Genomes and Genes
Summary: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.
- Pieczarka J, Nagamachi C, O Brien P, Yang F, Rens W, Barros R, et al. Reciprocal chromosome painting between two South American bats: Carollia brevicauda and Phyllostomus hastatus (Phyllostomidae, Chiroptera). Chromosome Res. 2005;13:339-47 pubmed..The use of chromosome painting is a modern way of genomic comparison on the cytological level, and will clarify the intense intergenus ..
- Neusser M, Munch M, Anzenberger G, Muller S. Investigation of marmoset hybrids (Cebuella pygmaea x Callithrix jacchus) and related Callitrichinae (Platyrrhini) by cross-species chromosome painting and comparative genomic hybridization. Cytogenet Genome Res. 2005;108:191-6 pubmed..We analyzed their karyotypes by multi-directional chromosome painting employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes...
- Vicari M, de Mello Pistune H, Castro J, de Almeida M, Bertollo L, Moreira Filho O, et al. New insights on the origin of B chromosomes in Astyanax scabripinnis obtained by chromosome painting and FISH. Genetica. 2011;139:1073-81 pubmed publisherb>Chromosome painting (CP) with a probe of B chromosome obtained by microdissection and fluorescence in situ hybridization (FISH) with probes of As51 satellite DNA, C( o )t-1 DNA, and 18S ..
- Mao X, Nie W, Wang J, Su W, Feng Q, Wang Y, et al. Comparative cytogenetics of bats (Chiroptera): the prevalence of Robertsonian translocations limits the power of chromosomal characters in resolving interfamily phylogenetic relationships. Chromosome Res. 2008;16:155-70 pubmed publisher..Here, the representatives of families Megadermatidae and Emballonuridae are studied by comparative chromosome painting for the first time...
- Kato A, Lamb J, Birchler J. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A. 2004;101:13554-9 pubmed..The same probe mixture identifies meiotic pachytene, late prophase I, and metaphase I chromosomes. The procedure could facilitate the study of chromosomal structure and behavior and be adapted for other plant species. ..
- Switonski M, Andersson M, Nowacka Woszuk J, Szczerbal I, Sosnowski J, Kopp C, et al. Identification of a new reciprocal translocation in an AI bull by synaptonemal complex analysis, followed by chromosome painting. Cytogenet Genome Res. 2008;121:245-8 pubmed publisher..No association between the tetravalent and XY bivalent was observed. Chromosome painting, with the use of bovine whole chromosome painting probes, conjugated with DAPI staining, facilitated a ..
- Robinson T, Ruiz Herrera A. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data. Chromosome Res. 2008;16:1133-41 pubmed publisher..Our analyses clarify the distinction between shared-ancestral and shared-derived homology in the eutherian ancestral karyotype. ..
- Diniz D, Laudicina A, Cioffi M, Bertollo L. Microdissection and whole chromosome painting. Improving sex chromosome analysis in Triportheus (Teleostei, Characiformes). Cytogenet Genome Res. 2008;122:163-8 pubmed publisher..This probe was used for WCP (whole chromosome painting) through fluorescent in situ hybridization (FISH) in several other Triportheus species, to analyze the ..
- Romanenko S, Sitnikova N, Serdukova N, Perelman P, Rubtsova N, Bakloushinskaya I, et al. Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). II. The genome homology of two mole voles (genus Ellobius), the field vole and golden hamster revealed by comparative chromosome painting. Chromosome Res. 2007;15:891-7 pubmedUsing cross-species chromosome painting, we have carried out a comprehensive comparison of the karyotypes of two Ellobius species with unusual sex determination systems: the Transcaucasian mole vole, Ellobius lutescens (2n = 17, X in ..
- Stanyon R, Yang F, Morescalchi A, Galleni L. Chromosome painting in the long-tailed field mouse provides insights into the ancestral murid karyotype. Cytogenet Genome Res. 2004;105:406-11 pubmed..It would be desirable to have a richer phylogenetic array of species before any final conclusions are drawn about the Muridae ancestral karyotype. The ancestral karyotype presented here should be considered as a working hypothesis. ..
- Ventura K, O Brien P, Yonenaga Yassuda Y, Ferguson Smith M. 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 Res. 2009;17:1063-78 pubmed publisher..Hence, comparative chromosome painting has become the method of choice for genome comparisons at the cytogenetic level since it allows complete ..
- MacQueen A, Phillips C, Bhalla N, Weiser P, Villeneuve A, Dernburg A. Chromosome sites play dual roles to establish homologous synapsis during meiosis in C. elegans. Cell. 2005;123:1037-50 pubmed..We speculate that concentration of these activities at one region per chromosome may have coevolved with the loss of a point centromere to safeguard karyotype stability. ..
- Stephens P, Greenman C, Fu B, Yang F, Bignell G, Mudie L, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011;144:27-40 pubmed publisher..We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer. ..
- Gerbault Serreau M, Bonnet Garnier A, Richard F, Dutrillaux B. Chromosome painting comparison of Leontopithecus chrysomelas (Callitrichine, Platyrrhini) with man and its phylogenetic position. Chromosome Res. 2004;12:691-701 pubmed..Six chromosomal rearrangements would have occurred during the period of this network evolution. Finally, the karyotype of the last common ancestor to all Callitrichines has been reconstructed. It possessed 48 chromosomes. ..
- Nie W, Wang J, Su W, Wang Y, Yang F. Chromosomal rearrangements underlying karyotype differences between Chinese pangolin (Manis pentadactyla) and Malayan pangolin (Manis javanica) revealed by chromosome painting. Chromosome Res. 2009;17:321-9 pubmed publisher..pentadactyla, was established by chromosome painting for the first time...
- Giovannotti M, Caputo V, O Brien P, Lovell F, Trifonov V, Cerioni P, et al. Skinks (Reptilia: Scincidae) have highly conserved karyotypes as revealed by chromosome painting. Cytogenet Genome Res. 2009;127:224-31 pubmed publisher..In this study cross-species chromosome painting using Scincus scincus (2n = 32) as the source genome, was used to detect the chromosomal rearrangements and ..
- Noronha R, Nagamachi C, O Brien P, Ferguson Smith M, Pieczarka J. Meiotic analysis of XX/XY and neo-XX/XY sex chromosomes in Phyllostomidae by cross-species chromosome painting revealing a common chromosome 15-XY rearrangement in Stenodermatinae. Chromosome Res. 2010;18:667-76 pubmed publisher..The tail corresponds to the pairing of the 15 P. hastatus autosomal bivalent, which are translocated to the sex chromosomes. Probably the non-pairing is responsible for the meiotic silencing of these segments. ..
- Ye J, Nie W, Wang J, Su W, Jing M, Graphodatsky A, et al. Genome-wide comparative chromosome map between human and the Forrest's pika (Ochotona forresti) established by cross-species chromosome painting: further support for the Glires hypothesis. Cytogenet Genome Res. 2011;132:41-6 pubmed publisher..chromosomal homologies between human and the Forrest's pika (Ochotona forresti, 2n = 54) by cross-species chromosome painting. Integration of our map with the published comparative chromosome map between human and rabbit has enabled ..
- Rab P, Rábová M, Pereira C, Collares Pereira M, Pelikánová S. Chromosome studies of European cyprinid fishes: interspecific homology of leuciscine cytotaxonomic marker-the largest subtelocentric chromosome pair as revealed by cross-species painting. Chromosome Res. 2008;16:863-73 pubmed publisher..The probe consistently hybridized to the distal part of the short arm of the marker chromosome, indicating sequence homology. ..
- Volleth M, Yang F, Muller S. High-resolution chromosome painting reveals the first genetic signature for the chiropteran suborder Pteropodiformes (Mammalia: Chiroptera). Chromosome Res. 2011;19:507-19 pubmed publisher..now, the composition of synteny-conserved segments in chiropteran karyotypes was studied by cross-species chromosome painting with probes derived from whole human (HSA) or chiropteran chromosomes only...
- Nie W, Wang J, Su W, Wang D, Tanomtong A, Perelman P, et al. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting. Heredity (Edinb). 2012;108:17-27 pubmed publisherChromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in ..
- Pieczarka J, Gomes A, Nagamachi C, Rocha D, Rissino J, O Brien P, et al. A phylogenetic analysis using multidirectional chromosome painting of three species (Uroderma magnirostrum, U. bilobatum and Artibeus obscurus) of subfamily Stenodermatinae (Chiroptera-Phyllostomidae). Chromosome Res. 2013;21:383-92 pubmed publisher..The genome-wide comparative maps based on chromosome painting and chromosome banding reveal the chromosome forms that characterize each taxonomic level within the ..
- Wallis M, Delbridge M, Pask A, Alsop A, Grutzner F, O Brien P, et al. Mapping platypus SOX genes; autosomal location of SOX9 excludes it from sex determining role. Cytogenet Genome Res. 2007;116:232-4 pubmed..The autosomal localization of platypus SOX9 in this study contradicts the hypothesis that SOX9 acts as the sex determining switch in platypus. ..
- Biltueva L, Yang F, Vorobieva N, Graphodatsky A. Comparative map between the domestic pig and dog. Mamm Genome. 2004;15:809-18 pubmedCross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig...
- Darai Ramqvist E, Díaz de Ståhl T, Sandlund A, Mantripragada K, Klein G, Dumanski J, et al. Array-CGH and multipoint FISH to decode complex chromosomal rearrangements. BMC Genomics. 2006;7:330 pubmed..Although our chr3 BAC/PAC array could identify single copy number changes even in pentaploid cells, mpFISH provided a more accurate analysis in the dissection of complex karyotypes at high ploidy levels. ..
- Rens W, O Brien P, Grützner F, Clarke O, Graphodatskaya D, Tsend Ayush E, et al. The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biol. 2007;8:R243 pubmed..In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping.
- Szinay D, Bai Y, Visser R, de Jong H. FISH applications for genomics and plant breeding strategies in tomato and other solanaceous crops. Cytogenet Genome Res. 2010;129:199-210 pubmed publisher..In the next steps in comparative genomics, we now can detect smaller chromosomal and DNA rearrangements, diminutions and amplifications of repeats and changes of the epigenetic status of introgressed regions. ..
- Bosma A, de Haan N, Arkesteijn G, Yang F, Yerle M, Zijlstra C. Comparative chromosome painting between the domestic pig (Sus scrofa) and two species of peccary, the collared peccary (Tayassu tajacu) and the white-lipped peccary (T. pecari): a phylogenetic perspective. Cytogenet Genome Res. 2004;105:115-21 pubmed..Cross-species chromosome painting was performed between the domestic pig (Sus scrofa; 2n = 38), a representative of the Suidae, and two ..
- Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol. 2013;30:1454-64 pubmed publisher..Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome ..
- Ferguson Smith M, Yang F, Rens W, O Brien P. The impact of chromosome sorting and painting on the comparative analysis of primate genomes. Cytogenet Genome Res. 2005;108:112-21 pubmed..We review here the contributions that this technology has made to the analysis of primate genomes. ..
- Kato A, Lamb J, Albert P, Danilova T, Han F, Gao Z, et al. Chromosome painting for plant biotechnology. Methods Mol Biol. 2011;701:67-96 pubmed publisher..This chapter details the labeling procedures and chromosome preparation techniques used to produce high-quality FISH signals on somatic metaphase and meiotic pachytene spreads. ..
- Adamovic T, Trossö F, Roshani L, Andersson L, Petersen G, Rajaei S, et al. Oncogene amplification in the proximal part of chromosome 6 in rat endometrial adenocarcinoma as revealed by combined BAC/PAC FISH, chromosome painting, zoo-FISH, and allelotyping. Genes Chromosomes Cancer. 2005;44:139-53 pubmed..We applied rat and mouse chromosome painting probes onto tumor cell metaphase preparations in order to detect and characterize gross RNO6 aberrations...
- Pampalona J, Soler D, Genesca A, Tusell L. Telomere dysfunction and chromosome structure modulate the contribution of individual chromosomes in abnormal nuclear morphologies. Mutat Res. 2010;683:16-22 pubmed publisher..Few micronuclei emerged in this cell system thus validating the scoring of nucleoplasmic bridges and nuclear buds for measuring chromosome instability in telomere-dysfunction cell environments...
- Howarth K, Blood K, Ng B, Beavis J, Chua Y, Cooke S, et al. Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene. 2008;27:3345-59 pubmed..Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer. ..
- Kellogg M, Burkett S, Dennis T, Stone G, Gray B, McGuire P, et al. Chromosome painting in the manatee supports Afrotheria and Paenungulata. BMC Evol Biol. 2007;7:6 pubmed..Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee.
- Adega F, Chaves R, Kofler A, Krausman P, Masabanda J, Wienberg J, et al. High-resolution comparative chromosome painting in the Arizona collared peccary (Pecari tajacu, Tayassuidae): a comparison with the karyotype of pig and sheep. Chromosome Res. 2006;14:243-51 pubmedWe used chromosome painting with chromosome-specific probes derived from domestic sheep and pig for a high-resolution cytogenetic comparison with the karyotype of collared peccary (Pecari tajacu sonoriensis)...
- Kulemzina A, Yang F, Trifonov V, Ryder O, Ferguson Smith M, Graphodatsky A. Chromosome painting in Tragulidae facilitates the reconstruction of Ruminantia ancestral karyotype. Chromosome Res. 2011;19:531-9 pubmed publisher..the first genome-wide comparative map of the Java mouse deer (Tragulus javanicus, Tragulidae) revealed by chromosome painting with human and dromedary probes...
- Thalhammer S, Langer S, Speicher M, Heckl W, Geigl J. Generation of chromosome painting probes from single chromosomes by laser microdissection and linker-adaptor PCR. Chromosome Res. 2004;12:337-43 pubmed..Furthermore, the capability of these probes to detect even small translocations (<3 Mb) suggests that the dissected regions are completely represented in the generated painting probes. ..
- Chaves R, Frönicke L, Guedes Pinto H, Wienberg J. Multidirectional chromosome painting between the Hirola antelope (Damaliscus hunteri, Alcelaphini, Bovidae), sheep and human. Chromosome Res. 2004;12:495-503 pubmed..antelope ( Damaliscus hunteri ) derived by flow sorting of chromosomes were used in multi directional chromosome painting experiments to better define the karyological relationship within Bovidae species (specifically, Caprini ..
- Pokorná M, Giovannotti M, Kratochvíl L, Caputo V, Olmo E, Ferguson Smith M, et al. Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting. Chromosoma. 2012;121:409-18 pubmed publisher..In this project, we used comparative chromosome painting to determine how widely this synteny is conserved across nine families covering most of the main lineages ..
- de Oliveira E, de Moura S, dos Anjos L, Nagamachi C, Pieczarka J, O Brien P, et al. Comparative chromosome painting between chicken and spectacled owl (Pulsatrix perspicillata): implications for chromosomal evolution in the Strigidae (Aves, Strigiformes). Cytogenet Genome Res. 2008;122:157-62 pubmed publisher..to define homologies between Gallus gallus and Pulsatrixperspicillata (Strigiformes, Strigidae), we used chromosome painting with chicken DNA probes of chromosomes 1-10 and Z and telomeric sequences...
- Badenhorst D, Dobigny G, Adega F, Chaves R, O Brien P, Ferguson Smith M, et al. Chromosomal evolution in Rattini (Muridae, Rodentia). Chromosome Res. 2011;19:709-27 pubmed publisher..Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ..
- Lysak M, Koch M, Pecinka A, Schubert I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 2005;15:516-25 pubmed..The presumed hexaploidization event occurred after the Arabidopsis-Brassiceae split, between 7.9 and 14.6 Mya. ..
- Gilbert C, O Brien P, Bronner G, Yang F, Hassanin A, Ferguson Smith M, et al. Chromosome painting and molecular dating indicate a low rate of chromosomal evolution in golden moles (Mammalia, Chrysochloridae). Chromosome Res. 2006;14:793-803 pubmed..Using G-banding and chromosome painting we provide a comprehensive comparison of the karyotypes of five species representing five of the nine ..
- Teruel M, Cabrero J, Montiel E, Acosta M, Sanchez A, Camacho J. Microdissection and chromosome painting of X and B chromosomes in Locusta migratoria. Chromosome Res. 2009;17:11-8 pubmed publisher..microdissection of the B and X chromosomes, DNA amplification by one (B) or two (X) different methods, and chromosome painting. The results showed that B chromosomes share at least two types of repetitive DNA sequences with the A ..
- Kim M, Kim S, Kim H, Hoang I, Oh W, Koh J, et al. Characterization of the TSU-PR1 cell line by chromosome painting and flow cytometry. Cancer Genet Cytogenet. 2005;163:17-22 pubmed..These numbers are also in accordance with the chromosome copy numbers determined with FISH: 2.98 +/- 0.23, 2.91 +/- 0.44, 2.74 +/- 0.44, 3.93 +/- 0.38, and 5.05 +/- 0.78 for chromosomes 4, 6, 7, 17, and 20, respectively (P > 0.05). ..
- Nie W, O Brien P, Ng B, Fu B, Volobouev V, Carter N, et al. 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 Res. 2009;17:99-113 pubmed publisher..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...
- Lysak M, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci U S A. 2006;103:5224-9 pubmed..chromosome complements can be resolved by genome sequencing, comparative genetic mapping, and comparative chromosome painting. Previously, comparison of genetic maps and gene-based phylogenies suggested that the karyotypes of ..
- Yang F, Graphodatsky A, Li T, Fu B, Dobigny G, Wang J, et al. Comparative genome maps of the pangolin, hedgehog, sloth, anteater and human revealed by cross-species chromosome painting: further insight into the ancestral karyotype and genome evolution of eutherian mammals. Chromosome Res. 2006;14:283-96 pubmedTo better understand the evolution of genome organization of eutherian mammals, comparative maps based on chromosome painting have been constructed between human and representative species of three eutherian orders: Xenarthra, Pholidota, ..
- Ruiz Herrera A, Garcia F, Aguilera M, Garcia M, Ponsà Fontanals M. Comparative chromosome painting in Aotus reveals a highly derived evolution. Am J Primatol. 2005;65:73-85 pubmed..The homologies between these two Aotus KMs and human chromosomes were established, indicating that KM3 has a more derived karyotype than KM9 with respect to the ancestral Platyrrhini karyotype. ..
- Nie W. Molecular cytogenetic studies in strepsirrhine primates, Dermoptera and Scandentia. Cytogenet Genome Res. 2012;137:246-58 pubmed publisherSince the first chromosome painting study between human and strepsirrhine primates was performed in 1996, nearly 30 species in Strepsirrhini, Dermoptera and Scandentia have been analyzed by cross-species chromosome painting...
- Nie W, O Brien P, Fu B, Wang J, Su W, Ferguson Smith M, et al. Chromosome painting between human and lorisiform prosimians: evidence for the HSA 7/16 synteny in the primate ancestral karyotype. Am J Phys Anthropol. 2006;129:250-9 pubmedMultidirectional chromosome painting with probes derived from flow-sorted chromosomes of humans (Homo sapiens, HSA, 2n = 46) and galagos (Galago moholi, GMO, 2n = 38) allowed us to map evolutionarily conserved chromosomal segments among ..
- Pardini A, O Brien P, Fu B, Bonde R, Elder F, Ferguson Smith M, et al. Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria. Proc Biol Sci. 2007;274:1333-40 pubmed..Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), ..