authors.forename: Asato
authors.initials: A
authors.lastname: Kuroiwa
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics; D050173:Genes, Y-Linked / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D051189:Murinae / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D018626:Retroelements / Q000235:genetics; D019849:Sex Determination Processes / Q000235:genetics*; D051876:Sex-Determining Region Y Protein / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics; D014178:Translocation, Genetic / Q000235:genetics*; D014960:X Chromosome / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*
chemical_list: D018626:Retroelements; D051876:Sex-Determining Region Y Protein
keywords: BAC; RNA-seq; evolution; gene amplification; sex chromosome; translocation