Insertion Hot Spots of DIRS1 Retrotransposon and Chromosomal Diversifications among the Antarctic Teleosts Nototheniidae

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.

Single Copies of the 5S rRNA Inserted into 45S rDNA Intergenic Spacers in the Genomes of Nototheniidae (Perciformes, Actinopterygii)

In the vast majority of Animalia genomes, the 5S rRNA gene repeats are located on chromosomes outside of the 45S rDNA arrays of the nucleolar organiser (NOR). We analysed the genomic databases available and found that a 5S rDNA sequence is inserted into the intergenic spacer (IGS) between the 45S rDNA repeats in ten species of the family Nototheniidae (Perciformes, Actinopterigii). We call this sequence the NOR-5S rRNA gene. Along with Testudines and Crocodilia, this is the second case of a close association between four rRNA genes within one repetitive unit in deuterostomes. In both cases, NOR-5S is oriented opposite the 45S rDNA. None of the three nucleotide substitutions compared to the canonical 5S rRNA gene influenced the 5S rRNA secondary structure. In transcriptomes of the Patagonian toothfish, we only found NOR-5S rRNA reads in ovaries and early embryos, but not in testis or somatic tissues of adults. Thus, we consider the NOR-5S gene to be a maternal-type 5S rRNA template. The colocalization of the 5S and 45S ribosomal genes appears to be essential for the equimolar production of all four rRNAs in the species that show rDNA amplification during oogenesis. Most likely, the integration of 5S and NOR rRNA genes occurred prior to Nototheniidae lineage diversification.

Pathways to polar adaptation in fishes revealed by long-read sequencing

Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.

Transposable Element Tissue-Specific Response to Temperature Stress in the Stenothermal Fish Puntius tetrazona

Ray-finned fish represent a very interesting group of vertebrates comprising a variety of organisms living in different aquatic environments worldwide. In the case of stenothermal fish, thermal fluctuations are poorly tolerated, thus ambient temperature represents a critical factor. In this paper, we considered the tiger barb Puntius tetrazona, a freshwater fish belonging to the family Cyprinidae, living at 21-28 °C. We analyzed the available RNA-Seq data obtained from specimens exposed at 27 °C and 13 °C to investigate the transcriptional activity of transposable elements (TEs) and genes encoding for proteins involved in their silencing in the brain, gill, and liver. TEs are one of the tools generating genetic variability that underlies biological evolution, useful for organisms to adapt to environmental changes. Our findings highlighted a different response of TEs in the three analyzed tissues. While in the brain and gill, no variation in TE transcriptional activity was observed, a remarkable increase at 13 °C was recorded in the liver. Moreover, the transcriptional analysis of genes encoding proteins involved in TE silencing such as heterochromatin formation, the NuRD complex, and the RISC complex (e.g., AGO and GW182 proteins) highlighted their activity in the hepatic tissue. Overall, our findings suggested that this tissue is a target organ for this kind of stress, since TE activation might regulate the expression of stress-induced genes, leading to a better response of the organism to temperature changes. Therefore, this view corroborates once again the idea of a potential role of TEs in organism rapid adaptation, hence representing a promising molecular tool for species resilience.

Physical Mapping of Repeated Sequences on Fish Chromosomes by Fluorescence In Situ Hybridization (FISH)

The opportunity to map genes and noncoding DNA sequences on the chromosomes by fluorescence in situ hybridization (FISH) has greatly enhanced the potential for fish karyotyping and comparative cytogenetics. The use of FISH allowed for significant advances in our understanding of the fish genome architecture, especially when applied to the study of the repetitive component of the genome, that is generally underestimated in the bioinformatic assembly. Here we provide a step-by-step protocol for FISH of repeated sequences onto chromosomes of fish species.

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.

Mobile Elements in Ray-Finned Fish Genomes

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

Multiple independent chromosomal fusions accompanied the radiation of the Antarctic teleost genus Trematomus (Notothenioidei:Nototheniidae)

Background

Chromosomal rearrangements are thought to be an important driving force underlying lineage diversification, but their link to speciation continues to be debated. Antarctic teleost fish of the family Nototheniidae (Notothenioidei) diversified in a changing environmental context, which led to ecological, morphological, and genetic differentiation among populations. In addition, extensive chromosomal repatterning accompanied species divergence in several clades. The most striking karyotypic changes involved the recent species radiation (about 10 My) of the genus Trematomus, with chromosomal pair numbers ranging between 29 and 12. These dramatic reductions in chromosome number resulted mostly from large-scale chromosome fusions. Multiple centric and/or tandem fusions have been hypothesized in at least seven of the twelve recognized Trematomus species. To reconstruct their evolutionary history, we employed comparative cytogenomics (BAC-FISH and chromosome painting) to reveal patterns of interspecific chromosomal orthologies across several notothenioid clades.

Results

We defined orthologous chromosomal segments of reference, termed Structural Units (SUs). SUs were identified in a total of 18 notothenioid species. We demonstrated for the first time that SUs were strongly conserved across every specimen examined, with chromosomal syntenies highlighting a paucity of intrachromosomal macro-rearrangements. Multiple independent fusions of these SUs were inferred in the Trematomus species, in contrast to the shared SU fusions in species of the sister lineage Notothenia.

Conclusions

The SU segments were defined units of chromosomal rearrangement in the entire family Nototheiidae, which diverged from the other notothenioid families 20 My ago. Some of the identified chromosomal syntenies within the SUs were even conserved in their closest relatives, the family Eleginopsidae. Comparing the timing of acquisition of the fusions in the closely related genera Notothenia and Trematomus of the nototheniid species family, we conclude that they exhibit distinct chromosomal evolutionary histories, which may be relevant to different speciation scenarios.

Cytogenetic characterization of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902) through analysis of mitotic chromosomes from early larvae

This paper describes the cytogenetic features of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902), a keystone species of the Antarctic coastal marine ecosystem. Conventional cytogenetic analyses and physical mapping of repetitive DNA sequences were performed on metaphase plates obtained through direct chromosome preparation from P. antarctica early larvae. The Antarctic silverfish have a diploid number (2n) = 48, and a karyotype made up of a majority of two-armed chromosomes (karyotype formula36m/sm + 10st + 2a, fundamental number = 94). Major ribosomal gene repeats were detected on three chromosome pairs (20, 21, and 23), in correspondence of dim DAPI stained regions. Long Interspersed Nuclear Elements (LINEs) were abundant and wide spread over all chromosomes. Overall, the cytogenetic data presented herein are consistent with a long independent cytogenetic and evolutionary history for the species. The large number of two-armed chromosomes, indicative of highly-rearranged karyotype, coupled with a diploid number of 48, a presumed primitive character for this fish group, and the spread of the major ribosomal genes on three chromosome pairs, make the Antarctic silverfish distinct from all other notothenioid species.