Liehr T, Mrasek K, Kosyakova N, Ogilvie CM, Vermeesch J, Trifonov V, et al. Small supernumerary marker chromosomes (sSMC) in humans; are there B chromosomes hidden among them. Mol Cytogenet. 2008;1:12.
Article
PubMed
PubMed Central
Google Scholar
Balaban-Malenbaum G, Gilbert F. Double minute chromosomes and the homogeneously staining regions in chromosomes of a human neuroblastoma cell line. Science. 1977;198:739–41.
Article
CAS
PubMed
Google Scholar
Camacho JPM, Sharbel TF, Beukeboom LW. B-chromosome evolution. Philos Trans R Soc Lond B Biol Sci. 2000;355:163–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Graphodatsky AS, Kukekova AV, Yudkin DV, Trifonov VA, Vorobieva NV, Beklemisheva VR, et al. The proto-oncogene C-KIT maps to canid B-chromosomes. Chromosome Res. 2005;13:113–22.
Article
CAS
PubMed
Google Scholar
Yudkin DV, Trifonov VA, Kukekova AV, Vorobieva NV, Rubtsova NV, Yang F, et al. Mapping of KIT adjacent sequences on canid autosomes and B chromosomes. Cytogenet Genome Res. 2007;116:100–3.
Article
CAS
PubMed
Google Scholar
Duke Becker SE, Thomas R, Trifonov VA, Wayne RK, Graphodatsky AS, Breen M. Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. Chromosome Res. 2011;19:685–708.
Article
CAS
Google Scholar
Trifonov VA, Dementyeva PV, Larkin DM, O’Brien PC, Perelman PL, Yang F, et al. Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus). BMC Biol. 2013;11:1–11.
Article
Google Scholar
Banaei-Moghaddam AM, Martis MM, Macas J, Gundlach H, Himmelbach A, Altschmied L, et al. Genes on B chromosomes: old questions revisited with new tools. Biochim Biophys Acta. 1849;2015:64–70.
Google Scholar
Makunin AI, Dementyeva PV, Graphodatsky AS, Volobouev VT, Kukekova AV, Trifonov VA. Genes on B chromosomes of vertebrates. Mol Cytogenet. 2014;7:99.
Article
PubMed
PubMed Central
Google Scholar
Neitzel H. Chromosome evolution of Cervidae: karyotypic and molecular aspects. In: Obe G, Basler A, editors. Cytogenetics - Basic and applied aspects. Berlin Heidelberg New York: Springer; 1987. p. 90–112.
Google Scholar
Duarte JMB, Jorge W. Chromosomal polymorphism in several populations of deer (genus Mazama) from Brazil. Arch Zootec. 1996;45:281–7.
Google Scholar
Abril VV, Duarte JMB. Chromosome polymorphism in the Brazilian dwarf brocket deer, Mazama nana (Mammalia, Cervidae). Genet Mol Biol. 2008;31:53–7.
Article
Google Scholar
Duarte JMB, Jorge W. Morphologic and cytogenetic description of the small red brocket (Mazama bororo Duarte, 1996) in Brazil. Mammalia. 2003;67:403–10.
Article
Google Scholar
Fiorillo BF, Sarria-Perea JA, Abril VV, Duarte JMB. Cytogenetic description of the Amazonian brown brocket Mazama nemorivaga (Artiodactyla, Cervidae). Comp Cytogenet. 2013;7:25.
Article
PubMed
PubMed Central
Google Scholar
Sokolov VE, Prikhod’ko VI. [Taxonomy of the musk deer (Artiodactyla, Mammalia)]. Izv Akad Nauk Seriia Biol Akad Nauk. 1998;1:37–46.
Google Scholar
Valente GT, Conte MA, Fantinatti BEA, Cabral-de-Mello DC, Carvalho RF, Vicari MR, et al. Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses. Mol Biol Evol. 2014;31:2061–72.
Article
CAS
PubMed
Google Scholar
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry. Nature. 2008;456:53–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Telenius H, Carter NP, Bebb CE, Nordenskjo¨ld M, Ponder BAJ, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer. Genomics. 1992;13:718–25.
Article
CAS
PubMed
Google Scholar
Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics. 2012;13:178.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Bourcy CFA, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR. A quantitative comparison of single-cell whole genome amplification methods. PLoS One. 2014;9:e105585.
Article
PubMed
PubMed Central
Google Scholar
Martis MM, Klemme S, Banaei-Moghaddam AM, Blattner FR, Macas J, Schmutzer T, et al. Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc Natl Acad Sci. 2012;109:13343–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, et al. High-throughput sequencing of microdissected chromosomal regions. Eur J Hum Genet EJHG. 2010;18:457–62.
Article
PubMed
Google Scholar
Graphodatsky AS, Yang F, O’Brien PCM, Serdukova N, Milne BS, Trifonov V, et al. A comparative chromosome map of the Arctic fox, red fox and dog defined by chromosome painting and high resolution G-banding. Chromosome Res. 2000;8:253–63.
Article
CAS
PubMed
Google Scholar
Durkin K, Coppieters W, Drögemüller C, Ahariz N, Cambisano N, Druet T, et al. Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature. 2012;482:81–4.
Article
CAS
PubMed
Google Scholar
Sokolov VE, Orlov VN, Chudinovskaya GA, Danilkin AA. Chromosomal differences between two roe subspecies (Capreolus capreolus L. and Capreolus capreolus pygargus Pall.). Zoologicheskii Zhurnal. 1978;57:1109–1112.
Yang F, O’Brien PCM, Wienberg J, Neitzel H, Lin CC, Ferguson-Smith MA. Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi). Chromosoma. 1997;106:37–43.
Article
CAS
PubMed
Google Scholar
Dementyeva PV, Trifonov VA, Kulemzina AI, Graphodatsky AS. Reconstruction of the putative Cervidae ancestral karyotype by chromosome painting of Siberian roe deer (Capreolus pygargus) with dromedary probes. Cytogenet Genome Res. 2010;128:228–35.
Article
CAS
PubMed
Google Scholar
Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014;46:858–65.
Article
CAS
PubMed
Google Scholar
Kawahara-Miki R, Tsuda K, Shiwa Y, Arai-Kichise Y, Matsumoto T, Kanesaki Y, et al. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics. 2011;12:103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kropatsch R, Dekomien G, Akkad DA, Gerding WM, Petrasch-Parwez E, Young ND, et al. SOX9 Duplication Linked to Intersex in Deer. PLoS One. 2013;8:e73734.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danilkin AA, Hewison AM. Behavioural ecology of Siberian and European roe deer. London: Chapman & Hall; 1996.
Google Scholar
Matosiuk M, Borkowska A, Świsłocka M, Mirski P, Borowski Z, Krysiuk K, et al. Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer. Mol Ecol. 2014;23:2559–72.
Article
CAS
PubMed
Google Scholar
Olano-Marin J, Plis K, Sönnichsen L, Borowik T, Niedziałkowska M, Jędrzejewska B. Weak Population Structure in European Roe Deer (Capreolus capreolus) and Evidence of Introgressive Hybridization with Siberian Roe Deer (C. pygargus) in Northeastern Poland. PLoS One. 2014;9:e109147.
Article
PubMed
PubMed Central
Google Scholar
Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013;29:792–3.
Article
PubMed
Google Scholar
Novák P, Neumann P, Macas J. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics. 2010;11:378.
Article
PubMed
PubMed Central
Google Scholar
Ferguson-Smith MA. Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications. Eur J Hum Genet EJHG. 1997;5:253–65.
CAS
PubMed
Google Scholar
Graphodatsky AS, Trifonov VA, Stanyon R. The genome diversity and karyotype evolution of mammals. Mol Cytogenet. 2011;4:22.
Article
PubMed
PubMed Central
Google Scholar
Veltman IM, Veltman JA, Arkesteijn G, Janssen IM, Vissers LE, de Jong PJ, et al. Chromosomal breakpoint mapping by arrayCGH using flow-sorted chromosomes. Biotechniques. 2003;35:1066–70.
CAS
PubMed
Google Scholar
Gribble SM, Kalaitzopoulos D, Burford DC, Prigmore E, Selzer RR, Ng BL, et al. Ultra-high resolution array painting facilitates breakpoint sequencing. J Med Genet. 2007;44:51–8.
Article
CAS
PubMed
Google Scholar
Collard JG, Philippus E, Tulp A, Lebo RV, Gray JW. Separation and analysis of human chromosomes by combined velocity sedimentation and flow sorting applying single-and dual-laser flow cytometry. Cytometry. 1984;5:9–19.
Article
CAS
PubMed
Google Scholar
Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, et al. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol. 2009;10:R112.
Article
PubMed
PubMed Central
Google Scholar
Brinkrolf K, Rupp O, Laux H, Kollin F, Ernst W, Linke B, et al. Chinese hamster genome sequenced from sorted chromosomes. Nat Biotechnol. 2013;31:694–5.
Article
CAS
PubMed
Google Scholar
Puritz JB, Matz MV, Toonen RJ, Weber JN, Bolnick DI, Bird CE. Demystifying the RAD fad. Mol Ecol. 2014;23:5937–42.
Article
CAS
PubMed
Google Scholar
Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, et al. Mapping translocation breakpoints by next-generation sequencing. Genome Res. 2008;18:1143–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H, et al. Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Eur J Hum Genet. 2010;18:539–43.
Article
CAS
PubMed
Google Scholar
Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishiguro S, et al. Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science. 1998;279:577–80.
Article
CAS
PubMed
Google Scholar
Sihto H, Sarlomo-Rikala M, Tynninen O, Tanner M, Andersson LC, Franssila K, et al. KIT and platelet-derived growth factor receptor alpha tyrosine kinase gene mutations and KIT amplifications in human solid tumors. J Clin Oncol. 2005;23:49–57.
Article
CAS
PubMed
Google Scholar
Johnson JL, Kozysa A, Kharlamova AV, Gulevich RG, Perelman PL, Fong HWF, et al. Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT. Anim Genet. 2015;46:190–9.
Article
CAS
PubMed
Google Scholar
Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007;7:233–45.
Article
CAS
PubMed
Google Scholar
Liu Z. The role of PI3K p110alpha and p110beta isoforms in oncogenesis. Harvard University; 2007
Kumar A, Fernandez-Capetillo O, Carrera AC. Nuclear phosphoinositide 3-kinase β controls double-strand break DNA repair. Proc Natl Acad Sci. 2010;107:7491–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salaverria I, Royo C, Carvajal-Cuenca A, Clot G, Navarro A, Valera A, et al. CCND2 rearrangements are the most frequent genetic events in cyclin D1-mantle cell lymphoma. Blood. 2013;121:1394–402.
Article
CAS
PubMed
PubMed Central
Google Scholar
Both J, Krijgsman O, Bras J, Schaap GR, Baas F, Ylstra B, et al. Focal chromosomal copy number aberrations identify CMTM8 and GPR177 as new candidate driver genes in osteosarcoma. PLoS One. 2014;9:e115835.
Article
PubMed
PubMed Central
Google Scholar
Lockwood WW, Chari R, Coe BP, Girard L, Macaulay C, Lam S, et al. DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene. 2008;27:4615–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res. 2009;19:770–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gilbert C, Ropiquet A, Hassanin A. Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): systematics, morphology, and biogeography. Mol Phylogenet Evol. 2006;40:101–17.
Article
CAS
PubMed
Google Scholar
Duarte JMB, González S, Maldonado JE. The surprising evolutionary history of South American deer. Mol Phylogenet Evol. 2008;49:17–22.
Article
CAS
PubMed
Google Scholar
Graphodatsky AS, Sharshov AA, Shutov VV. [Karyotypic relations of Cervidae]. Zool. Zhurnal. 1990;69:101–14.
Google Scholar
Randi E, Pierpaoli M, Danilkin A. Mitochondrial DNA polymorphism in populations of Siberian and European roe deer (Capreolus pygargus and C. capreolus). Heredity. 1998;80:429–37.
Article
CAS
PubMed
Google Scholar
Trifonov VA, Dementyeva PV, Beklemisheva VR, Yudkin DV, Vorobieva NV, Graphodatsky AS. Supernumerary chromosomes, segmental duplications, and evolution. Russ J Genet. 2010;46:1094–6.
Article
CAS
Google Scholar
Yang F, O’Brien PCM, Milne BS, Graphodatsky AS, Solanky N, Trifonov V, et al. A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps. Genomics. 1999;62:189–202.
Article
CAS
PubMed
Google Scholar
Yang F, Trifonov V, Ng BL, Kosyakova N, Carter NP. Generation of paint probes by flow-sorted and microdissected chromosomes. Fluoresc. Situ Hybrid. FISH—Application Guide. Springer; 2009. p. 35–52.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17:10–2.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinforma Oxf Engl. 2010;26:841–2.
Article
CAS
Google Scholar
Seshan VE, Olsen A. DNAcopy: DNA copy number data analysis. R package version 1.24.0. 2011. http://www.Bioconductor.org/packages/release/bioc/html/DNAcopy.html.
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
Article
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1–13.
Article
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC genome browser database: 2014 update. Nucleic Acids Res. 2014;42:D764–70.
Article
CAS
PubMed
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv Prepr. ArXiv13033997 [Internet]. 2013 [cited 2015 May 27]; Available from: http://arxiv.org/abs/1303.3997