Genomic Access to the Diversity of Fishes

Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits

Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.

Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus

The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin

Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.

Expression of the sodium iodide symporter (NIS) in reproductive and neural tissues of teleost fish

Iodine, an essential component of thyroid hormones, can only be obtained through the diet. The sodium iodide symporter (NIS) transports iodide across mammalian intestinal and thyroid epithelia to deliver iodide for thyroid hormone production. Using reverse transcription-polymerase chain reaction (RT-PCR) we confirmed that mRNA for a homolog of mammalian NIS is expressed in comparable locations, both sub-pharyngeal thyroid tissue and intestine, in multiple teleost fish species, supporting a conserved mechanism for intestinal-thyroid iodine transport across vertebrates. To determine when in embryogenesis NIS expression is initiated we utilized in situ hybridization (ISH) during development of zebrafish (Danio rerio) embryos. This revealed expression of nis as early as 2 days post fertilization (dpf) along the dorsal surface of the yolk sac, suggesting a function to import iodine from yolk. To evaluate the potential for maternal deposition of iodine in yolk, RT-PCR and further in situ staining of ovarian tissue in gravid female zebrafish confirmed NIS mRNA presence in the ooplasm and granulosa layer of early stage follicles. This further suggests that maternally-deposited NIS mRNA may be available for early embryogenesis. Unexpectedly, ISH in embryos revealed robust nis expression in the central nervous system throughout days 2-5 days post fertilization, with adult whole brain ISH localizing expression in the hypothalamus, cerebellum, and optic tectum. RT-PCR on whole brain tissue from five species of adult fish representing three taxonomic orders likewise revealed robust CNS expression. These unexpected locations of nis expression suggest novel, as yet undescribed reproductive and neural functions of NIS in teleost species.