Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula).

BackgroundAcipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, high chromosome numbers, presence of numerous microchromosomes and propensity to interspecific hybridization. The presumed palaeotetraploidy of the American paddlefish was recently validated by molecular phylogeny and Hox genes analyses. A whole genome duplication in the paddlefish lineage was estimated at approximately 42 Mya and was found to be independent from several genome duplications evidenced in its sister lineage, i.e. sturgeons. We tested the ploidy status of available chromosomal markers after the expected rediploidization. Further we tested, whether paralogs of Hox gene clusters originated from this paddlefish specific genome duplication are cytogenetically distinguishable.ResultsWe found that both paralogs HoxA alpha and beta were distinguishable without any overlapping of the hybridization signal - each on one pair of large metacentric chromosomes. Of the HoxD, only the beta paralog was unequivocally identified, whereas the alpha paralog did not work and yielded only an inconclusive diffuse signal. Chromosomal markers on three diverse ploidy levels reflecting different stages of rediploidization were identified: quadruplets retaining their ancestral tetraploid condition, semi-quadruplets still reflecting the ancestral tetraploidy with clear signs of advanced rediploidization, doublets were diploidized with ancestral tetraploidy already blurred. Also some of the available microsatellite data exhibited diploid allelic band patterns at their loci whereas another locus showed more than two alleles.ConclusionsOur exhaustive staining of paddlefish chromosomes combined with cytogenetic mapping of ribosomal genes and Hox paralogs and with microsatellite data, brings a closer look at results of the process of rediploidization in the course of paddlefish genome evolution. We show a partial rediploidization represented by a complex mosaic structure comparable with segmental paleotetraploidy revealed in sturgeons (Acipenseridae). Sturgeons and paddlefishes with their high propensity for whole genome duplication thus offer suitable animal model systems to further explore evolutionary processes that were shaping the early evolution of all vertebrates

The second highest chromosome count among vertebrates is observed in cultured sturgeon and is associated with genome plasticity

Additional file 1: Table S1. Genotyping results with highlighted private dam and sire microsatellite alleles observed at all analysed loci for parental individuals, and for pentaploid (5n) and heptaploid (7n) full siblings

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.</p

Human-aided dispersal has altered but not erased the phylogeography of the tench

Human-aided dispersal can result in phylogeographic patterns that do not reflect natural historical processes, particularly in species prone to intentional translocations by humans. Here, we use a multiple-gene sequencing approach to assess the effects of human-aided dispersal on phylogeography of the tench Tinca tinca, a widespread Eurasian freshwater fish with a long history in aquaculture. Spatial genetic analysis applied to sequence data from four unlinked loci and 67 geographic localities (38–382 gene copies per locus) defined two groups of populations that were little structured geographically but were significantly differentiated from each other, and it identified locations of major genetic breaks, which were concordant across genes and were driven by distributions of two phylogroups. This pattern most reasonably reflects isolation in two major glacial refugia and subsequent range expansions, with the Eastern and Western phylogroups remaining largely allopatric throughout the tench range. However, this phylogeographic variation was also present in all 17 cultured breeds studied, and some populations at the western edge of the native range contained the Eastern phylogroup. Thus, natural processes have played an important role in structuring tench populations, but human-aided dispersal has also contributed significantly, with the admixed genetic composition of cultured breeds most likely contributing to the introgression

Fish sperm motility assessment as a tool for aquaculture research, a historical approach

[EN] Fish sperm motility is nowadays considered the best biomarker for the quality of fish spermatozoa, and sperm motion parameters from more than 300 fish species have been reported in more than 1500 scientific articles covering a wide range of topics, from molecular biology to ecology. The most studied topics have been (i) the sperm storage (involving both the use of chilled¿storage protocols for short¿term periods and sperm cryopreservation techniques for long¿term storage), (ii) the sperm physiology (fathom in the spermatozoa activation process and the whole propulsion machinery of the sperm cells) and (iii) the broodstock management (covering aspects such as rearing conditions, dietary requirements or hormonal induction treatments). In addition, other aquaculture and ecological topics, such as (iv) the knowledge of the breeding cycle of the species, (v) the phenomenon of the sperm competition and (vi) ecotoxicological studies for the evaluation of aquatic environments, have also been approached from the evaluation of sperm motion performance. Therefore, fish sperm motility assessment can serve as a potential tool for aquaculture and ecological purposes, covering key topics of fundamental and applied research. This review gives an overview of the major research areas in which fish sperm motility has been applied successfully.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 642893 (IMPRESS). VG has a postdoc grant from the UPV (PAID-10-16).Gallego Albiach, V.; Asturiano Nemesio, JF. (2018). Fish sperm motility assessment as a tool for aquaculture research, a historical approach. Reviews in Aquaculture (Online). 1-28. https://doi.org/10.1111/raq.12253S12

NATO-Russia Relationship after the Annexing of Crimea from Nuclear Weapons Perspective

The aim of this work is to determine the influence of nuclear weapons possession in 1) Russia's foreign policy in the Ukraine crisis, 2) relations between NATO and Russia. For this purpose the work monitors the development of NATO - Russia relations from the Budapest memorandum until present. The work also creates typology of russian signalling activities based on the theoretical basis of the nuclear deterrence conceptions and especially on the models of crisis signalling, which is closely linked to these conceptions. After monitoring these activities the work concludes that Russia is indeed using threats of nuclear weapons employment in the framework of it's attitude towards Ukraine crisis and also the intensity of signalling shows similar development as the relations with NATO