The Experts below are selected from a list of 3759 Experts worldwide ranked by ideXlab platform
Fengtang Yang - One of the best experts on this subject based on the ideXlab platform.
-
Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional Chromosome Painting.
BMC evolutionary biology, 2018Co-Authors: Anderson José Baia Gomes, Malcolm A. Ferguson-smith, Fengtang Yang, C.y. Nagamachi, Patricia Caroline Mary O’brien, Luis Reginaldo Ribeiro Rodrigues, Julio Cesar PieczarkaAbstract:The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use Chromosome Painting with whole Chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published Chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole Chromosome probes allows us to track some syntenic associations prior to the emergence of this family.
-
Chromosome Painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes
2018Co-Authors: Talita Fernanda Augusto Ribas, Fengtang Yang, C.y. Nagamachi, Alexandre Aleixo, Melquizedec Luiz Silva Pinheiro, Patricia Caroline Mary O´brien, Malcolm Andrew Ferguson-smith, Pablo Suarez, Julio Cesar PieczarkaAbstract:Glyphorynchus spirurus (GSP), also called the Wedge-billed Woodcreeper (Furnariidae) has an extensive distribution in the Americas, including the Atlantic coast of Brazil. Nevertheless, there is no information about its karyotype or genome organization. To contribute to the knowledge of chromosomal evolution in Passeriformes we analysed the karyotype of Glyphorynchus spirurus by classic and molecular cytogenetics methods. We show that Glyphorynchus spirurus has a 2n = 80 karyotype with a fundamental number (FN) of 84, similar to the avian putative ancestral karyotype (PAK). Glyphorynchus spirurus pair 1 was heteromorphic in the Tapajós population whereby the short arms varied in sizes, possibly due to a pericentric inversion, as described in other Furnariidae birds. FISH with the Histone H5 probe revealed a signal in the pericentromeric region of G. spirurus Chromosome 5 and rDNA 18S showed interstitial signal in GSP-1. Chromosome Painting with Gallus gallus (GGA) macroChromosomes 1–9 probes showed disruption of Chromosome syntenies of GGA-1, 2 and 4 by fission in Glyphorynchus spirurus. Our results confirm that the GGA1 centric fission is a synapomorphic character for the phylogenetic branch composed of Strigiformes, Passeriformes, Columbiformes and Falconiformes. On the other hand, the GGA-2 fission is reported here for the first time in Passeriformes. Chromosome Painting with BOE whole Chromosome probes confirmed these rearrangements in Glyphorynchus spirurus revealed by Gallus gallus 1–9 probes, in addition to enabling the establishment of genome-wide homology map.
-
Karyotypic Evolution in Malagasy Flying Foxes (Pteropodidae, Chiroptera) and Their Hipposiderid Relatives as Determined by Comparative Chromosome Painting.
Cytogenetic and genome research, 2016Co-Authors: Leigh R. Richards, Fengtang Yang, Ramugondo V. Rambau, Steven M. Goodman, Peter J. Taylor, Jennifer M. LambAbstract:Pteropodidae and Hipposideridae are 2 of the 9 chiropteran families that occur on Madagascar. Despite major advancements in the systematic study of the island's bat fauna, few karyotypic data exist for endemic species. We utilized G- and C-banding in combination with Chromosome Painting with Myotismyotis probes to establish a genome-wide homology among Malagasy species belonging to the families Pteropodidae (Pteropus rufus 2n = 38; Rousettus madagascariensis, 2n = 36), Hipposideridae (Hipposideros commersoni s.s., 2n = 52), and a single South African representative of the Rhinolophidae (Rhinolophus clivosus, 2n = 58). Painting probes of M. myotis detected 26, 28, 28, and 29 regions of homology in R. madagascariensis, P. rufus, H. commersoni s.s, and R. clivosus, respectively. Translocations, pericentric inversions, and heterochromatin additions were responsible for karyotypic differences amongst the Malagasy pteropodids. Comparative Chromosome Painting revealed a novel pericentric inversion on P. rufus Chromosome 4. Chromosomal characters suggest a close evolutionary relationship between Rousettus and Pteropus. H. commersoni s.s. shared several chromosomal characters with extralimital congeners but did not exhibit 2 chromosomal synapomorphies proposed for Hipposideridae. This study provides further insight into the ancestral karyotypes of pteropodid and hipposiderid bats and corroborates certain molecular phylogenetic hypotheses.
-
karyotypic evolution in family hipposideridae chiroptera mammalia revealed by comparative Chromosome Painting g and c banding
Zoological Research, 2010Co-Authors: Jinhuan Wang, Weiting Su, Yingxiang Wang, Fengtang YangAbstract:Comparing to its sister-family (Rhinolophidae), Hipposideridae was less studied by cytogenetic approaches. Only a few high-resolution G-banded karyotypes have been reported so far, and most of the conclusions on the karyotypic evolution in Hipposideridae were based on conventional Giemsa-staining. In this study, we applied comparative Chromosome Painting, a method of choice for genome-wide comparison at the molecular level, and G- and C-banding to establish comparative map between five hipposiderid species from China, using a whole set of Chromosome-specific Painting probes from one of them (Aselliscus stoliczkanus). G-band and C-band comparisons between homologous segments defined by Chromosome Painting revealed that Robertsonian translocations, paracentric inversions and heterochromatin addition could be the main mechanism of Chromosome evolution in Hipposideridae. Comparative analysis of the conserved chromosomal segments among five hipposiderid species and outgroup species suggests that bi-armed Chromosomes should be included into the ancestral karyotype of Hipposideridae, which was previously believed to be exclusively composed of acrocentric Chromosomes.
-
avian comparative genomics reciprocal Chromosome Painting between domestic chicken gallus gallus and the stone curlew burhinus oedicnemus charadriiformes an atypical species with low diploid number
Chromosome Research, 2009Co-Authors: Wenhui Nie, Malcolm A Fergusonsmith, V. Volobouev, Patricia C M Obrien, Nigel P Carter, Fengtang YangAbstract:The chicken is the most extensively studied species in birds and thus constitutes an ideal reference for comparative genomics in birds. Comparative cytogenetic studies indicate that the chicken has retained many Chromosome characters of the ancestral avian karyotype. The homology between chicken macroChromosomes (1–9 and Z) and their counterparts in more than 40 avian species of 10 different orders has been established by Chromosome Painting. However, the avian homologues of chicken microChromosomes remain to be defined. Moreover, no reciprocal Chromosome Painting in birds has been performed due to the lack of Chromosome-specific probes from other avian species. Here we have generated a set of Chromosome-specific paints using flow cytometry that cover the whole genome of the stone curlew (Burhinus oedicnemus, Charadriiformes), a species with one of the lowest diploid number so far reported in birds, as well as paints from more microChromosomes of the chicken. A genome-wide comparative map between the chicken and the stone curlew has been constructed for the first time based on reciprocal Chromosome Painting. The results indicate that extensive Chromosome fusions underlie the sharp decrease in the diploid number in the stone curlew. To a lesser extent, Chromosome fissions and inversions occurred also during the evolution of the stone curlew. It is anticipated that this complete set of Chromosome Painting probes from the first Neoaves species will become an invaluable tool for avian comparative cytogenetics.
Malcolm A Fergusonsmith - One of the best experts on this subject based on the ideXlab platform.
-
Chromosome Painting does not support a sex Chromosome turnover in lacerta agilis linnaeus 1758
Cytogenetic and Genome Research, 2020Co-Authors: Artem P. Lisachov, Malcolm A Fergusonsmith, Jorge C. Pereira, Massimo Giovannotti, Svetlana A Romanenko, Daria A Andreyushkova, P M Borodin, Vladimir A. TrifonovAbstract:Reptiles show a remarkable diversity of sex determination mechanisms and sex Chromosome systems, derived from different autosomal pairs. The origin of the ZW sex Chromosomes of Lacerta agilis, a widespread Eurasian lizard species, is a matter of discussion: is it a small macroChromosome from the 11-18 group common to all lacertids, or does this species have a unique ZW pair derived from the large Chromosome 5? Using independent molecular cytogenetic methods, we investigated the karyotype of L. agilis exigua from Siberia, Russia, to identify the sex Chromosomes. FISH with a flow-sorted Chromosome Painting probe derived from L. strigata and specific to Chromosomes 13, 14, and Z confirmed that the Z Chromosome of L. agilis is a small macroChromosome, the same as in L. strigata. FISH with the telomeric probe showed an extensive accumulation of the telomere-like repeat in the W Chromosome in agreement with previous studies, excluding the possibility that the lineages of L. agilis studied in different works could have different sex Chromosome systems due to a putative intra-species polymorphism. Our results reinforce the idea of the stability of the sex Chromosomes and lack of evidence for sex-Chromosome turnovers in known species of Lacertidae.
-
Chromosome Painting does not support a sex Chromosome turnover in lacerta agilis linnaeus 1758
bioRxiv, 2019Co-Authors: Artem P. Lisachov, Malcolm A Fergusonsmith, Jorge C. Pereira, Massimo Giovannotti, Svetlana A Romanenko, Daria A Andreyushkova, P M Borodin, Vladimir A. TrifonovAbstract:Reptiles show a remarkable diversity of sex determination mechanisms and sex Chromosome systems, derived from different autosomal pairs. The origin of the ZW sex Chromosomes of Lacerta agilis, a widespread Eurasian lizard species, is a matter of discussion: is it a small macroChromosome from the 11-18 group, common to all lacertids, or this species has unique ZW pair derived from the large Chromosome 5. Using independent molecular cytogenetic methods, we investigated the karyotype of L. agilis exigua from Siberia, Russia, to identify the sex Chromosomes. FISH with the flow-sorted Chromosome Painting probe, derived from L. strigata and specific to Chromosomes 13, 14, and Z, confirmed that the Z Chromosome of L. agilis is a small macroChromosome, the same as in L. strigata. FISH with the telomeric probe showed an extensive accumulation of the telomeric repeat on the W Chromosome in agreement with previous studies, excluding the possibility that the lineages of L. agilis studied in different works could have different sex Chromosome systems due to a putative intra-species polymorphism. Our results reinforce the idea of the stability of the sex Chromosomes and lack of evidence for sex-Chromosome turnovers in known species of Lacertidae.
-
Chromosome Painting in tyrant flycatchers confirms a set of inversions shared by oscines and suboscines aves passeriformes
Cytogenetic and Genome Research, 2018Co-Authors: Benilson Silva Rodrigues, Malcolm A Fergusonsmith, Rafael Kretschmer, Ricardo José Gunski, Analía Del Valle Garnero, Patricia C M Obrien, Edivaldo Herculano Corrêa OliveiraAbstract:Tyrannidae is the largest family of Passeriformes in the Neotropical region. However, despite an interesting chromosomal diversity, there are only few cytogenetic studies of this family, and most of these are based on conventional cytogenetics. Hence, we analyzed here the chromosomal diversity and karyotypical evolution of this group by Chromosome Painting in 3 different species - Pitangus sulphuratus , Serpophaga subcristata , and Satrapa icterophrys - and make comparisons with previous data. In addition to Chromosome Painting with Gallus gallus (GGA) and Leucopternis albicollis (LAL) probes, karyotypes were analyzed by conventional staining, C-banding, and FISH with 18S rDNA and telomeric probes. Although this family is characterized by extensive chromosomal variation, we found similar karyotypes and diploid numbers ranging from 2n = 80 in P. sulphuratus to 2n = 82 in S. subcristata and S. icterophrys . Constitutive heterochromatin was located centromerically in all 3 species. Clusters of 18S rDNA were present in 1 pair of microChromosomes, except in S. subcristata , where 2 pairs of microChromosomes were labeled. No interstitial telomeric sequences were detected. GGA and LAL whole-Chromosome probes revealed the occurrence of fissions and both paracentric and pericentric inversions commonly seen in other Passeriformes. In general terms, tyrants show the typical karyotype found in Passeriformes, suggesting that the observed rearrangements occurred before the division of the suborders Oscines and Suboscines.
-
extensive homology of chicken macroChromosomes in the karyotypes of trachemys scripta elegans and crocodylus niloticus revealed by Chromosome Painting despite long divergence times
Cytogenetic and Genome Research, 2012Co-Authors: Fumio Kasai, P C M Obrien, S Martin, Malcolm A FergusonsmithAbstract:We report extensive Chromosome homology revealed by Chromosome Painting between chicken ( Gallus gallus domesticus , GGA, 2n = 78) macroChromosomes (representing 70% of the chicken ge
-
Chromosome homologies of the highly rearranged karyotypes of four akodon species rodentia cricetidae resolved by reciprocal Chromosome Painting the evolution of the lowest diploid number in rodents
Chromosome Research, 2009Co-Authors: Karen Ventura, Patricia C M Obrien, Yatiyo Yonenagayassuda, Malcolm A FergusonsmithAbstract:Traditionally comparative cytogenetic studies are based mainly on banding patterns. Nevertheless, when dealing with species with highly rearranged genomes, as in Akodon species, or with other highly divergent species, cytogenetic comparisons of banding patterns prove inadequate. Hence, comparative Chromosome Painting has become the method of choice for genome comparisons at the cytogenetic level since it allows complete Chromosome probes of a species to be hybridized in situ onto Chromosomes of other species, detecting homologous genomic regions between them. In the present study, we have explored the highly rearranged complements of the Akodon species using reciprocal Chromosome Painting through species-specific Chromosome probes obtained by Chromosome sorting. The results revealed complete homology among the complements of Akodon sp. n. (ASP), 2n = 10; Akodon cursor (ACU), 2n = 15; Akodon montensis (AMO), 2n = 24; and Akodon paranaensis (APA), 2n = 44, and extensive Chromosome rearrangements have been detected within the species with high precision. Robertsonian and tandem rearrangements, pericentric inversions and/or centromere repositioning, paracentric inversion, translocations, insertions, and breakpoints, where chromosomal rearrangements, seen to be favorable, were observed. Chromosome Painting using the APA set of 21 autosomes plus X and Y revealed eight syntenic segments that are shared with A. montensis, A. cursor, and ASP, and one syntenic segment shared by A. montensis and A. cursor plus five exclusive Chromosome associations for A. cursor and six for ASP Chromosome X, except for the heterochromatin region of ASP X, and even Chromosome Y shared complete homology among the species. These data indicate that all those closely related species have experienced a recent extensive process of autosomal rearrangement in which, except for ASP, there is still complete conservation of sex Chromosomes homologies.
Malcolm A. Ferguson-smith - One of the best experts on this subject based on the ideXlab platform.
-
Comparative Chromosome Painting in hummingbirds (Trochilidae).
Genetics and molecular biology, 2020Co-Authors: Tiago Marafiga Degrandi, Patricia C. M. O’brien, Malcolm A. Ferguson-smith, Ivanete Oliveira Furo, Ricardo José Gunski, Jorge C. Pereira, Edivaldo Herculano Correia De Oliveira, Alice Lemos Costa, Analía Del Valle Garnero, Roberto Ferreira ArtoniAbstract:Hummingbirds (Trochilidae) are one of the most enigmatic avian groups, and also among the most diverse, with approximately 360 recognized species in 106 genera, of which 43 are monotypic. This fact has generated considerable interest in the evolutionary biology of the hummingbirds, which is reflected in a number of DNA-based studies. However, only a few of them explored chromosomal data. Given this, the present study provides an analysis of the karyotypes of three species of Neotropical hummingbirds, Anthracothorax nigricollis (ANI), Campylopterus largipennis (CLA), and Hylocharis chrysura (HCH), in order to analyze the chromosomal processes associated with the evolution of the Trochilidae. The diploid number of ANI is 2n=80 Chromosomes, while CLA and HCH have identical karyotypes, with 2n=78. Chromosome Painting with Gallus gallus probes (GGA1-12) shows that the hummingbirds have a karyotype close to the proposed ancestral bird karyotype. Despite this, an informative rearrangement was detected: an in-tandem fusion between GGA7 and GGA9 found in CLA and HCH, but absent in ANI. A comparative analysis with the tree of life of the hummingbirds indicated that this fusion must have arisen following the divergence of a number of hummingbird species.
-
Chromosomal phylogeny and comparative Chromosome Painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia.
BMC evolutionary biology, 2019Co-Authors: Willam Oliveira Da Silva, Malcolm A. Ferguson-smith, Julio Cesar Pieczarka, Patricia Caroline Mary O’brien, Marlyson Jeremias Rodrigues Da Costa, Ana Cristina Mendes-oliveira, Rogério Vieira Rossi, C.y. NagamachiAbstract:The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and Chromosome Painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by Chromosome Painting with Hylaeamys megacephalus (HME) whole-Chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. The comparative Chromosome Painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X Chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by Chromosome Painting among the karyotypes. Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.
-
Chromosomal polymorphism and comparative Chromosome Painting in the rufous-collared sparrow (Zonotrichia capensis).
Genetics and molecular biology, 2018Co-Authors: Sandra Eloisa Bülau, Patricia C. M. O’brien, Malcolm A. Ferguson-smith, Rafael Kretschmer, Ricardo José Gunski, Edivaldo Herculano Corrêa Oliveira, Analía Del Valle Garnero, Thales Renato Ochotorena FreitasAbstract:Zonotrichia capensis is widely distributed in the Neotropics. Previous cytogenetic studies demonstrated the presence of polymorphisms in two Chromosome pairs (ZCA2 and ZCA4). Here, we report results based on comparative Chromosome Painting, using probes derived from Gallus gallus and Leucopternis albicollis, focused on characterizing the Chromosome organization of Z. capensis. Our results demonstrate the conservation of ancestral syntenies as observed previously in other species of passerine. Syntenies were rearranged by a series of inversions in the second Chromosome as described in other Passeriformes, but in this species, by using probes derived from L. albicollis we observed an extra inversion in the second Chromosome that had not previously been reported. We also report a paracentric inversion in pair 3; this Chromosome corresponds to the second Chromosome in Zonotrichia albicollis and may indicate the presence of ancestral inversions in the genus. The chromosomal inversions we found might be important for understanding the phenotypic variation that exists throughout the distribution of Z. capensis.
-
Comparative Chromosome Painting in Columbidae (Columbiformes) reinforces divergence in Passerea and Columbea
Chromosome Research, 2018Co-Authors: Rafael Kretschmer, Malcolm A. Ferguson-smith, Ivanete Oliveira Furo, Ricardo José Gunski, Analía Valle Garnero, Jorge C. Pereira, Patricia C. M. O’brien, Edivaldo Herculano Corrêa Oliveira, Thales Renato Ochotorena FreitasAbstract:Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the karyotype evolution within Columbiformes remains unclear. To delineate the synteny-conserved segments and karyotypic differences among four Columbidae species, we used Chromosome Painting from Gallus gallus (GGA, 2n = 78) and Leucopternis albicollis (LAL, 2n = 68). Besides that, a set of Painting probes for the eared dove, Zenaida auriculata (ZAU, 2n = 76), was generated from flow-sorted Chromosomes. Chromosome Painting with GGA and ZAU probes showed conservation of the first ten ancestral pairs in Z. auriculata , Columba livia , and Columbina picui , while in Leptotila verreauxi , fusion of the ancestral Chromosomes 6 and 7 was observed. However, LAL probes revealed a complex reorganization of ancestral Chromosome 1, involving paracentric and pericentric inversions. Because of the presence of similar intrachromosomal rearrangements in the Chromosomes corresponding to GGA1q in the Columbidae and Passeriformes species but without a common origin, these results are consistent with the recent proposal of divergence within Neoaves (Passerea and Columbea). In addition, inversions in Chromosome 2 were identified in C. picui and L. verreauxi . Thus, in four species of distinct genera of the Columbidae family, unique chromosomal rearrangements have occurred during karyotype evolution, confirming that despite conservation of the ancestral syntenic groups, these Chromosomes have been modified by the occurrence of intrachromosomal rearrangements.
-
Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional Chromosome Painting.
BMC evolutionary biology, 2018Co-Authors: Anderson José Baia Gomes, Malcolm A. Ferguson-smith, Fengtang Yang, C.y. Nagamachi, Patricia Caroline Mary O’brien, Luis Reginaldo Ribeiro Rodrigues, Julio Cesar PieczarkaAbstract:The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use Chromosome Painting with whole Chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published Chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole Chromosome probes allows us to track some syntenic associations prior to the emergence of this family.
Alexander S. Graphodatsky - One of the best experts on this subject based on the ideXlab platform.
-
The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora).
PLOS ONE, 2016Co-Authors: Violetta R Beklemisheva, Vladimir N Burkanov, Natalia A. Lemskaya, Anastasia I. Kulemzina, Polina L Perelman, Anastasia A Proskuryakova, Alexander S. GraphodatskyAbstract:Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However Chromosome Painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative Chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-Chromosome Painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome Painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative Chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published Chromosome Painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.
-
The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora) - Table 1
2016Co-Authors: Violetta R Beklemisheva, Vladimir N Burkanov, Natalia A. Lemskaya, Anastasia I. Kulemzina, Polina L Perelman, Anastasia A Proskuryakova, Alexander S. GraphodatskyAbstract:The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora) - Table
-
DOI: 10.1007/s10577-008-1270-2 Chromosome Painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes
2014Co-Authors: P. L. Perelman, Alexander S. Graphodatsky, Gary Stone, P. C. M. O'brien, Natalya A. Serdyukova, Pietro Cavagna, A. Menotti, J. W. Dragoo, W. Nie, Jun WangAbstract:The karyotypic relationships of skunks (Mephitidae) with other major clades of carnivores are not yet established. Here, multi-directional Chromosome Painting was used to reveal the karyological relationships among skunks and between Mephitidae (skunks) and Procyonidae (raccoons). Representative species from three genera of Mephitidae (Mephitis mephitis, 2n = 50; Mephitis macroura, 2n = 50; Conepatus leuconotus, 2n=46; Spilogale gracilis, 2n = 60) and one species of Procyonidae (Procyon lotor, 2n = 38) were studied. Chromosomal homology was mapped by hybridization of five sets of whole-Chromosome paints derived from stone marten (Martes foina, 2n = 38), cat, skunks (M. mephitis; M. macroura) and human. The karyotype of the raccoon i
-
Comparative Chromosome Painting in Carnivora and Pholidota.
Cytogenetic and genome research, 2012Co-Authors: Polina L Perelman, Violetta R Beklemisheva, Dmitry V. Yudkin, T.n. Petrina, V.v. Rozhnov, Wenhui Nie, Alexander S. GraphodatskyAbstract:The order of Carnivora has been very well characterized with over 50 species analyzed by Chromosome Painting and with Painting probe sets made for 9 Carnivora species. Representatives of almost all families have been studied with few exceptions (Otariidae, Odobenidae, Nandiniidae, Prionodontidae). The patterns of Chromosome evolution in Carnivora are discussed here. Overall, many Carnivora species retained karyotypes that only slightly differ from the ancestral carnivore karyotype. However, there are at least 3 families in which the ancestral carnivore karyotype has been severely rearranged – Canidae, Ursidae and Mephitidae. Here we report Chromosome Painting of yet another Carnivora species with a highly rearranged karyotype, Genetta pardina. Recurrent rearrangements make it difficult to define the ancestral chromosomal arrangement in several instances. Only 2 species of pangolins (Pholidota), a sister order of Carnivora, have been studied by Chromosome Painting. Future use of whole-genome sequencing data is discussed in the context of solving the questions that are beyond resolution of conventional banding techniques and Chromosome Painting.
-
reconstruction of the putative cervidae ancestral karyotype by Chromosome Painting of siberian roe deer capreolus pygargus with dromedary probes
Cytogenetic and Genome Research, 2010Co-Authors: P V Dementyeva, Anastasia I. Kulemzina, Vladimir A. Trifonov, Alexander S. GraphodatskyAbstract:The Siberian roe deer (Capreolus pygargus) is one of a few deer species presumably preserving the ancestral cervid karyotype. The comparative genomic data of the Siberian roe deer are critical for our understanding of the karyotypic relationships within artiodactyls. We have established chromosomal homologies between the Siberian roe deer and the dromedary (Camelus dromedarius) by cross-species Chromosome Painting with dromedary Chromosome-specific Painting probes. Dromedary Chromosome paints detected 53 autosomal homologies in the genome of the Siberian roe deer. The identification of chromosomal homologies between the Siberian roe deer and cattle resulted from previously detected cattle-dromedary homologies. We have found 8 chromosomal rearrangements (6 fissions in the Siberian roe deer, 1 fission in the cattle and 1 inversion on the CPY11) that have separated the karyotypes of the cattle and the Siberian roe deer. The inversion on CPY11 might be an apomorphic trait of cervids, since we detected its presence in the gray brocket deer (Mazama gouazoubira). Thus our data further prove the scenario of chromosomal rearrangements that was previously proposed and add some new data.
C.y. Nagamachi - One of the best experts on this subject based on the ideXlab platform.
-
Chromosomal phylogeny and comparative Chromosome Painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia.
BMC evolutionary biology, 2019Co-Authors: Willam Oliveira Da Silva, Malcolm A. Ferguson-smith, Julio Cesar Pieczarka, Patricia Caroline Mary O’brien, Marlyson Jeremias Rodrigues Da Costa, Ana Cristina Mendes-oliveira, Rogério Vieira Rossi, C.y. NagamachiAbstract:The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and Chromosome Painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by Chromosome Painting with Hylaeamys megacephalus (HME) whole-Chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. The comparative Chromosome Painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X Chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by Chromosome Painting among the karyotypes. Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.
-
Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional Chromosome Painting.
BMC evolutionary biology, 2018Co-Authors: Anderson José Baia Gomes, Malcolm A. Ferguson-smith, Fengtang Yang, C.y. Nagamachi, Patricia Caroline Mary O’brien, Luis Reginaldo Ribeiro Rodrigues, Julio Cesar PieczarkaAbstract:The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use Chromosome Painting with whole Chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published Chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole Chromosome probes allows us to track some syntenic associations prior to the emergence of this family.
-
Chromosome Painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes
2018Co-Authors: Talita Fernanda Augusto Ribas, Fengtang Yang, C.y. Nagamachi, Alexandre Aleixo, Melquizedec Luiz Silva Pinheiro, Patricia Caroline Mary O´brien, Malcolm Andrew Ferguson-smith, Pablo Suarez, Julio Cesar PieczarkaAbstract:Glyphorynchus spirurus (GSP), also called the Wedge-billed Woodcreeper (Furnariidae) has an extensive distribution in the Americas, including the Atlantic coast of Brazil. Nevertheless, there is no information about its karyotype or genome organization. To contribute to the knowledge of chromosomal evolution in Passeriformes we analysed the karyotype of Glyphorynchus spirurus by classic and molecular cytogenetics methods. We show that Glyphorynchus spirurus has a 2n = 80 karyotype with a fundamental number (FN) of 84, similar to the avian putative ancestral karyotype (PAK). Glyphorynchus spirurus pair 1 was heteromorphic in the Tapajós population whereby the short arms varied in sizes, possibly due to a pericentric inversion, as described in other Furnariidae birds. FISH with the Histone H5 probe revealed a signal in the pericentromeric region of G. spirurus Chromosome 5 and rDNA 18S showed interstitial signal in GSP-1. Chromosome Painting with Gallus gallus (GGA) macroChromosomes 1–9 probes showed disruption of Chromosome syntenies of GGA-1, 2 and 4 by fission in Glyphorynchus spirurus. Our results confirm that the GGA1 centric fission is a synapomorphic character for the phylogenetic branch composed of Strigiformes, Passeriformes, Columbiformes and Falconiformes. On the other hand, the GGA-2 fission is reported here for the first time in Passeriformes. Chromosome Painting with BOE whole Chromosome probes confirmed these rearrangements in Glyphorynchus spirurus revealed by Gallus gallus 1–9 probes, in addition to enabling the establishment of genome-wide homology map.
-
Chromosome Painting reveals multiple rearrangements between Gymnotus capanema and Gymnotus carapo (Gymnotidae, Gymnotiformes).
Cytogenetic and genome research, 2013Co-Authors: C.y. Nagamachi, Susana Suely Rodrigues Milhomem, Julio Cesar Pieczarka, Patricia Caroline Mary O’brien, Jéssica Almeida Batista, Malcolm A. Ferguson-smithAbstract:The genus Gymnotus (Gymnotiformes) is a group of fishes with karyotypic plasticity, demonstrated by cytogenetic studies using whole Chromosome probes of G. carapo (GCA, 2n = 42) that were obtained by flow-sorting from fibroblast cultures. In the present work we undertook comparative mapping of the karyotype of G. capanema (GCP, 2n = 34) with GCA, 2n = 42 Painting probes. The results demonstrate that the karyotype of G. capanema is extensively rearranged when compared to G. carapo. From the 12 Chromosome pairs of G. carapo that can be individually differentiated (GCA1-3, 6, 7, 9, 14, 16 and 18-21), only 4 pairs (GCA6, 7, 19, and 20) maintained conserved synteny in G. capanema. From these 4, GCA6 and GCA20 correspond to individual Chromosomes (GCP8 and GCP15), while the other 2 share homology with parts of GCP1 and GCP2, respectively. The remaining GCP Chromosomes showed more complex hybridization patterns with homologies to other GCA pairs. These results demonstrate that the level of reorganization in the genome of G. capanema is much greater than in GCA, 2n = 42 and in karyomorph GCA, 2n = 40 which was previously analyzed by Chromosome Painting.
-
A phylogenetic analysis using multidirectional Chromosome Painting of three species (Uroderma magnirostrum, U. bilobatum and Artibeus obscurus) of subfamily Stenodermatinae (Chiroptera-Phyllostomidae)
Chromosome Research, 2013Co-Authors: A. J. B. Gomes, C.y. Nagamachi, Jorge Das Dores Rissino, P. C. M. O’brien, F. Yang, D. C. C. Rocha, Malcolm A. Ferguson-smithAbstract:The species of genera Uroderma and Artibeus are medium-sized bats belonging to the family Phyllostomidae and subfamily Stenodermatinae (Mammalia, Chiroptera) from South America. They have a wide distribution in the Neotropical region, with two currently recognized species in Uroderma and approximately 20 species in Artibeus . These two genera have different rates of Chromosome evolution, with Artibeus probably having retained the ancestral karyotype for the subfamily. We used whole Chromosome paint probe sets from Carollia brevicauda and Phyllostomus hastatus on Uroderma magnirostrum , Uroderma bilobatum , and Artibeus obscurus . With the aim of testing the previous phylogenies of these bats using cytogenetics, we compared these results with published Painting maps on Phyllostomidae. The genome-wide comparative maps based on Chromosome Painting and Chromosome banding reveal the Chromosome forms that characterize each taxonomic level within the Phyllostomidae and show the Chromosome evolution of this family. Based on this, we are able to suggest an ancestral karyotype for Phyllostomidae. Our cladistic analysis is an independent confirmation using multidirectional Chromosome Painting of the previous Phyllostomidae phylogenies.