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Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications.

Symonová R, Majtánová Z, Sember A, Staaks GB, Bohlen J, Freyhof J, Rábová M, Ráb P - BMC Evol. Biol. (2013)

Bottom Line: Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments.We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis.We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic. radka.symonova@natur.cuni.cz

ABSTRACT

Background: Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution.

Results: Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8-10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species.

Conclusion: We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation. Such causal interplay between genome differentiation, retrotransposons (re)activation and environmental conditions may become a topic to be explored in a broader genomic context in future evolutionary studies.

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Metaphase plates and karyograms of C. albula and C. fontanae showing Chromomycin A3/DAPI staining, FISH and CGH experiments. Chromomycin A3 (CMA3) fluorescent staining (green) and DAPI (blue) staining in C. albula (a) and C. fontanae (b). FISH with the 28S rDNA (300 bp probe) (red), DAPI counterstaining (blue) in C. albula (c). FISH with the 28S rDNA (800 bp probe) (red), DAPI counterstaining (blue) in C. fontanae (d). A set of reciprocal comparative genomic hybridization (CGH) experiments to C. albula chromosomes (e) and C. fontanae chromosomes (f). In both (e, f), the C. albula genomic DNA was labelled in red and the C. fontanae genomic DNA in green. Bar = 5 μm.
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Figure 3: Metaphase plates and karyograms of C. albula and C. fontanae showing Chromomycin A3/DAPI staining, FISH and CGH experiments. Chromomycin A3 (CMA3) fluorescent staining (green) and DAPI (blue) staining in C. albula (a) and C. fontanae (b). FISH with the 28S rDNA (300 bp probe) (red), DAPI counterstaining (blue) in C. albula (c). FISH with the 28S rDNA (800 bp probe) (red), DAPI counterstaining (blue) in C. fontanae (d). A set of reciprocal comparative genomic hybridization (CGH) experiments to C. albula chromosomes (e) and C. fontanae chromosomes (f). In both (e, f), the C. albula genomic DNA was labelled in red and the C. fontanae genomic DNA in green. Bar = 5 μm.

Mentions: Karyotypes of both examined ciscoes were very similar (2n = 80 in both species) and both belong to the karyotype category A sensu[13]. They both had 8 pairs of meta- (m) to submetacentric (sm) and 32 pairs of acrocentric (a) chromosomes (both sexes in C. fontanae, only males in C. albula were available), The NF was 96 in both species (Figure 2a-d). The sequential Chromomycin A3 (CMA3, particularly specific for CG rich regions) and DAPI (specific for AT rich regions) stainings revealed in both species a varying number of 6–8 sites with CMA3+/DAPI- signals. The signals occurred at telomeric regions of 3–4 metacentric chromosomes and at pericentromeric regions of 3–4 acrocentric/submetacentric chromosomes (Figure 3a, b). In some nuclei, several other weakly CMA3+ regions not corresponding to DAPI- signals mostly with pericentromeric locations were observed (Figure 3a). This variability occurs on the inter-individual as well as on the intra-individual level.


Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications.

Symonová R, Majtánová Z, Sember A, Staaks GB, Bohlen J, Freyhof J, Rábová M, Ráb P - BMC Evol. Biol. (2013)

Metaphase plates and karyograms of C. albula and C. fontanae showing Chromomycin A3/DAPI staining, FISH and CGH experiments. Chromomycin A3 (CMA3) fluorescent staining (green) and DAPI (blue) staining in C. albula (a) and C. fontanae (b). FISH with the 28S rDNA (300 bp probe) (red), DAPI counterstaining (blue) in C. albula (c). FISH with the 28S rDNA (800 bp probe) (red), DAPI counterstaining (blue) in C. fontanae (d). A set of reciprocal comparative genomic hybridization (CGH) experiments to C. albula chromosomes (e) and C. fontanae chromosomes (f). In both (e, f), the C. albula genomic DNA was labelled in red and the C. fontanae genomic DNA in green. Bar = 5 μm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585787&req=5

Figure 3: Metaphase plates and karyograms of C. albula and C. fontanae showing Chromomycin A3/DAPI staining, FISH and CGH experiments. Chromomycin A3 (CMA3) fluorescent staining (green) and DAPI (blue) staining in C. albula (a) and C. fontanae (b). FISH with the 28S rDNA (300 bp probe) (red), DAPI counterstaining (blue) in C. albula (c). FISH with the 28S rDNA (800 bp probe) (red), DAPI counterstaining (blue) in C. fontanae (d). A set of reciprocal comparative genomic hybridization (CGH) experiments to C. albula chromosomes (e) and C. fontanae chromosomes (f). In both (e, f), the C. albula genomic DNA was labelled in red and the C. fontanae genomic DNA in green. Bar = 5 μm.
Mentions: Karyotypes of both examined ciscoes were very similar (2n = 80 in both species) and both belong to the karyotype category A sensu[13]. They both had 8 pairs of meta- (m) to submetacentric (sm) and 32 pairs of acrocentric (a) chromosomes (both sexes in C. fontanae, only males in C. albula were available), The NF was 96 in both species (Figure 2a-d). The sequential Chromomycin A3 (CMA3, particularly specific for CG rich regions) and DAPI (specific for AT rich regions) stainings revealed in both species a varying number of 6–8 sites with CMA3+/DAPI- signals. The signals occurred at telomeric regions of 3–4 metacentric chromosomes and at pericentromeric regions of 3–4 acrocentric/submetacentric chromosomes (Figure 3a, b). In some nuclei, several other weakly CMA3+ regions not corresponding to DAPI- signals mostly with pericentromeric locations were observed (Figure 3a). This variability occurs on the inter-individual as well as on the intra-individual level.

Bottom Line: Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments.We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis.We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic. radka.symonova@natur.cuni.cz

ABSTRACT

Background: Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution.

Results: Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8-10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species.

Conclusion: We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation. Such causal interplay between genome differentiation, retrotransposons (re)activation and environmental conditions may become a topic to be explored in a broader genomic context in future evolutionary studies.

Show MeSH
Related in: MedlinePlus