Identification of the sex chromosome pair in chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha)

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.

Evolution of the sex-determining gene in the teleostean genus Oryzias

In the genetic sex determination of vertebrates, the gonadal sex depends on the combination of sex chromosomes that a zygote possesses. Despite the discovery of the sex-determining gene (SRY/Sry) in mammals in 1990s, the sex-determining gene in non-mammalian vertebrates remained an enigma for over a decade. In most mammals, the male-inducing master sex-determining gene is located on the Y chromosome and is therefore absent from XX females. A second sex-determining gene, Dmy, was described in the Oryzias latipes in 2002 and has a DNA-binding motif that is different from the motif in the mammalian sex-determining gene SRY or Sry. Dmy is also located on the Y chromosome and is therefore absent in XX females. Seven other sex-determining genes, including candidate genes, are now known in birds, a frog species, and 5 fish species. These findings over the past twenty years have increased our knowledge of sex-determining genes and sex chromosomes among vertebrates. Here, we review recent advances in our understanding of sex-determining genes and genetic sex determination systems in fish, especially those of the Oryzias species, which are described in detail. The facts suggest some patterns of how new sex-determining genes emerged and evolved. We believe that these facts are common not only in Oryzias but also in other fish species. This knowledge will help to elucidate the conserved mechanisms from which various sex-determining mechanisms have evolved.

Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescence in situ hybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

Whole chromosome painting reveals independent origin of sex chromosomes in closely related forms of a fish species

The wolf fish Hoplias malabaricus includes well differentiated sex systems (XY and X(1)X(2)Y in karyomorphs B and D, respectively), a nascent XY pair (karyomorph C) and not recognized sex chromosomes (karyomorph A). We performed the evolutionary analysis of these sex chromosomes, using two X chromosome-specific probes derived by microdissection from the XY and X(1)X(2)Y sex systems. A putative-sex pair in karyomorph A was identified, from which the differentiated XY system was evolved, as well as the clearly evolutionary relationship between the nascent XY system and the origin of the multiple X(1)X(2)Y chromosomes. The lack of recognizable signals on the sex chromosomes after the reciprocal cross-FISH experiments highlighted that they evolved independently from non-homologous autosomal pairs. It is noteworthy that these distinct pathways occur inside the same nominal species, thus exposing the high plasticity of sex chromosome evolution in lower vertebrates. Possible mechanisms underlying this sex determination liability are also discussed.

Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes

Background

The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X₁X₂Y sex systems in Hoplias malabaricus and Erythrinus erythrinus. At first, the occurrence of a same sex chromosome system within a family suggests that the sex chromosomes are correlated and originated from ancestral XY chromosomes that were either homomorphic or at an early stage of differentiation. To identify the origin and evolution of these X₁X₂Y sex chromosomes, we performed reciprocal cross-species FISH experiments with two sex-chromosome-specific probes designed from microdissected X₁ and Y chromosomes of H. malabaricus and E. erythrinus, respectively.

Results

Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X₁X₂Y sex systems that are currently present.

Conclusions

Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.

Linkage analysis reveals the independent origin of Poeciliid sex chromosomes and a case of atypical sex inheritance in the guppy (Poecilia reticulata)

Among different teleost fish species, diverse sex-determining mechanisms exist, including environmental and genetic sex determination, yet chromosomal sex determination with male heterogamety (XY) prevails. Different pairs of autosomes have evolved as sex chromosomes among species in the same genus without evidence for a master sex-determining locus being identical. Models for evolution of Y chromosomes predict that male-advantageous genes become linked to a sex-determining locus and suppressed recombination ensures their co-inheritance. In the guppy, Poecilia reticulata, a set of genes responsible for adult male ornaments are linked to the sex-determining locus on the incipient Y chromosome. We have identified >60 sex-linked molecular markers to generate a detailed map for the sex linkage group of the guppy and compared it with the syntenic autosome 12 of medaka. We mapped the sex-determining locus to the distal end of the sex chromosome. We report a sex-biased distribution of recombination events in female and male meiosis on sex chromosomes. In one mapping cross, we observed sex ratio and male phenotype deviations and propose an atypical mode of genetic sex inheritance as its basis.

Different origins of ZZ/ZW sex chromosomes in closely related medaka fishes, Oryzias javanicus and O. hubbsi

Although the sex-determining gene DMY has been identified on the Y chromosome in the medaka, Oryzias latipes, this gene is absent in most Oryzias species. Recent comparative studies have demonstrated that, in the javanicus species group, Oryzias dancena and Oryzias minutillus have an XX/XY sex determination system, while Oryzias hubbsi has a ZZ/ZW system. Furthermore, sex chromosomes were not homologous in these species. Here, we investigated the sex determination mechanism in Oryzias javanicus, another species in the javanicus group. Linkage analysis of isolated sex-linked DNA markers showed that this species has a ZZ/ZW sex determination system. The sex-linkage map showed a conserved synteny to the linkage group 16 of O. latipes, suggesting that the sex chromosomes in O. javanicus are not homologous to those in any other Oryzias species. Fluorescence in-situ hybridization analysis confirmed that the ZW sex chromosomes of O. javanicus and O. hubbsi are not homologous, and showed that O. javanicus has the morphologically heteromorphic sex chromosomes, in which the W chromosome has 4,6-diamino-2-phenylindole-positive heterochromatin at the centromere. These findings suggest the repeated evolution of new sex chromosomes from autosomes in Oryzias, probably through the emergence of new sex-determining genes.