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On the Origin and Evolution of the Extant System of B Chromosomes in Oryzomyini Radiation (Rodentia, Sigmodontinae).

Ventura K, O'Brien PC, do Nascimento Moreira C, Yonenaga-Yassuda Y, Ferguson-Smith MA - PLoS ONE (2015)

Bottom Line: The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes.The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys flavescens and Sooretamys angouya lacking OSHR in Bs.The species-specific pattern of Bs is probably a consequence of their independent evolutionary origin.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil; Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom; Instituto de Recursos Naturais - Universidade Federal de Itajubá, Itajubá, Minas Gerais, Brazil.

ABSTRACT
Heterogeneous supernumerary chromosomes (Bs) are recognized in the oryzomyines Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens and Sooretamys angouya, representing about 10% of all known B-containing rodent species. They provide an outstanding model for understanding the origin, evolution and diversity of Bs in a phylogenetic context. Therefore, whole chromosome-specific probes were generated from flow-sorted Holochilus brasiliensis (HBR) autosomes 11 and 25+26 and chromosomes X, Y and Bs. Hybridizations were performed on male metaphases of 15 Oryzomyini species of which 3 are B-containing species. The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes. The OSHR is also present on Bs of Holochilus brasiliensis, Nectomys rattus and N. squamipes but not on Bs of O. flavescens and S. angouya. Two distinct additional OSHR/autosome associations are observed on S. angouya. The three species that are OSHR negative belong to an outgroup. Molecular dating suggests that the OSHR originated between 7.8 and 3 Mya on ancestral sex chromosomes. A tentative explanation for the OSHR-positive nature of B regions in three species could be that transposable elements (TEs) from this specific sex chromosome region may have invaded existing B chromosomes. The presence of the OSHR on entire Xp and Yp adjacent to interstitial telomeric sequences at pericentromeric positions, as observed in Drymoreomys albimaculatus, show a similar organization as on B chromosomes in Nectomys squamipes. The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys flavescens and Sooretamys angouya lacking OSHR in Bs. The species-specific pattern of Bs is probably a consequence of their independent evolutionary origin.

No MeSH data available.


Karyotype and characterization of HBR probes.(a) GTG-banded karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). Black square with B1 and B2 after telomeric FISH. Inset, supernumeraries B1 and B2, and sex chromosomes in RBG and CBG-banding pattern. (b) Flow karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). The peaks containing the single HBR B1, B2, X, Y and 11 and the two chromosomes HBR 25, 26 are indicated in bold.
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pone.0136663.g001: Karyotype and characterization of HBR probes.(a) GTG-banded karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). Black square with B1 and B2 after telomeric FISH. Inset, supernumeraries B1 and B2, and sex chromosomes in RBG and CBG-banding pattern. (b) Flow karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). The peaks containing the single HBR B1, B2, X, Y and 11 and the two chromosomes HBR 25, 26 are indicated in bold.

Mentions: The whole chromosome-specific painting probes of Holochilus brasiliensis (HBR) HBR X, HBR Y, HBR supernumeraries (B1 and B2) and the two autosomal probes (HBR 11 and HBR 25, 26) were generated from flow-sorted chromosomes at the Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, UK. The primary fibroblast cell lines came from one male Holochilus brasiliensis with 2n = 56+2Bs (Fig 1A and 1B). The chromosomes of HBR were arranged by size according to their position in the flow karyotype. On the hybridized metaphases, the HBR chromosomes were identified by 4′,6- diamidino-2-phenylindole (DAPI) differential staining. The chromosome-specific paints were made by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) on flow-sorted chromosomes [37, 38]. Briefly, the chromosomes were stained with Hoechst 33258 (2 μg/ml) and Chromomycin A3 (40 μg/ml) in the presence of magnesium sulfate (2.5 mmol/l) for 2 h. Sodium sulfite (25 mmol/l) and sodium citrate (10 mmol/l) were added 15 min prior to flow sorting. Chromosome sorting was performed using a dual-laser cell sorter (MoFlo; Beckman Coulter). Approximately 400 chromosomes were sorted from each peak in the flow karyotypes directly into PCR tubes containing 30 μl of distilled water. Each sample was amplified by DOP-PCR using the primer 6MW [37]. Primary PCR products were labeled using cyanine 3 (Cy3)-dUTP (GE Healthcare Lifesciences) or fluorescein isothiocyanate (FITC)-12-dUTP (Roche)–final concentration 0,1mM—by taking 1 μl of product to a second DOP-PCR using the same primer.


On the Origin and Evolution of the Extant System of B Chromosomes in Oryzomyini Radiation (Rodentia, Sigmodontinae).

Ventura K, O'Brien PC, do Nascimento Moreira C, Yonenaga-Yassuda Y, Ferguson-Smith MA - PLoS ONE (2015)

Karyotype and characterization of HBR probes.(a) GTG-banded karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). Black square with B1 and B2 after telomeric FISH. Inset, supernumeraries B1 and B2, and sex chromosomes in RBG and CBG-banding pattern. (b) Flow karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). The peaks containing the single HBR B1, B2, X, Y and 11 and the two chromosomes HBR 25, 26 are indicated in bold.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549248&req=5

pone.0136663.g001: Karyotype and characterization of HBR probes.(a) GTG-banded karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). Black square with B1 and B2 after telomeric FISH. Inset, supernumeraries B1 and B2, and sex chromosomes in RBG and CBG-banding pattern. (b) Flow karyotype of a male Holochilus brasiliensis (2n = 56+2Bs). The peaks containing the single HBR B1, B2, X, Y and 11 and the two chromosomes HBR 25, 26 are indicated in bold.
Mentions: The whole chromosome-specific painting probes of Holochilus brasiliensis (HBR) HBR X, HBR Y, HBR supernumeraries (B1 and B2) and the two autosomal probes (HBR 11 and HBR 25, 26) were generated from flow-sorted chromosomes at the Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, UK. The primary fibroblast cell lines came from one male Holochilus brasiliensis with 2n = 56+2Bs (Fig 1A and 1B). The chromosomes of HBR were arranged by size according to their position in the flow karyotype. On the hybridized metaphases, the HBR chromosomes were identified by 4′,6- diamidino-2-phenylindole (DAPI) differential staining. The chromosome-specific paints were made by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) on flow-sorted chromosomes [37, 38]. Briefly, the chromosomes were stained with Hoechst 33258 (2 μg/ml) and Chromomycin A3 (40 μg/ml) in the presence of magnesium sulfate (2.5 mmol/l) for 2 h. Sodium sulfite (25 mmol/l) and sodium citrate (10 mmol/l) were added 15 min prior to flow sorting. Chromosome sorting was performed using a dual-laser cell sorter (MoFlo; Beckman Coulter). Approximately 400 chromosomes were sorted from each peak in the flow karyotypes directly into PCR tubes containing 30 μl of distilled water. Each sample was amplified by DOP-PCR using the primer 6MW [37]. Primary PCR products were labeled using cyanine 3 (Cy3)-dUTP (GE Healthcare Lifesciences) or fluorescein isothiocyanate (FITC)-12-dUTP (Roche)–final concentration 0,1mM—by taking 1 μl of product to a second DOP-PCR using the same primer.

Bottom Line: The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes.The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys flavescens and Sooretamys angouya lacking OSHR in Bs.The species-specific pattern of Bs is probably a consequence of their independent evolutionary origin.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil; Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom; Instituto de Recursos Naturais - Universidade Federal de Itajubá, Itajubá, Minas Gerais, Brazil.

ABSTRACT
Heterogeneous supernumerary chromosomes (Bs) are recognized in the oryzomyines Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens and Sooretamys angouya, representing about 10% of all known B-containing rodent species. They provide an outstanding model for understanding the origin, evolution and diversity of Bs in a phylogenetic context. Therefore, whole chromosome-specific probes were generated from flow-sorted Holochilus brasiliensis (HBR) autosomes 11 and 25+26 and chromosomes X, Y and Bs. Hybridizations were performed on male metaphases of 15 Oryzomyini species of which 3 are B-containing species. The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes. The OSHR is also present on Bs of Holochilus brasiliensis, Nectomys rattus and N. squamipes but not on Bs of O. flavescens and S. angouya. Two distinct additional OSHR/autosome associations are observed on S. angouya. The three species that are OSHR negative belong to an outgroup. Molecular dating suggests that the OSHR originated between 7.8 and 3 Mya on ancestral sex chromosomes. A tentative explanation for the OSHR-positive nature of B regions in three species could be that transposable elements (TEs) from this specific sex chromosome region may have invaded existing B chromosomes. The presence of the OSHR on entire Xp and Yp adjacent to interstitial telomeric sequences at pericentromeric positions, as observed in Drymoreomys albimaculatus, show a similar organization as on B chromosomes in Nectomys squamipes. The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys flavescens and Sooretamys angouya lacking OSHR in Bs. The species-specific pattern of Bs is probably a consequence of their independent evolutionary origin.

No MeSH data available.