Longley AE. Supernumerary chromosomes in Zea mays. J Agric Res. 1927;35:769–84.
Google Scholar
Ahmad S, Martins C. The modern view of B chromosomes under the impact of high scale omics analyses. Cells. 2019;8:156.
PubMed Central
CAS
Google Scholar
Wilson EB. Studies on chromosomes. V. the chromosomes of metapodius. A contribution to the hypothesis of the genetic continuity of chromosomes. J Exp Zool. 1909;6:147–205.
Google Scholar
Camacho JPM. B chromosomes. In: Gregory TR, editor. The evolution of the genome; 2005. p. 223–86.
Google Scholar
D’Ambrosio U, Alonso-Lifante MP, Barros K, Kovařík A, Mas de Xaxars G, Garcia S. B-chrom: A database on B-chromosomes of plants, animals and fungi. New Phytol. 2017;216:635–42.
PubMed
Google Scholar
Jones RN, Rees H. B chromosomes. London: Academic; 1982.
Randolph LF. Genetic characteristics of the B chromosomes in maize. Genetics. 1941;26:608–31.
Nur U, Werren JH, Eickbush DG, Burke WD, Eickbush TH. A “selfish” B chromosome that enhances its transmission by eliminating the paternal genome. Science. 1988;240:512–4.
PubMed
CAS
Google Scholar
Leach CR, Houben A, Field B, Pistrick K, Demidov D, Timmis JN. Molecular evidence for transcription of genes on a B chromosome in Crepis capillaris. Genetics. 2005;171:269–78.
PubMed
PubMed Central
CAS
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. Chromosom Res. 2005;13:113–22.
CAS
Google Scholar
Ruiz-Estévez M, López-León MD, Cabrero J, Camacho JP. B-chromosome ribosomal DNA is functional in the grasshopper Eyprepocnemis plorans. PLoS One. 2012;7:e36600.
PubMed
PubMed Central
Google Scholar
Trifonov VA, Dementyeva PV, Larkin DM, O’Brien PCM, 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;11:90.
PubMed
PubMed Central
Google Scholar
Mestriner CA, Galetti PM, Valentini SR, Ruiz IRG, Abel LDS, Moreira-Filho O, et al. Structural and functional evidence that a B chromosome in the characid fish Astyanax scabripinnis is an isochromosome. Heredity. 2000;85:1–9.
PubMed
CAS
Google Scholar
Silva DMZA, Utsunomia R, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosomal mapping of repetitive DNA sequences in five species of Astyanax (Characiformes, Characidae) reveals independent location of U1 and U2 snRNA sites and association of U1 snRNA and 5S rDNA. Cytogenet Genome Res. 2015;146:144–52.
PubMed
CAS
Google Scholar
Duílio DMZ, Daniel SN, Camacho JPM, Utsunomia R, Ruiz-Ruano FJ, Penitente M, et al. Origin of B chromosomes in the genus Astyanax (Characiformes, Characidae) and the limits of chromosome painting. Mol Gen Genomics. 2016;291:1407–18.
Google Scholar
Pazza R, Dergam JA, Kavalco KF. Trends in karyotype evolution in Astyanax (Teleostei, Characiformes, Characidae): insights from molecular data. Front Genet. 2018;9:131.
Paiz LM, Baumgärtner L, da Graça WJ, Margarido VP. Basic cytogenetics and physical mapping of ribosomal genes in four Astyanax species (Characiformes, Characidae) collected in middle Paraná river, Iguassu National Park: considerations on taxonomy and systematics of the genus. Comp Cytogenet. 2015;9:54–65.
Google Scholar
Romero A, Paulson KM. It’s a wonderful hypogean life: a guide to the troglomorphic fishes of the world. Environ Biol Fish. 2001;62:13–41.
Google Scholar
Jeffery WR. Cavefish as a model system in evolutionary developmental biology. Dev Biol. 2001;231:1–12.
PubMed
CAS
Google Scholar
Kavalco KF, De Almeida-Toledo LF. Molecular cytogenetics of blind Mexican tetra and comments on the karyotypic characteristics of genus Astyanax (Teleostei, Characidae). Zebrafish. 2007;4:103–11.
PubMed
CAS
Google Scholar
De Silva DMZA, Utsunomia R, Ruiz-Ruano FJ, Daniel SN, Porto-Foresti F, Hashimoto DT, et al. High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. Sci Rep. 2017;7:12726.
Palestis BG, Cabrero J, Trivers R, et al. Prevalence of B chromosomes in Orthoptera is associated with shape and number of a chromosomes. Genetica. 2010;138:1181–9.
PubMed
Google Scholar
Cella DM, Ferreira A. The cytogenetics of Abracris flavolineata (Orthoptera, Caelifera, Ommatolampinae, Abracrini). Rev Bras Genet. 1991;14:315–29.
Google Scholar
Bueno D, Palacios-Gimenez OM, Cabral-de-Mello DC. Chromosomal mapping of repetitive DNAs in the grasshopper Abracris flavolineata reveal possible ancestry of the B chromosome and H3 histone spreading. PLoS One. 2013;8(6):e66532.
Milani D, Bardella VB, Ferretti ABSM, Palacios-Gimenez OM, Melo ADS, Moura RC, Loreto V, Song H, Cabral-de-Mello DC. Satellite DNAs unveil clues about the ancestry and composition of B chromosomes in three grasshopper species. Genes. 2018;9:523.
PubMed Central
Google Scholar
Ruiz-Ruano FJ, Castillo-Martínez J, Cabrero J, Gómez R, Camacho JPM, López-León MD. High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats. Chromosoma. 2018;127:323–40.
PubMed
CAS
Google Scholar
Potapov VA, Solovyev VV, Romanshchenko AG, Sosnovtsev SV, Ivanov SV. The structural and evolutional features of complex tandemly arranged Bsp-repeats in fox genome. II. Tissue-specific and recombinational sites in the BamHI-dimer. Mol Biol. 1991;25:116–32.
CAS
Google Scholar
Peppers JA, Wiggins LE, Baker RJ. Nature of B chromosomes in the harvest mouse Reithrodontomys megalotis by fluorescence in situ hybridization (FISH). Chromosom Res. 1997;5:475–9.
CAS
Google Scholar
Wurster-Hill DH, Ward OG, Davis BH, Park JP, Moyzis RK, Meyne J. Fragile sites, telomeric DNA sequences, B chromosomes, and DNA content in raccoon dogs, Nyctereutes procyonoides, with comparative notes on foxes, coyote, wolf, and raccoon: (with i color plate). Cytogenet Genome Res. 1988;49:278–81.
CAS
Google Scholar
Szczerbal I, Switonski M. B chromosomes of the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray) contain inactive NOR-like sequences. Caryologia. 2003;56:213–6.
Google Scholar
Stitou S. Díaz De La Guardia R, Jiménez R, Burgos M. inactive ribosomal cistrons are spread throughout the B chromosomes of Rattus rattus (Rodentia, Muridae). Implications for their origin and evolution. Chromosom Res. 2000;8:305–11.
Article
CAS
Google Scholar
Rubtsov NB, Karamysheva TV, Andreenkova OV, Bochkaerev MN, Kartavtseva IV, Roslik GV, et al. Comparative analysis of micro and macro B chromosomes in the Korean field mouse Apodemus peninsulae (Rodentia, Murinae) performed by chromosome microdissection and FISH. Cytogenet Genome Res. 2004;106:289–94.
Article
PubMed
CAS
Google Scholar
Teruel M, Cabrero J, Perfectti F, Camacho JPM. B chromosome ancestry revealed by histone genes in the migratory locust. Chromosoma. 2010;119:217–25.
Article
PubMed
CAS
Google Scholar
Trifonov VA, Perelman PL, Kawada SI, Iwasa MA, Oda SI, Graphodatsky AS. Complex structure of B-chromosomes in two mamalian species: Apodemus peninsulae (Rodentia) and Nyctereutes procyonoides (Carnivora). Chromosom Res. 2002;10:109–16.
Article
CAS
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 U S A. 2012;109:13343–6.
Article
PubMed
PubMed Central
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
PubMed
CAS
Google Scholar
Navarro-Domínguez B, Ruiz-Ruano FJ, Cabrero J, Corral JM, López-León MD, Sharbel TF, et al. Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Sci Rep. 2017;7:45200.
Huang W, Du Y, Zhao X, Jin W. B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.). BMC Plant Biol. 2016;16:88.
Li Y, Jing XA, Aldrich JC, Clifford C, Chen J, Akbari OS, et al. Unique sequence organization and small RNA expression of a “selfish” B chromosome. Chromosoma. 2017;126:753–68.
Article
PubMed
CAS
Google Scholar
Aldrich JC, Leibholz A, Cheema MS, Ausió J, Ferree PM. A “selfish” B chromosome induces genome elimination by disrupting the histone code in the jewel wasp Nasonia vitripennis. Sci Rep. 2017;7:42551.
Ramos É, Cardoso AL, Brown J, Marques DF, Fantinatti BEA, Cabral-de-Mello DC, et al. The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. Chromosoma. 2017;126:313–23.
PubMed
CAS
Google Scholar
Navarro-Domínguez B, Martín-Peciña M, Ruiz-Ruano FJ, Cabrero J, Corral JM, López-León MD, et al. Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects. Chromosoma. 2019;128:53–67.
PubMed
Google Scholar
Hong ZJ, Xiao JX, Peng SF, Lin YP, Cheng YM. Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome. Mol Gen Genomics. 2020;295:313–25.
CAS
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.
PubMed
Google Scholar
Gore AV, Tomins KA, Iben J, Ma L, Castranova D, Davis AE, et al. An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol. 2018;2:1155–60.
PubMed
PubMed Central
Google Scholar
Goel M, Sun H, Jiao W, et al. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019;20:277.
PubMed
PubMed Central
Google Scholar
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, et al. The cavefish genome reveals candidate genes for eye loss. Nat Commun. 2014;5:5307.
Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, et al. Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol. 2007;5:932–44.
CAS
Google Scholar
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 2011;477:207–10.
PubMed
PubMed Central
CAS
Google Scholar
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012;484:55–61.
PubMed
PubMed Central
CAS
Google Scholar
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013;496:498–503.
PubMed
PubMed Central
CAS
Google Scholar
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013;45:415–21.
PubMed
PubMed Central
CAS
Google Scholar
Friebe B, Jiang J, Gill B. Detection of 5S rDNA and other repeated DNA on supernumerary B chromosomes of Triticum species (Poaceae). Plant Syst Evol. 1995;196:131–9 23.
CAS
Google Scholar
Cabrero J, Bakkali M, Bugrov A, Warchalowska-Sliwa E, López-León MD, Perfectti F, et al. Multiregional origin of B chromosomes in the grasshopper Eyprepocnemis plorans. Chromosoma. 2003;112:207–11.
PubMed
CAS
Google Scholar
Bugrov AG, Karamysheva TV, Perepelov EA, Elisaphenko EA, Rubtsov DN, Warchałowska-Śliwa E, et al. DNA content of the B chromosomes in grasshopper Podisma kanoi Storozh. (Orthoptera, Acrididae). Chromosom Res. 2007;15:315–26.
CAS
Google Scholar
Oliveira NL, Cabral-De-Mello DC, Rocha MF, Loreto V, Martins C, Moura RC. Chromosomal mapping of rDNAs and H3 histone sequences in the grasshopper Rhammatocerus brasiliensis (acrididae, gomphocerinae): extensive chromosomal dispersion and co-localization of 5S rDNA/H3 histone clusters in the a complement and B chromosome. Mol Cytogenet. 2011;4:24.
Kour G, Kaul S, Dhar MK. Molecular characterization of repetitive DNA sequences from B chromosome in Plantago lagopus L. Cytogenet Genome Res. 2014;142:121–8.
PubMed
CAS
Google Scholar
Houben A, Banaei-Moghaddam AM, Klemme S, Timmis JN. Evolution and biology of supernumerary B chromosomes. Cell Mol Life Sci. 2014;71(3):467–78.
Coan RLB, Martins C. Landscape of transposable elements focusing on the B chromosome of the cichlid fish Astatotilapia latifasciata. Genes. 2018;9:269.
PubMed Central
Google Scholar
Banaei-Moghaddam AM, Meier K, Karimi-Ashtiyani R, Houben A. Formation and expression of pseudogenes on the B chromosome of rye. Plant Cell. 2013;25:2536–44.
PubMed
PubMed Central
CAS
Google Scholar
Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M, et al. B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes. PLoS Genet. 2011;7:e1002203.
PubMed
PubMed Central
CAS
Google Scholar
Jehangir M, Ahmad SF, Cardoso AL, Ramos E, Valente GT, Martins C. De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes. Chromosoma. 2019;128:81–96.
PubMed
CAS
Google Scholar
Protas M, Conrad M, Gross JB, Tabin C, Borowsky R. Regressive evolution in the Mexican cave tetra, Astyanax mexicanus. Curr Biol. 2007;17:452–4.
PubMed
PubMed Central
CAS
Google Scholar
Castro JP, Hattori RS, Yoshinaga TT, de A Silva DMZ, Ruiz-Ruano FJ, Foresti F, et al. Differential expression of genes related to sexual determination can modify the reproductive cycle of Astyanax scabripinnis (Characiformes: Characidae) in b chromosome carrier individuals. Genes (Basel). 2019;10.
Clemente M, Garma C, De Sola BG, Henriques-Gil N. Steep variation in mitochrondrial DNA and B chromosomes among natural populations of Eyprepocnemis plorans (Acrididae). Hereditas. 2001;134:135–40.
PubMed
CAS
Google Scholar
Ma W, Gabriel TS, Martis MM, Gursinsky T, Schubert V, Vrána J, et al. Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its a chromosome paralog. New Phytol. 2017;213:916–28.
PubMed
CAS
Google Scholar
Sumner AT. A simple technique for demonstrating centromeric heterochromatin. Exp Cell Res. 1972;75:304–6.
PubMed
CAS
Google Scholar
Gordon A and Hannon GJ, FASTX-Toolkit. 2014. http://hannonlab.cshl.edu/fastx_toolkit.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
PubMed
PubMed Central
CAS
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
Google Scholar
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, et al. Ensembl 2019. Nucleic Acids Res. 2019;47:745–51.
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:1–18.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
PubMed
PubMed Central
CAS
Google Scholar
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, et al. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019;20:224.
PubMed
PubMed Central
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. 2009;19:1630–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics. 2014;30:2808–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smit A, Hubley R, Green P. RepeatMasker Open-4.0. 2013–2015 . http://www.repeatmasker.org. 2013.
Google Scholar
Pinkel D, Straume T, Gray JW. Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci U S A. 1986;83:2934–8.
PubMed
PubMed Central
CAS
Google Scholar
Nguyen P, Sykorova M, Sichova J, Kůta V, Dalíková M, Čapková Frydrychová R, Neven LG, Sahara K, Marec F. Neo-sex chromosomes and adaptive potential in tortricid pests. Proc Natl Acad Sci U S A. 2013;110:6931–6.
PubMed
PubMed Central
CAS
Google Scholar
Montiel EE, Cabrero J, Ruiz-Estévez M, Burke WD, Eickbush TH, Camacho JPM, et al. Preferential occupancy of R2 retroelements on the B chromosomes of the grasshopper Eyprepocnemis plorans. PLoS One. 2014;9:e91820.
PubMed
PubMed Central
Google Scholar
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, et al. Correction: chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genet. 2016;12:e1006500.
PubMed
PubMed Central
Google Scholar
Rajičić M, Romanenko SA, Karamysheva TV, Blagojević J, Adnadević T, Budinski I, et al. The origin of B chromosomes in yellownecked mice (Apodemus flavicollis)-break rules but keep playing the game. PLoS One. 2017;12(3):e0172704.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10.
Google Scholar
Wang X, Fang X, Yang P, Jiang X, Jiang F, Zhao D, et al. The locust genome provides insight into swarm formation and long-distance flight. Nat Commun. 2014;5:2957.
PubMed
Google Scholar
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, et al. Modernizing reference genome assemblies. PLoS Biol. 2011;9:e1001091.
PubMed
PubMed Central
CAS
Google Scholar
Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–77.
PubMed
PubMed Central
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
PubMed
CAS
Google Scholar
Brionne A, Juanchich A, Hennequet-Antier C. ViSEAGO: a bioconductor package for clustering biological functions using gene ontology and semantic similarity. BioData Min. 2019;12:16.
McDonald J. Fisher’s exact test of independence. Handbook of biological statistics. Baltimore: Sparky House Publ; 2014.
Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007;23:1274–81.
PubMed
CAS
Google Scholar
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics. 2011;27:1571–2.
PubMed
PubMed Central
CAS
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.
Cheong WH, Tan YC, Yap SJ, Ng KP. ClicO FS: An interactive web-based service of Circos. Bioinformatics. 2015;31:3685–7.
PubMed
PubMed Central
CAS
Google Scholar
Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E. SynMap2 and SynMap3D: web-based whole-genome synteny browsers. Bioinformatics. 2017;33:2197–8.
PubMed
CAS
Google Scholar
Lysak MA, 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
PubMed Central
CAS
Google Scholar