pubmed.ncbi.nlm.nih.gov

Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes - PubMed

Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes

Eskeatnaf Mulugeta et al. Genome Res. 2016 Sep.

Abstract

The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.

© 2016 Mulugeta et al.; Published by Cold Spring Harbor Laboratory Press.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.

Phylogenetic relationship and geographic ranges of Ellobius species. (A) Phylogenetic tree (based on Zfx and Atrx) showing that the loss of the Y Chromosome occurred independently in Ellobius talpinus and Ellobius lutescens. Bootstrap values are shown on three nodes. (B) Present habitats of E. lutescens and E. talpinus separated by the Caspian Sea and the Caspian Mountains 8–7 Mya (obtained from the IUCN Red List of Threatened Species Version 2015.1;

http://www.iucnredlist.org

).

Figure 2.
Figure 2.

Y-derived genes in the genomes of E. lutescens and E. talpinus. (A) Y-derived ancestral and added genes identified in the genomes of E. lutescens and E. talpinus. (mc) Multicopy; (ps) pseudo gene. (B) Schematic representation of the mouse Y Chromosome. Genes indicated in pink are present in the E. lutescens genome. (C) The expression level of Y-Chromosomal genes and their X-Chromosomal homologs in testis of E. lutescens based on RNA sequencing data. E. lutescens testis RNA was assembled and annotated using mouse cDNA, and transcript abundance was quantified and plotted using the mouse chromosomal map. Low expressed genes (genes below the 25th percentile of the data) were removed before plotting. (FPKM) Fragments per kilobase of transcript per million fragments mapped. (D) Real-time quantitative RT-PCR on RNA isolated from ovary (Ov), testes (T), and female and male liver (Li F and Li M, respectively) for the E. lutescens homologs of mouse Eif2s3x and Eif2s3y (top graph), Zfx and Zfy (second from top), Usp9x and Usp9y (third from top), and Ssty (bottom graph). mRNA expression levels are normalized to beta actin; error bars, SD values from two separate animals.

Figure 3.
Figure 3.

Y-derived genes localize to the nonrecombining and meiotically silenced X Chromosome in E. lutescens. (A) Localization of FISH probes for E. lutescens homologs of mouse, Usp9y and Zfy (green) on the single X (encircled) in combination with an E. lutescens X-Chromosomal BAC FISH probe (red) in E. lutescens meiotic spreads also immunostained for SYCP3 (purple). Enlargements of indicated areas are shown on the right. DAPI counterstaining of the DNA is shown in the top and middle images. (B) Immunostaining for H2AFX and SYCP3 (top), polymerase (RNA) II (DNA-directed) polypeptide A (POLR2A) and SYCP3 (middle), and MLH1 and SYCP3 (bottom) on spread pachytene E. lutescens spermatocytes. Phosphorylated H2AFX marks the single X chromatin (encircled) in pachytene. POLR2A is depleted from the X Chromosome region in comparison with the rest of the nucleus. MLH1 marks crossover sites along the synaptonemal complexes of all autosomes. Enlargements of indicated areas are shown on the right. (C) Expression level of X-Chromosomal genes compared with autosomal genes. E. lutescens testis RNA was assembled and annotated using mouse cDNA; transcript abundance was quantified and plotted using the mouse chromosomal map. Low expressed genes (genes below the 25th percentile of the data) were removed before plotting. Expression level is expressed in FPKM (log2 scale). (D) Female E. lutescens reads were aligned to the male E. lutescens reference genome, and SNVs were called that are homozygous within the female but differ from the assembled male genome. High-quality SNVs were plotted using the mouse chromosome annotation and normalized to the number of coding genes per chromosome. None were found for the X Chromosome.

Figure 4.
Figure 4.

dN and dS analyses of autosomal and X-linked genes in E. lutescens. (A) Boxplots showing dN values of autosomal and X-Chromosomal E. lutescens orthologs of mouse genes. Values were averaged per chromosome and plotted using the mouse chromosomal map. (B) Boxplots showing dS values of autosomal and X-Chromosomal E. lutescens orthologs of mouse genes. Values were averaged per chromosome and plotted using the mouse chromosomal map. (C) Boxplots of dN (left) and dS (middle) values of all autosomal genes together compared with the X Chromosome, and the corresponding dN/dS values for the autosomal genes and the X-linked genes (right), calculated from the summed values. P values were calculated using R (Wilcoxon rank-sum test) and indicate significant differences between autosomal and X-Chromosomal values. (D) Scatter plot showing the distribution of dN and dS for the E. lutescens X Chromosome (green) and autosomes (red).

Similar articles

Cited by

References

    1. Arakawa Y, Nishida-Umehara C, Matsuda Y, Sutou S, Suzuki H. 2002. X-chromosomal localization of mammalian Y-linked genes in two XO species of the Ryukyu spiny rat. Cytogenet Genome Res 99: 303–309. - PubMed
    1. Bachtrog D. 2013. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet 14: 113–124. - PMC - PubMed
    1. Bagheri-Fam S, Sreenivasan R, Bernard P, Knower KC, Sekido R, Lovell-Badge R, Just W, Harley VR. 2012. Sox9 gene regulation and the loss of the XY/XX sex-determining mechanism in the mole vole Ellobius lutescens. Chromosome Res 20: 191–199. - PubMed
    1. Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, et al. 2014. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508: 494–499. - PMC - PubMed
    1. Blackmon H, Demuth JP. 2015. The fragile Y hypothesis: Y chromosome aneuploidy as a selective pressure in sex chromosome and meiotic mechanism evolution. Bioessays 37: 942–950. - PubMed

Publication types

MeSH terms

LinkOut - more resources