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The veiled chameleon (

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Para. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal de S?o Carlos. Departamento de Gen?tica e Evolu??o. S?o Carlos, SP, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Para. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. In contrast to the ?avian-like? diploid number (2n = 80), most toucans and aracaris (Piciformes: Ramphastidae) have divergent karyotypes, exhibiting a higher 2n. To identify the chromosomal rearrangements that shaped the karyotype of these species, we applied chicken macrochromosome paints 1?10 and 11 microsatellite sequences to the chromosomes of two representative species, Pteroglossus inscriptus and Ramphastos tucannus tucannus. Paints of chicken chromosomes revealed that at least the first five ancestral chromosomes have undergone fissions, and a fusion between a segment of chicken chromosome 1 and a segment from chromosome 3 occurred in both species. The microsatellite sequences were accumulated mainly in the Z chromosome and in several microchromosomes in both species. These results suggest that the genomes of the Ramphastidae have been shaped by extensive fissions and repetitive DNA accumulation as the main driving forces leading to the higher 2n as found in these species. Furthermore, our results suggest that the putative ancestral karyotype of Ramphastidae already had a high diploid number, probably close to 2n = 112, similar to that observed in P. inscriptus and R. t. tucannus.

Federal University of Par?. Faculty of Natural Sciences. Institute of Coastal Studies. Bragan?a PA, Brazil. Federal University of Par?. Faculty of Natural Sciences. Institute of Exact and Natural Sciences. Bel?m PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos. Ananindeua, PA, Brasil. Cambridge Resource Center for Comparative Genomics. Cambridge, United Kingdom. Federal University of Par?. Faculty of Natural Sciences. Institute of Coastal Studies. Bragan?a PA, Brazil. Federal University of Par?. Faculty of Natural Sciences. Institute of Coastal Studies. Bragan?a PA, Brazil / University of Porto. Agrarian Campus of Vair?o. Center for Research in Biodiversity and Genetic Resources. Associated Laboratory. Vair?o, Portugal. Federal University of Par?. Faculty of Natural Sciences. Institute of Exact and Natural Sciences. Bel?m PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos. Ananindeua, PA, Brasil. Federal University of Par?. Faculty of Natural Sciences. Institute of Coastal Studies. Bragan?a PA, Brazil. The family Centropomidae includes a number of fish species of high commercial value. One of these species, Centropomus undecimalis, is a target of artisanal, industrial, and sports fisheries and has also considerable potential for captive breeding, which has led to its inclusion in several aquaculture programs. While the biology and ecology of C. undecimalis are relatively well documented, few karyological data are available on this species, and they are still scarce for other centropomids. The few chromosomal data available on this family indicate a conserved karyotype 2n?=?48, but it is unclear whether the chromosome microstructure is also conserved. In this study, new cytogenetic data are presented on C. undecimalis from the Amazon coastal zone, including C-banding, Ag-NOR, in situ hybridization with repetitive DNA probes (5S and 18S ribosomal genes), and telomeric (TTAGGG)n sequences. The diploid number of the species was 2n?=?48, with heterochromatic blocks in the centromeric and pericentromeric regions, as well as distal signals; the nucleolus organizer regions (NORs) were associated with the heterochromatic region. The 18S and 5S recombinant DNA (rDNA) clusters were located in the distal region of chromosome pairs 1 and 11, respectively. The similarities of the karyotype macrostructure found among the centropomid species reinforce their exceptional chromosomal stability. However, the presence of heterochromatic blocks and location of NORs suggest the occurrence of structural rearrangements, which indicates that evolutionary dynamics at the microstructural level in this group may be relatively complex and should be evaluated carefully in any study that targets the production of hybrids for aquaculture.

Evolutionary history and taxonomic position for cryptic species may be clarified by using molecular and cytogenetic methods. The subterranean rodent, the Alay mole voleEllobiusalaicusVorontsov et al., 1969 is one of three sibling species constituting the subgenus Ellobius Fischer, 1814, all of which lost the Y chromosome and obtained isomorphic XX sex chromosomes in both males and females.E.alaicusis evaluated by IUCN as a data deficient species because their distribution, biology, and genetics are almost unknown. We revealed specific karyotypic variability (2n = 52–48) inE.alaicusdue to different Robertsonian translocations (Rbs). Two variants of hybrids (2n = 53, different Rbs) withE.tancreiBlasius, 1884 were found at the Northern slopes of the Alay Ridge and in the Naryn district, Kyrgyzstan. We described the sudden change in chromosome numbers from 2n = 50 to 48 and specific karyotype structure for mole voles, which inhabit the entrance to the Alay Valley (Tajikistan), and revealed their affiliation asE.alaicusby cytochromeband fragments of nuclearXISTandRspo1genes sequencing. To date, it is possible to expand the range ofE.alaicusfrom the Alay Valley (South Kyrgyzstan) up to the Ferghana Ridge and the Naryn Basin, Tien Shan at the north-east and to the Pamir-Alay Mountains (Tajikistan) at the west. The closeness ofE.tancreiandE.alaicusis supported, whereas specific chromosome and molecular changes, as well as geographic distribution, verified the species status forE.alaicus. The case ofEllobiusspecies accented an unevenness in rates of chromosome and nucleotide changes along with morphological similarity, which is emblematic for cryptic species.

Universidade Federal do Par?. Programa de P?s-Gradua??o em Biodiversidade e Biotecnologia da Rede Bionorte. Bel?m, PA, Brazil. Universidade Federal do Par?. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Department of Veterinary Medicine. Cambridge, UK. Universidade Federal do Par?. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil. Universidade Federal do Par?. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil. Universidade Federal do Par?. Programa de P?s-Gradua??o em Neuroci?ncias e Biologia Celular. Bel?m, PA, Brazil. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Department of Veterinary Medicine. Cambridge, UK. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Department of Veterinary Medicine. Cambridge, UK. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Par?. Faculdade de Ci?ncias Naturais. Bel?m, PA, Brazil. Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas (PPGCB). S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas (PPGCB). S?o Gabriel, RS, Brazil. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. 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

Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression., The genetic changes that occur in late stage metastatic melanoma are not well delineated. Here, the authors use rapid autopsy samples from metastatic melanoma patients and show that the late stage in the disease is characterised by whole genome doubling and aneuploidy.

We are grateful to the staff of Laborat?rio de Diversidade Gen?tica Animal from Universidade Federal do Pampa (Campus S?o Gabriel), CNPq (309699/2015-0), PROPESP-UFPA and CAPES for technical and financial support. This research was partially funded by a grant to EHCO from CNPq (307382/2019-2) and to MAFS from the Wellcome Trust in support of the Cambridge Resource Centre for Comparative Genomics and by the Biotechnology and Biological Sciences Research Council (BB/K008161/1) to the University of Kent, also by UIDB/CVT/00772/2020 funded by the Funda??o para Ci?ncia e Tecnologia (FCT). Universidade Federal Rural da Amaz?nia. Laborat?rio de Reprodu??o Animal. Parauapebas, PA, Brazil / University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil / University of Kent. School of Biosciences. Canterbury, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom / University of Tr?s-os-Montes and Alto Douro. Animal and Veterinary Research Centre. Vila Real, Portugal. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. University of Kent. School of Biosciences. Canterbury, United Kingdom. University of Kent. School of Biosciences. Canterbury, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus.

Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromosome-specific probes from this species have been used successfully to detect intrachromosomal rearrangements in different species of bird since 2010. However, some gaps were detected in this first set of probes. Here, we have obtained a new set of whole chromosome probes in order to improve the previous one; also, we have performed experiments using bacterial artificial chromosome (BAC) from chicken microchromosomes. Our results demonstrated that the microchromosomes were involved in fusion events. In addition, a new nomenclature has been proposed for the new set of probes and some inaccurate data were corrected.

The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.

This work was supported by the Conselho Nacional de Desenvolvimento Cient??fico e Tecnolo?gico (CNPq) Grant number 307382/2019- 02 to EHCO and the Coordenac??o de Aperfeic?oamento de Pessoal de N??vel Superior (CAPES) Universidade Federal do Par?. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Par?. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Pampa, Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa, Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Departamento de Gen?tica, Ecologia e Evolu??o, Laborat?rio de Citogen?mica Evolutiva. Belo Horizonte, MG, Brazil. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Department of Veterinary Medicine. Cambridge, United Kingdom. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Department of Veterinary Medicine. Cambridge, United Kingdom. Universidade Federal do Par?. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. The Cuckoos have a long history of difficult classification. The species of this order have been the subject of several studies based on osteology, behavior, ecology, morphology and molecular data. Despite this, the relationship between Cuculiformes and species of other orders remains controversial. In this work, two species of Cuculidae, Guira guira (Gmelin, 1788) and Piaya cayana (Linnaeus, 1766), were analyzed by means of comparative chromosome painting in order to study the chromosome evolution of this group and to undertake the first chromosome mapping of these species. Our results demonstrate high chromosomal diversity, with 2n = 76 in G. guira, with fission and fusion events involving ancestral syntenies, while P. cayana presented only fissions, which were responsible for the high diploid number of 2n = 90. Interestingly, there were no chromosomal rearrangements in common between these species. Our results, based on Giemsa staining, were compared with previous data for other cuckoos and also with taxa proposed as sister-groups of Cuculiformes (Otidiformes, Musophagiformes and Opisthocomiformes). Cytogenetic comparisons demonstrated that cuckoo species can be divided into at least three major groups. In addition, we found no evidence to place Cuculiformes close to the groups proposed previously as sister-groups.

This research was partially funded by a grant to EHCO from CNPq (307382/2019-2) and to MAFS from the Wellcome Trust in support of the Cambridge Resource Centre for comparative genomics Federal University of Par?. Post-Graduation Program in Genetics and Molecular Biology. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecido e Citogen?tica. Ananindeua, PA, Brasil / Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK / Federal University of Rio Grande do Sul. Pos-Graduation Program in Genetics and Molecular Biology. Porto Alegre, RS, Brazil. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecido e Citogen?tica. Ananindeua, PA, Brasil / Federal University of Par?. Faculty of Natural Sciences. Institute of Exact and Natural Sciences. Bel?m, PA, Brazil. Abstract: Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil / University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Paran?. Programa de P?s-gradua??o em Gen?tica. Laborat?rio de Citogen?tica e Gen?tica da Conserva??o Animal. Curitiba, PR, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. The order Charadriiformes comprises three major clades: Lari and Scolopaci as sister group to Charadrii. Until now, only three Charadriiformes species have been studied by chromosome painting: Larus argentatus (Lari), Burhinus oedicnemus and Vanellus chilensis (Charadrii). Hence, there is a lack of information concerning the third clade, Scolapaci. Based on this, and to gain a better understanding of karyotype evolution in the order Charadriiformes, we applied conventional and molecular cytogenetic approaches in a species belonging to clade Scolopaci - the wattled jacana (Jacana jacana) - using Gallus gallus and Zenaida auriculata chromosome-specific probes. Cross-species evaluation of J. jacana chromosomes shows extensive genomic reshuffling within macrochromosomes during evolution, with multiple fission and fusion events, although the diploid number remains at high level (2n=82). Interestingly, this species does not have the GGA7-8 fusion, which was found in two representatives of Charadrii clade, reinforcing the idea that this fusion may be exclusive to the Charadrii clade. In addition, it is shown that the chromosome evolution in Charadriiformes is complex and resulted in species with typical and atypical karyotypes. The karyotypic features of Scolopaci are very different from those of Charadrii and Lari, indicating that after divergence, each suborder has undergone different chromosome rearrangements.

Instituto Evandro Chagas; CAPES; CNPq Universidade Federal do Rio Grande do Sul. Programa de P?s-Gradua??o em Biologia Animal. Porto Alegre, RS, Brazil. Universidade Federal do Rio Grande do Sul. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Rio Grande do Sul. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge, United Kingdom. University of Cambridge. Department of Veterinary Medicine. Cambridge, United Kingdom. Universidade Federal do Pampa. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Bel?m, PA, Brasil / Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. Universidade Federal do Pampa. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Cytogenetic analyses of the Suboscines species are still scarce, and so far, there is no karyotype description of any species belonging to the family Conopophagidae. Thus, the aim of this study is to describe and analyze the karyotype of Conopophaga lineata by chromosome painting using Gallus gallus (GGA) probes and to identify the location of the 18/28S rDNA cluster. Metaphases were obtained from fibroblast culture from two individuals of C. lineata. We observed a diploid number of 2n=78. GGA probes showed that most ancestral syntenies are conserved, except for the fission of GGA1 and GGA2, into two distinct pairs each. We identified the location of 18S rDNA genes in a pair of microchromosomes. The fission of the syntenic group corresponding to GGA2 was observed in other Furnariida, and hence may correspond to a chromosomal synapomorphy for the species of Parvorder Furnariida.

Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico Universidade Estadual de Ponta Grossa. Programa de P?s-Gradua??o em Biologia Evolutiva. Ponta Grossa, PR, Brazil. Universidade Federal Rural da Amaz?nia. Laborat?rio de Reprodu??o Animal. Parauapebas, PA, Brazil / University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Universidade Federal do Par?. Programa de P?s-Gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Pampa. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. University of Tr?s?os?Montes and Alto Douro. Animal and Veterinary Research Centre. Vila Real, Portugal. Universidade Federal do Pampa. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Estadual de Ponta Grossa. Programa de P?s-Gradua??o em Biologia Evolutiva. Ponta Grossa, PR, Brazil. 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.

Supernumerary elements of the genome are often called B chromosomes. They usually consist of various autosomal sequences and, because of low selective pressure, are mostly pseudogenized and contain many repeats. There are numerous reports on B chromosomes in mammals, fish, invertebrates, plants, and fungi, but only a few of them have been studied using sequencing techniques. However, reptilian supernumerary chromosomes have been detected only cytogenetically and never sequenced or analyzed at the molecular level. One model squamate species with available genome sequence is Anolis carolinensis. The scope of the present article is to describe the genetic content of A. carolinensis supernumerary chromosomes. In this article, we confirm the presence of B chromosomes in this species by reverse painting and synaptonemal complex analysis. We applied low-pass high-throughput sequencing to analyze flow-sorted B chromosomes. Anole B chromosomes exhibit similar traits to other supernumerary chromosomes from different taxons: they contain two genes related to cell division control (INCENP and SPIRE2), are enriched in specific repeats, and show a high degree of pseudogenization. Therefore, the present study confirms that reptilian B chromosomes resemble supernumerary chromosomes of other taxons.

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.

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Par?. Faculdade de Ci?ncias Naturais. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Madingley Road, Cambridge, UK. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Madingley Road, Cambridge, UK. In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.

The hoatzin (Opisthocomus hoazin Müller, 1776) is a folivorous bird, endemic to the Amazonian region. It presents some unique characteristics, including wing claws and foregut fermentation, which make its phylogenetic relationship to other birds difficult to determine. There have been various attempts to place it among the Galliformes, Gruiformes, Musophagiformes, Cuculiformes, and Charadriiformes, but phylogenetic analyses always show low supporting values. Nowadays, the hoatzin is included in the monotypic order Opisthocomiformes, but the relationship of this order to other groups of birds is still unclear. Although its karyotype resembles the typical avian model, fissions of the syntenic groups corresponding to chicken chromosomes 1 and 2 and 2 fusions were found. The presence of 18S rDNA clusters in 2 pairs of microchromosomes is another derived character. Hence, different rearrangements were detected in the karyotype of the hoatzin, indicating it has been derived from the putative ancestral karyotype by the occurrence of fissions and fusions. However, as these rearrangements are not exclusive to O. hoazin, they do not clarify the phylogenetic position of this enigmatic species.

Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype, based on homology with GGA. Fissions occurred mainly in syntenic groups homologous to GGA1-GGA5. On the other hand, the majority of the microchromosomes were found fused to other chromosomal elements in STY, indicating these rearrangements played an important role in the reduction of the 2n to 68. Comparison with hybridization pattern of the Japanese-Mountain-Eagle (Nisaetus nipalensis orientalis), the only Aquilinae analyzed by comparative chromosome painting previously, did not reveal any synapomorphy that could represent a chromosome signature to this subfamily. Therefore, conclusions about karyotype evolution in Aquilinae require additional painting studies.

Trogons are forest birds with a wide distribution, being found in Africa, Asia, and America, and are included in the order Trogoniformes, family Trogonidae. Phylogenetic studies using molecular data have not been able to determine the phylogenetic relationship among the different genera of trogons. So far, no cytogenetic data for these birds exist. Hence, the aim of this study was to characterize the karyotype of Trogon surrucura surrucura by means of classical and molecular cytogenetics. We found a diploid chromosome number of 2n = 82, similar to most birds, with several derived features compared to chicken and the putative ancestral avian karyotype. T. s. surrucura showed 3 pairs of microchromosomes bearing 18S rDNA clusters. The Z and W sex chromosomes were of similar size but could readily be identified by morphological differences. Using chromosome painting with whole chromosome probes from Gallus gallus and Leucopternis albicollis, we found that the chromosomes homologous to chicken chromosomes 2 and 5 correspond to 2 different pairs in T. s. surrucura and L. albicollis, due to the occurrence of centric fissions. Paracentric inversions were detected in the segment homologous to chicken chromosome 1q, and we confirmed the recurrence of breakpoints when our results were compared to other species of birds already analyzed by FISH or by in silico genome assembly.

Here, for the first time, we describe the karyotype of Myiopsitta monachus (Psittacidae, Arini). We found 2n = 48, corresponding to the lowest diploid number observed in Neotropical Psittaciformes so far, with an uncommonly large W chromosome homomorphic to the Z. In order to better understand the evolution of the sex chromosomes in this species, we applied several molecular cytogenetic approaches, including C-banding, FISH mapping of repetitive DNAs (several microsatellite repeats), and whole-chromosome painting on metaphases of M. monachus. For comparison, another species belonging to the same tribe but with a smaller W chromosome (A. aestiva) was also analyzed. The results show that the constitutive heterochromatin has a very diverse distribution pattern in these species revealing heterochromatic blocks in the centromeric region of all chromosomes and in most of the length of the W chromosome in A. aestiva, while in M. monachus they were found in interstitial and telomeric regions. Concerning the microsatellites, only the sequence (CG)n produced signals on the W chromosome of A. aestiva, in the distal region of both arms. However, in M. monachus, (CAA)n, (CAG)n, and (CG)n probes were accumulated on the W chromosome, and, in addition, the sequence (CAG)n also hybridized to heterochromatic regions in macrochromosomes, as well as in microchromosomes. Based on these results, we suggest that the increase in length of the W chromosome in M. monachus is due to the amplification of repetitive elements, which highlights their significant role in the evolutionary process of sex chromosome differentiation.

The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous, consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation.

Chromosome homologies in reptiles have been investigated extensively by gene mapping and chromosome painting. Relative chromosome size can be estimated roughly from conventional karyotypes, but chromosome GC content cannot be evaluated by any of these approaches. However, GC content can be obtained by whole-genome sequencing, although complete data are available only for a limited number of reptilian species. Chromosomes can be characterized by size and GC content in bivariate flow karyotypes, in which the distribution of peaks represents the differences. We have analysed flow karyotypes from 9 representative squamate species and show chromosome profiles for each species based on the relationship between size and GC content. Our results reveal that the GC content of macrochromosomes is invariable in the 9 species. A higher GC content was found in microchromosomes, similar to profiles previously determined in crocodile, turtle, and chicken. The findings suggest that karyotype evolution in reptiles is characterized by unique features of chromosome GC content.

Extensive chromosome homologies revealed by cross-species chromosome painting between marsupials have suggested a high level of genome conservation during evolution. Surprisingly, it has been reported that marsupial genome sizes vary by more than 1.2 Gb between species. We have shown previously that individual chromosome sizes and GC content can be measured in flow karyotypes, and have applied this method to compare four marsupial species. Chromosome sizes and GC content were calculated for the grey short-tailed opossum (2n= 18), tammar wallaby (2n= 16), Tasmanian devil (2n= 14) and fat-tailed dunnart (2n= 14), resulting in genome sizes of 3.41, 3.31, 3.17 and 3.25 Gb, respectively. The findings under the same conditions allow a comparison between the four species, indicating that the genomes of these four species are 1–8% larger than human. We show that marsupial genomes are characterized by a low GC content invariable between autosomes and distinct from the higher GC content of the marsupial × chromosome.

The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences. Recently whole chromosome painting (WCP) has been used for tracking the chromosomal evolution of the genus, showing highly reorganized karyotypes and the conserved synteny of the NOR bearing par within the clade G. carapo. In this study, painting probes derived from the chromosomes of G. carapo (GCA, 2n = 42, 30 m/sm + 12 st/a) were hybridized to the mitotic metaphases of G. arapaima (GAR, 2n = 44, 24 m/sm + 20 st/a). Our results uncovered chromosomal rearrangements and a high number of repetitive DNA regions. From the 12 chromosome pairs of G. carapo that can be individually differentiated (GCA1-3, 6, 7, 9, 14, 16, and 18-21), six pairs (GCA 1, 9, 14, 18, 20, 21) show conserved homology with GAR, five pairs (GCA 1, 9, 14, 20, 21) are also shared with cryptic species G. carapo 2n = 40 (34 m/sm + 6 st/a) and only the NOR bearing pair (GCA 20) is shared with G. capanema (GCP 2n = 34, 20 m/sm + 14 st/a). The remaining chromosomes are reorganized in the karyotype of GAR. Despite the close phylogenetic relationships of these species, our chromosome painting studies demonstrate an extensive reorganization of their karyotypes.

The subfamily Arvicolinae consists of a great number of species with highly diversified karyotypes. In spite of the wide use of arvicolines in biological and medicine studies, the data on their karyotype structures are limited. Here, we made a set of painting probes from flow-sorted chromosomes of a male Palearctic collared lemming (Dicrostonyx torquatus, DTO). Together with the sets of painting probes made previously from the field vole (Microtus agrestis, MAG) and golden hamster (Mesocricetus auratus, MAU), we carried out a reciprocal chromosome painting between these three species. The three sets of probes were further hybridized onto the chromosomes of the Eurasian water vole (Arvicola amphibius) and northern red-backed vole (Myodes rutilus). We defined the diploid chromosome number in D. torquatus karyotype as 2n = 45 + Bs and showed that the system of sex chromosomes is X1X2Y1. The probes developed here provide a genomic tool-kit, which will help to investigate the evolutionary biology of the Arvicolinae rodents. Our results show that the syntenic association MAG1/17 is present not only in Arvicolinae but also in some species of Cricetinae; and thus, should not be considered as a cytogenetic signature for Arvicolinae. Although cytogenetic signature markers for the genera have not yet been found, our data provides insight into the likely ancestral karyotype of Arvicolinae. We conclude that the karyotypes of modern voles could have evolved from a common ancestral arvicoline karyotype (AAK) with 2n = 56 mainly by centric fusions and fissions.

Among birds, Tyrannidae comprises one of the most diverse and species-rich families. Although cytogenetic data have shown interesting results in this family, such as variations in the macrochromosome morphology and diploid number, only a few species have had their karyotypes described. In the present study, we report the characterization of the karyotype of Elaenia spectabilis (Passeriformes, Tyrannidae) by means of classical and molecular cytogenetics. The results show that syntenic groups of Gallus gallus (GGA) were conserved, except GGA1 and GGA4, which were divided into two different pairs each. However, the results obtained with Leucopternis albicollis probes revealed the occurrence of inversions in segments homologous to GGA1q, similar to those observed in other Passerifomes (Turdus), and one inversion in GGA1p. These results suggest that the centric fission in GGA1, as well as the inversions observed in segments homologous to GGA1q, appeared in the early history of Passeriformes because they could be detected in Oscine and Suboscine species. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115, 391–398.

The Southern lapwing (Vanellus chilensis) is endemic to America and is well-known because of the vast expansion of its geographical distribution and its involvement in air accidents. Despite its popularity, there is no information concerning the genomic organization and karyotype of this species. Hence, because other species of the genus Vanellus have variable diploid numbers from 2n = 58 to 76, the aim of this report was to analyze the karyotype of V. chilensis by means of classical and molecular cytogenetics. We found that 2n = 78 and chromosome painting using probes of Gallus gallus (GGA) and Leucopternis albicollis revealed an organization similar to the avian putative ancestral karyotype, except for the fusion of GGA7 and GGA8, also found in Burhinus oedicnemus, the only Charadriiforme species analyzed by FISH so far. This rearrangement may represent a cytogenetic signature for this group and, in addition, must be responsible for the difference between the diploid number found in the avian putative ancestral karyotype (2n = 80) and V. chilensis (2n = 78).

Universidade Federal do Par?. Faculdade de Ci?ncias Naturais. Instituto de Ci?ncias Exatas e Naturais. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Universidade Federal do Par?. Faculdade de Ci?ncias Naturais. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Pampa, Campus S?o Gabriel. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa, Campus S?o Gabriel. Programa de P?s-Gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Par?. Faculdade de Ci?ncias Naturais. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. 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.

The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences. Recently whole chromosome painting (WCP) has been used for tracking the chromosomal evolution of the genus, showing highly reorganized karyotypes and the conserved synteny of the NOR bearing par within the clade G. carapo. In this study, painting probes derived from the chromosomes of G. carapo (GCA, 2n = 42, 30 m/sm + 12 st/a) were hybridized to the mitotic metaphases of G. arapaima (GAR, 2n = 44, 24 m/sm + 20 st/a). Our results uncovered chromosomal rearrangements and a high number of repetitive DNA regions. From the 12 chromosome pairs of G. carapo that can be individually differentiated (GCA1–3, 6, 7, 9, 14, 16, and 18–21), six pairs (GCA 1, 9, 14, 18, 20, 21) show conserved homology with GAR, five pairs (GCA 1, 9, 14, 20, 21) are also shared with cryptic species G. carapo 2n = 40 (34 m/sm + 6 st/a) and only the NOR bearing pair (GCA 20) is shared with G. capanema (GCP 2n = 34, 20 m/sm + 14 st/a). The remaining chromosomes are reorganized in the karyotype of GAR. Despite the close phylogenetic relationships of these species, our chromosome painting studies demonstrate an extensive reorganization of their karyotypes.

Trogons are forest birds with a wide distribution, being found in Africa, Asia, and America, and are included in the order Trogoniformes, family Trogonidae. Phylogenetic studies using molecular data have not been able to determine the phylogenetic relationship among the different genera of trogons. So far, no cytogenetic data for these birds exist. Hence, the aim of this study was to characterize the karyotype of Trogon surrucura surrucura by means of classical and molecular cytogenetics. We found a diploid chromosome number of 2n = 82, similar to most birds, with several derived features compared to chicken and the putative ancestral avian karyotype. T. s. surrucura showed 3 pairs of microchromosomes bearing 18S rDNA clusters. The Z and W sex chromosomes were of similar size but could readily be identified by morphological differences. Using chromosome painting with whole chromosome probes from Gallus gallus and Leucopternis albicollis, we found that the chromosomes homologous to chicken chromosomes 2 and 5 correspond to 2 different pairs in T. s. surrucura and L. albicollis, due to the occurrence of centric fissions. Paracentric inversions were detected in the segment homologous to chicken chromosome 1q, and we confirmed the recurrence of breakpoints when our results were compared to other species of birds already analyzed by FISH or by in silico genome assembly.

The Coscoroba (Coscoroba coscoroba), endemic to southern South America, is traditionally considered as an early branch from the common ancestor leading to true geese and swans. Recently, an interesting association between the Coscoroba and Cape Barren goose (Cereopsis novaehollandiae) as sister groups has been proposed. We present here the characterization of the karyotype of C. coscoroba using whole chromosome probes derived from Gallus gallus macrochromosomes. Our data showed that C. coscoroba has the highest diploid number among Anseriformes (2n = 98), and the conservation of macrochromosome pairs 1–10 indicates that the increase in diploid number has occurred by fission events involving only the microchromosomes. Moreover, the similarity between the diploid numbers of C. coscoroba (2n = 98) and Cereopsis novaehollandiae (2n = 92) reinforces the phylogenetic position of these two species as sister groups, considering that other species of geese and swans have diploid numbers close to 2n = 80. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 274–279.

Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here, we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multiordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 17 MSY genes, most being constrained by negative selection for nearly 100 million years. The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved noncoding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.

Background B chromosomes are dispensable and variable karyotypic elements found in some species of animals, plants and fungi. They often originate from duplications and translocations of host genomic regions or result from hybridization. In most species, little is known about their DNA content. Here we perform high-throughput sequencing and analysis of B chromosomes of roe deer and brocket deer, the only representatives of Cetartiodactyla known to have B chromosomes. Results In this study we developed an approach to identify genomic regions present on chromosomes by high-throughput sequencing of DNA generated from flow-sorted chromosomes using degenerate-oligonucleotide-primed PCR. Application of this method on small cattle autosomes revealed a previously described KIT gene region translocation associated with colour sidedness. Implementing this approach to B chromosomes from two cervid species, Siberian roe deer (Capreolus pygargus) and grey brocket deer (Mazama gouazoubira), revealed dramatically different genetic content: roe deer B chromosomes consisted of two duplicated genomic regions (a total of 1.42-1.98 Mbp) involving three genes, while grey brocket deer B chromosomes contained 26 duplicated regions (a total of 8.28-9.31 Mbp) with 34 complete and 21 partial genes, including KIT and RET protooncogenes, previously found on supernumerary chromosomes in canids. Sequence variation analysis of roe deer B chromosomes revealed a high frequency of mutations and increased heterozygosity due to either amplification within B chromosomes or divergence between different Bs. In contrast, grey brocket deer B chromosomes were found to be more homogeneous and resembled autosomes in patterns of sequence variation. Similar tendencies were observed in repetitive DNA composition. Conclusions Our data demonstrate independent origins of B chromosomes in the grey brocket and roe deer. We hypothesize that the B chromosomes of these two cervid species represent different stages of B chromosome sequences evolution: probably nascent and similar to autosomal copies in brocket deer, highly derived in roe deer. Based on the presence of the same orthologous protooncogenes in canids and brocket deer Bs we argue that genomic regions involved in B chromosome formation are not random. In addition, our approach is also applicable to the characterization of other evolutionary and clinical rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2933-6) contains supplementary material, which is available to authorized users.

Squamate reptiles show a striking diversity in modes of sex determination, including both genetic (XY or ZW) and temperature-dependent sex determination systems. The genomes of only a handful of species have been sequenced, analyzed and assembled including the genome of Anolis carolinensis. Despite a high genome coverage, only macrochromosomes of A. carolinensis were assembled whereas the content of most microchromosomes remained unclear. Most of the Anolis species have homomorphic XY sex chromosome system. However, some species have large heteromorphic XY chromosomes (e.g., A. sagrei) and even multiple sex chromosomes systems (e.g. A. pogus), that were shown to be derived from fusions of the ancestral XY with microautosomes. We applied next generation sequencing of flow sorting-derived chromosome-specific DNA pools to characterize the content and composition of microchromosomes in A. carolinensis and A. sagrei. Comparative analysis of sequenced chromosome-specific DNA pools revealed that the A. sagrei XY sex chromosomes contain regions homologous to several microautosomes of A. carolinensis. We suggest that the sex chromosomes of A. sagrei are derived by fusions of the ancestral sex chromosome with three microautosomes and subsequent loss of some genetic content on the Y chromosome.