Evidence of hexaploid karyotype in shortnose sturgeon

Fontana, Francesco; Congiu, Leonardo; Mudrak, Vincent A. MudrakV.A.; Quattro, Joseph M.; Smith, Theodore I. J.; Ware, Kent WareK.; Doroshov, Serge I.

doi:10.1139/g07-112

Cited by 72 publications

(65 citation statements)

References 42 publications

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“…The apparently limited fraction of successfully annotated sequences with GO terms (16%) might be due to the very ancient separation (about 250 MYBP) of sturgeons from any other species for which a relevant genomic information is available. Additionally, following the sturgeon-specific Whole Genome Duplications [4] part of the redundant genetic information probably underwent a functional divergence that may have further decreased the fraction of successfully annotable ESTs. Beside the evolutionary interest of a database obtained from a member of the Chondrostean, certainly applied genetics studies on sturgeons will benefit from this resource.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

et al. 2013

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BackgroundSturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females.ResultsThe 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs.ConclusionsThis study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs.

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Section: Discussionmentioning

confidence: 99%

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

et al. 2013

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“…During this process, a partial retention of 4n features is observable, like chromosome numbers and their external morphology (e.g. [17]). Distinct signs of ongoing and to different extent advanced rediploidization can be found in other cytogenomic markers – e.g.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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Background: Acipenseriformes 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. Results: We 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. Conclusions: Our 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.

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“…Gene duplication and subsequent functional divergence is a fundamental process of adaptive evolution [16] and is particularly relevant in the Acipenseridae where the presence of evolutionary polyploidy ranging in a series from 4n-8n-12n times the ancestral haploid number [17] presents significant challenges for investigating the evolutionary processes shaping the nuclear genomes [4], [18], [19]. It is unclear whether these polyploid events resulted from complete genome duplications (autopolyploid), hybridization between species of different ploidy levels combined with genome doubling (allopolyploidy), or a combination of these processes [20].…”

Section: Introductionmentioning

confidence: 99%

“…These authors, however, could not determine the species' exact level of polysomy (hexaploid or dodecaploid). Contemporary cytogenetic techniques (including signals from fluorescent in situ hybridization) suggest A. brevirostrum is a hexaploid species [19]. While immensely complex, nuclear DNA-based approaches to A. brevirostrum conservation could identify significant levels of informative genetic variation because certain duplicated loci and repetitive DNA may lack functional constraints, thus allowing rapid accumulation of differentiation in DNA sequences [32].…”

Section: Introductionmentioning

confidence: 99%

A Nuclear DNA Perspective on Delineating Evolutionarily Significant Lineages in Polyploids: The Case of the Endangered Shortnose Sturgeon (Acipenser brevirostrum)

King

Henderson²,

Kynard³

et al. 2014

PLoS ONE

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The shortnose sturgeon, Acipenser brevirostrum, oft considered a phylogenetic relic, is listed as an “endangered species threatened with extinction” in the US and “Vulnerable” on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.

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Evidence of hexaploid karyotype in shortnose sturgeon

Cited by 72 publications

References 42 publications

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

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

A Nuclear DNA Perspective on Delineating Evolutionarily Significant Lineages in Polyploids: The Case of the Endangered Shortnose Sturgeon (Acipenser brevirostrum)

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