Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus

Abstract

Sex chromosomes are a peculiar constituent of the genome because the evolutionary forces that fix the primary sex-determining gene cause genic degeneration and accumulation of junk DNA in the heterogametic partner. One of the most spectacular phenomena in sex chromosome evolution is the occurrence of neo-Y chromosomes, which lead to X1X2Y sex-determining systems. Such neo-sex chromosomes are critical for understanding the processes of sex chromosome evolution because they rejuvenate their total gene content. We assembled the male and female genomes at the chromosome level of the spotted knifejaw (Oplegnathus punctatus), which has a cytogenetically recognized neo-Y chromosome. The full assembly and annotation of all three sex chromosomes allowed us to reconstruct their evolutionary history. Contrary to other neo-Y chromosomes, the fusion to X2 is quite ancient, estimated at 48 Ma. Despite its old age and being even older in the X1 homologous region which carries a huge inversion that occurred as early as 55-48 Ma, genetic degeneration of the neo-Y appears to be only moderate. Transcriptomic analysis showed that sex chromosomes harbor 87 genes, which may serve important functions in the testis. The accumulation of such male-beneficial genes, a large inversion on the X1 homologous region and fusion to X2 appear to be the main drivers of neo-Y evolution in the spotted knifejaw. The availability of high-quality assemblies of the neo-Y and both X chromosomes make this fish an ideal model for a better understanding of the variability of sex determination mechanisms and of sex chromosome evolution.

Keywords: evolution; genome; neo-Y; spotted knifejaw.

Fig. 1.

The male and female genome assembly of the spotted knifejaw. (a) Synteny relationship of male (left side, blue) and female (right side, pink) chromosomes. Lines linking two chromosomes indicate the location of homologs, with gray lines connecting autosomes and multicolored lines representing the relationship between sex chromosomes of male and female (red for X1, yellow for X2, blue for gametologs of X1 and neo-Y, green for gametologs of X2 and neo-Y). (b) One-to-two synteny relationships of the two arms of neo-Y with X1/X2. MchrY designates neo-Y (light blue), whereas FchrX1 and FchrX2 are the X chromosomes (pink). Synteny relationships of the inversion region are shown in purple and brown, whereas those of the PARs are in light gray, the centromere region is in dark gray, and the other regions are in blue. (c) Repetitive sequence analysis. The upper depicts MchrY (Y), the lower depicts FchrX1 (X1) and FchrX2 (X2). Repetitive sequence types are indicated on the right. Note that the enrichment of LINE and LTR at the fusion point on neo-Y and regions on the corresponding centromeric regions of X1 and X2.

Fig. 2.

Genome-wide distribution of SNPs from 73 male and 124 female individuals. (a) Principal component analysis of 197 individuals using SNPs. (b) Phylogenetic tree showing relationships of male (blue) and female (orange) SNPs. (c) Average sequencing depth ratio between females and males. The read depth distribution in both female and male was similar for all autosomes, whereas it was decreased for most of X1 and the proximal region of X2. (d) Genome-wide scan of fixation index (F_ST) matching the result from the read depth distribution.

Fig. 3.

Divergence times along the neo-Y in a sliding window of 100 kb. SA: section A, SB: section B, SC: section C, SD: section D, SE: section E. Yellow bar: fusion region. SA, SB, and SC correspond to the inversion region. The region to the left of the yellow bar shows divergence times between X1 and Y, whereas the region to the right shows divergence times between X2 and Y. The synteny relationships between neo-Y and Xs (X1HDR and X2HDR) are shown in the upper part as described in the legend of figure 1. Note: The mutation rate (8.18 × 10⁻¹⁰ per site per year) of the spotted knifejaw was estimated through the comparative genomics analysis using ten other fish species. The genetic distance was calculated using collinearity blocks between the X1/X2 and the neo-Y within a 100 kb sliding window. The divergence time of each window between the X1/X2 and the neo-Y was calculated as follows: T = D/2μ.

Fig. 4.

Model for the evolution of the Y chromosome in spotted knifejaw.

Fig. 5

DEGs specifically expressed in male gonads based on the transcriptomic analysis. Fifty-four genes with gametologs on X chromosomes and the Y chromosome are shown. Forty-nine genes are in the inversion region (∼23 Mb) of the Y chromosome in X1HDR, whereas five are in the Y chromosome in X2HDR (∼17 Mb). The color bar shows the TPM values from 1 to 64. Red lines linking two chromosomes indicate the location of gametologs of the DEGs specifically expressed in the males.