Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

Romanenko, Svetlana A.; Biltueva, Larisa S.; Serdyukova, Natalia A.; Kulemzina, Anastasia I.; Beklemisheva, Violetta R.; Gladkikh, Olga L.; Lemskaya, Natalya A.; Интересова, Е. А.; Korentovich, Marina A.; Vorobieva, Nadezhda V.; Graphodatsky, Alexander S.; Trifonov, Vladimir A.

doi:10.1186/s13039-015-0194-8

Cited by 51 publications

(80 citation statements)

References 53 publications

(69 reference statements)

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“…So far, no sex-specific heteromorphic chromosomes could be revealed in sterlet or in other sturgeons Romanenko et al, 2015]. Early sex identification is important for commercially valuable sturgeon species, but the type of sex determination in sturgeons remains unknown.…”

confidence: 99%

“…The need for standardization of the sterlet karyotype is urgent and might represent a starting point for chromosomal studies in the whole family because of the basal karyotype status. In our previous study, we presented GTG-and CBG-banded sterlet karyotypes with homologous chromosomes arranged according to their size [Romanenko et al, 2015] which may serve as a basis for molecular marker mapping. Distinction between individual chromosome pairs could possibly be achieved by studying the pattern of repeat sequence distribution [Wang et al, 2015].…”

confidence: 99%

“…Current evolution of paleopolyploid sturgeons includes functional diploidization and genome reduction occurring at different rates in various parts of the genome [Ludwig et al, 2001;Crow et al, 2012]. Extended blocks of the sterlet genome exist in both tetraploid and diploid states, which can be partly degenerated and subjected to translocations [Romanenko et al, 2015;Trifonov et al, 2016].…”

confidence: 99%

“…To date, only few studies addressed the characterization of repetitive sequences in sturgeon genomes, and they were mostly focused on common types of repeats such as telomere and ribosomal DNA [Fontana et al, 1998;Romanenko et al, 2015]. Clear differences in the distribution of repetitive elements between small and large chromosomes in sterlet were revealed by physical mapping of the C 0 t30 DNA fraction [Romanenko et al, 2015] and by comparative genomic hybridization (CGH) in sturgeon hybrids [Symonová et al, 2013]. A high level of sequence conservation within the Hin dIII [de la and Pst I [Robles et al, 2004] families (ancient satellite DNAs which are preserved in sturgeons for more than 100 million years) affirms slow molecular evolution rates of the repetitive genome fraction [Krieger and Fuerst, 2002].…”

confidence: 99%

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Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

Biltueva

Prokopov

Makunin

et al. 2017

Cytogenet Genome Res

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Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.

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confidence: 99%

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Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

Biltueva

Prokopov

Makunin

et al. 2017

Cytogenet Genome Res

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Hybridization and Polyploidization in Sturgeon

Havelka

Arai

2018

Sex Control in Aquaculture

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

et al. 2016

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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.

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Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

Cited by 51 publications

References 53 publications

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet<b> </b>(<b><i>Acipenser ruthenus</i></b>)

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet<b> </b>(<b><i>Acipenser ruthenus</i></b>)

Hybridization and Polyploidization in Sturgeon

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

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