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

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

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

Diploid, triploid and tetraploid silver crucian carp Carassius auratus from the lower reach of Dyje River: the first results of reproductive characteristics and experimental hybridization

Diploid, triploid and tetraploid males of silver crucian carp, Carassius auratus, produced live motile spermatozoa, capable of fertilization. Flow cytometry for the relative DNA content in male gametes revealed spermatozoa of diploid males to be haploid, those of triploid males to be aneuploid and those of tetraploid male to be aneuploid and/or diploid. Concentration of spermatozoa and the percentage of live spermatozoa showed a tendency to drop with increasing ploidy level and this effect was significant for the tetraploid male compared to those of lower ploidy levels

Ploidy Levels and Fitness-Related Traits in Purebreds and Hybrids Originating from Sterlet (Acipenser ruthenus) and Unusual Ploidy Levels of Siberian Sturgeon (A. baerii)

The present study aimed to investigate and compare fitness-related traits and ploidy levels of purebreds and hybrids produced from sturgeon broodstock with both normal and abnormal ploidy levels. We used diploid Acipenser ruthenus and tetraploid A. baerii males and females to produce purebreds and reciprocal hybrids of normal ploidy levels. Likewise, we used diploid A. ruthenus and tetraploid A. baerii females mated to pentaploid and hexaploid A. baerii males to produce hybrids of abnormal ploidy levels. Fertilization of ova of A. ruthenus and A. baerii of normal ploidy with the sperm of pentaploid and hexaploid A. baerii produced fully viable progeny with ploidy levels that were intermediate between those of the parents as was also found in crosses of purebreds and reciprocal hybrids of normal ploidy levels. The A. ruthenus &times; pentaploid A. baerii and A. ruthenus &times; hexaploid A. baerii hybrids did not survive after 22 days post-hatch (dph). Mean body weight and cumulative survival were periodically checked at seven-time intervals. The recorded values of mean body weight were significantly higher in A. baerii &times; pentaploid A. baerii hybrids than other groups at three sampling points (160, 252 and 330 dph). In contrast, the highest cumulative survival was observed in A. baerii &times; A. ruthenus hybrids at all sampling points (14.47 &plusmn; 5.70 at 497 dph). Overall, most of the studied sturgeon hybrids displayed higher mean BW and cumulative survival compared to the purebreds. The utilization of sturgeon hybrids should be restricted to aquaculture purposes because they can pose a significant genetic threat to native populations through ecological interactions

Polyploid fish and shellfish: Production, biology and applications to aquaculture for performance improvement and genetic containment

32 pages, 8 figures, 6 tables.-- Printed version published Aug 16, 2009.This review originated following the presentations and subsequent discussions made at an international workshop on the "Genetics of domestication, breeding and enhancement of performance of fish and shellfish", organized within the EU-funded project "Genimpact" (RICA-CT-2005-022802. http://genimpact.imr.no), held in Viterbo, Italy, 12–17 June 2006.Polyploids can be defined as organisms with one or more additional chromosome sets with respect to the number most frequently found in nature for a given species. Triploids, organisms with three sets of homologous chromosomes, are found spontaneously in both wild and cultured populations and can be easily induced in many commercially relevant species of fish and shellfish. The major consequence of triploidy is gonadal sterility, which is of advantage in the aquaculture of molluscs since it can result in superior growth. In fish, the induction of triploidy is mainly used to avoid problems associated with sexual maturation such as lower growth rates, increased incidence of diseases and deterioration of the organoleptic properties. Triploidy can also be used to increase the viability of some hybrids, and is regarded as a potential method for the genetic containment of farmed shellfish and fish. This review focuses on some current issues related to the application of induced polyploidy in aquaculture, namely: 1) the artificial induction of polyploidy and the effectiveness of current triploidisation techniques, including the applicability of tetraploidy to generate auto- and allotriploids; 2) the performance capacity of triploids with respect to diploids; 3) the degree and permanence of gonadal sterility in triploids; and 4) the prospects for the potential future generalised use of triploids to avoid the genetic impact of escapees of farmed fish and shellfish on wild populations. Finally, directions for future research on triploids and their implementation are discussed.Studies in the laboratory of M.F. discussed here were supported in part by grants MSM6007665809 and GACR 523/08/0824. Research at the laboratory of F.P. is partially funded by the Consolider-Ingenio 2010 project "Aquagenomics".Peer reviewe

MOESM2 of The second highest chromosome count among vertebrates is observed in cultured sturgeon and is associated with genome plasticity

Additional file 2: Table S2. Species with the highest chromosome count in vertebrate families and their nuclear DNA content. Asterisks denote references to DNA content

Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish

Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process.publishe