{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T03:08:13Z","timestamp":1771211293547,"version":"3.50.1"},"reference-count":199,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2021,4,29]],"date-time":"2021-04-29T00:00:00Z","timestamp":1619654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, Portugal","award":["SFRH\/BD\/147488\/2019"],"award-info":[{"award-number":["SFRH\/BD\/147488\/2019"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, Portugal","award":["Scientific Employment Stimulus 2017 junior research contract in the biological sciences field"],"award-info":[{"award-number":["Scientific Employment Stimulus 2017 junior research contract in the biological sciences field"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric\/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.<\/jats:p>","DOI":"10.3390\/ijms22094707","type":"journal-article","created":{"date-parts":[[2021,4,29]],"date-time":"2021-04-29T04:30:11Z","timestamp":1619670611000},"page":"4707","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3994-5090","authenticated-orcid":false,"given":"Mariana","family":"Lopes","sequence":"first","affiliation":[{"name":"Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2245-8453","authenticated-orcid":false,"given":"Sandra","family":"Louzada","sequence":"additional","affiliation":[{"name":"Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0365-6916","authenticated-orcid":false,"given":"Margarida","family":"Gama-Carvalho","sequence":"additional","affiliation":[{"name":"Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5970-7428","authenticated-orcid":false,"given":"Raquel","family":"Chaves","sequence":"additional","affiliation":[{"name":"Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1126\/science.161.3841.529","article-title":"Repeated sequences in DNA","volume":"161","author":"Britten","year":"1968","journal-title":"Science"},{"key":"ref_2","first-page":"366","article-title":"So much\u2019junk\u2019DNA in our genome. In Proceedings of Evolution of Genetic Systems","volume":"23","author":"Ohno","year":"1972","journal-title":"Brookhaven Symp. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Palazzo, A.F., and Gregory, T.R. (2014). The case for junk DNA. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004351"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1159\/000337118","article-title":"The repetitive DNA content of eukaryotic genomes","volume":"Volume 7","year":"2012","journal-title":"Repetitive DNA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s10577-018-9582-3","article-title":"Alpha satellite DNA biology: Finding function in the recesses of the genome","volume":"26","author":"McNulty","year":"2018","journal-title":"Chromosome Res. Int. J. Mol. Supramol. Evol. Asp. Chromosome Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"10994","DOI":"10.1093\/nar\/gkz841","article-title":"Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases","volume":"47","author":"Star","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_7","unstructured":"Heitz, E. (1928). Das Heterochromatin der Moose, Borntr\u00e4ger."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1134\/S0006297918040156","article-title":"Who Needs This Junk, or Genomic Dark Matter","volume":"83","author":"Podgornaya","year":"2018","journal-title":"Biochem. Biokhimiia"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/S0022-2836(61)80075-2","article-title":"Equilibrium sedimentation in density gradients of DNA preparations from animal tissues","volume":"3","author":"Kit","year":"1961","journal-title":"J. Mol. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1101\/SQB.1961.026.01.009","article-title":"Compositional correlation between deoxyribonucleic acid and protein","volume":"26","author":"Sueoka","year":"1961","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.gene.2007.11.013","article-title":"Satellite DNAs between selfishness and functionality: Structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin","volume":"409","author":"Plohl","year":"2008","journal-title":"Gene"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/0014-4827(74)90249-3","article-title":"Localization of repeated DNA sequences in CsCl gradients by hybridization with complementary RNA","volume":"88","author":"Yasmineh","year":"1974","journal-title":"Exp. Cell Res."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Hartley, G., and O\u2019Neill, R.J. (2019). Centromere repeats: Hidden gems of the genome. Genes, 10.","DOI":"10.3390\/genes10030223"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1101\/sqb.2017.82.034504","article-title":"Function of Junk: Pericentromeric Satellite DNA in Chromosome Maintenance","volume":"82","author":"Jagannathan","year":"2017","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3073","DOI":"10.1093\/gbe\/evx212","article-title":"FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes","volume":"9","author":"Chaves","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.gde.2005.01.004","article-title":"Centromeric chromatin: What makes it unique?","volume":"15","author":"Henikoff","year":"2005","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1159\/000337122","article-title":"Satellite DNA evolution","volume":"Volume 7","author":"Plohl","year":"2012","journal-title":"Repetitive DNA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1007\/s10577-015-9494-4","article-title":"Transcription of tandemly repetitive DNA: Functional roles","volume":"23","author":"Biscotti","year":"2015","journal-title":"Chromosome Res. Int. J. Mol. Supramol. Evol. Asp. Chromosome Biol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Ferreira, D., Escudeiro, A., Adega, F., Anjo, S.I., Manadas, B., and Chaves, R. (2019). FA-SAT ncRNA interacts with PKM2 protein: Depletion of this complex induces a switch from cell proliferation to apoptosis. Cell. Mol. Life Sci.","DOI":"10.1007\/s00018-019-03234-x"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/s10577-015-9482-8","article-title":"Satellite non-coding RNAs: The emerging players in cells, cellular pathways and cancer","volume":"23","author":"Ferreira","year":"2015","journal-title":"Chromosome Res. Int. J. Mol. Supramol. Evol. Asp. Chromosome Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"226","DOI":"10.5808\/GI.2012.10.4.226","article-title":"Transposable elements: No more \u2018Junk DNA\u2019","volume":"10","author":"Kim","year":"2012","journal-title":"Genom. Inform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/S0378-1119(00)00436-4","article-title":"Genomic scrap yard: How genomes utilize all that junk","volume":"259","year":"2000","journal-title":"Gene"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1134\/S1022795419080155","article-title":"The Role of Satellite DNA in Causing Structural Rearrangements in Human Karyotype","volume":"56","author":"Puppo","year":"2020","journal-title":"Russ. J. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"704","DOI":"10.3389\/fgene.2019.00704","article-title":"Copy number variation of human satellite III (1q12) with Aging","volume":"10","author":"Veiko","year":"2019","journal-title":"Front. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Yand\u0131m, C., and Karak\u00fclah, G. (2019). Expression dynamics of repetitive DNA in early human embryonic development. BMC Genom., 20.","DOI":"10.1186\/s12864-019-5803-1"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"312","DOI":"10.3389\/fcell.2020.00312","article-title":"Functional Significance of Satellite DNAs: Insights from Drosophila","volume":"8","author":"Shatskikh","year":"2020","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3390\/genes5010033","article-title":"The Past, Present, and Future of Human Centromere Genomics","volume":"5","author":"Sullivan","year":"2014","journal-title":"Genes"},{"key":"ref_28","first-page":"1","article-title":"Discovery of 33mer in chromosome 21\u2013the largest alpha satellite higher order repeat unit among all human somatic chromosomes","volume":"9","author":"Paar","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/s004390050508","article-title":"Human centromeric DNAs","volume":"100","author":"Lee","year":"1997","journal-title":"Hum. Genet."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0022-2836(86)90224-X","article-title":"Sequence relationships of three human satellite DNAs","volume":"187","author":"Prosser","year":"1986","journal-title":"J. Mol. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1159\/000133374","article-title":"A satellite III sequence shared by human chromosomes 13, 14, and 21 that is contiguous with \u03b1 satellite DNA","volume":"61","author":"Vissel","year":"1992","journal-title":"Cytogenet. Genome Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1007\/s00412-014-0462-0","article-title":"Centromere identity from the DNA point of view","volume":"123","author":"Plohl","year":"2014","journal-title":"Chromosoma"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2943","DOI":"10.1016\/j.celrep.2017.02.072","article-title":"Demethylated HSATII DNA and HSATII RNA foci sequester PRC1 and MeCP2 into cancer-specific nuclear bodies","volume":"18","author":"Hall","year":"2017","journal-title":"Cell Rep."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.devcel.2017.07.001","article-title":"Human Centromeres Produce Chromosome-Specific and Array-Specific Alpha Satellite Transcripts that Are Complexed with CENP-A and CENP-C","volume":"42","author":"McNulty","year":"2017","journal-title":"Dev. Cell"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"15148","DOI":"10.1073\/pnas.1518008112","article-title":"Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer","volume":"112","author":"Bersani","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Delpu, Y., McNamara, T., Griffin, P., Kaleem, S., Narayan, S., Schildkraut, C., Miga, K., and Tahiliani, M. (2019). Chromosomal rearrangements at hypomethylated Satellite 2 sequences are associated with impaired replication efficiency and increased fork stalling. bioRxiv, 554410.","DOI":"10.1101\/554410"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"11502","DOI":"10.1093\/nar\/gku835","article-title":"Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome","volume":"42","author":"Erliandri","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_38","first-page":"2668","article-title":"Regular higher order repeat structures in beetle Tribolium castaneum genome","volume":"9","author":"Paar","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Miga, K.H. (2019). Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population. Genes, 10.","DOI":"10.3390\/genes10050352"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Warburton, P.E., Hasson, D., Guillem, F., Lescale, C., Jin, X., and Abrusan, G. (2008). Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genom., 9.","DOI":"10.1186\/1471-2164-9-533"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Altemose, N., Miga, K.H., Maggioni, M., and Willard, H.F. (2014). Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Comput. Biol., 10.","DOI":"10.1371\/journal.pcbi.1003628"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3929","DOI":"10.1093\/nar\/15.9.3929","article-title":"Hypervariable lengths of human DNA associated with a human satellite III sequence found in the 3.4 kb Y-specific fragment","volume":"15","author":"Fowler","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1002\/ajmg.1320260116","article-title":"Chromosomal polymorphisms of 1, 9, 16, and Y in 4 major ethnic groups: A large prenatal study","volume":"26","author":"Hsu","year":"1987","journal-title":"Am. J. Med Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/BF00278966","article-title":"The quantitative analysis of polymorphism on human chromosomes 1, 9, 16, and Y. IV. Heterogeneity of a normal population","volume":"54","author":"Podugolnikova","year":"1980","journal-title":"Hum. Genet."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/BF00201662","article-title":"Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes","volume":"93","author":"Tagarro","year":"1994","journal-title":"Hum. Genet."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/hmg\/2.10.1639","article-title":"Long-range analyses of the centromeric regions of human chromosomes 13, 14 and 21: Identification of a narrow domain containing two key centromeric DNA elements","volume":"2","author":"Trowell","year":"1993","journal-title":"Hum. Mol. Genet."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1007\/BF00284102","article-title":"Chromosomal location by in situ hybridization of the human Sau3A family of DNA repeats","volume":"75","author":"Agresti","year":"1987","journal-title":"Hum. Genet."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3177","DOI":"10.1093\/nar\/6.10.3177","article-title":"Cloning of human satellite III DNA: Different components are on different chromosomes","volume":"6","author":"Cooke","year":"1979","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/0014-4827(75)90648-5","article-title":"The location of four human satellite DNAs on human chromosomes","volume":"92","author":"Gosden","year":"1975","journal-title":"Exp. Cell Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/0888-7543(88)90139-5","article-title":"A subfamily of alphoid repetitive DNA shared by the NOR-bearing human chromosomes 14 and 22","volume":"3","author":"Jones","year":"1988","journal-title":"Genomics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/BF00210595","article-title":"Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides","volume":"93","author":"Tagarro","year":"1994","journal-title":"Hum. Genet."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Garrido-Ramos, M.A. (2017). Satellite DNA: An Evolving Topic. Genes, 8.","DOI":"10.3390\/genes8090230"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/0022-2836(71)90403-7","article-title":"DNA strand reassociation and polyribonucleotide binding in the African green monkey, Cercopithecus aethiops","volume":"56","author":"Maio","year":"1971","journal-title":"J. Mol. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/BF00285813","article-title":"Chromosomal localization of complex and simple repeated human DNAs","volume":"66","author":"Manuelidis","year":"1978","journal-title":"Chromosoma"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1101\/sqb.2003.68.141","article-title":"Sequence organization and functional annotation of human centromeres","volume":"68","author":"Rudd","year":"2003","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_56","first-page":"524","article-title":"Chromosome-specific organization of human alpha satellite DNA","volume":"37","author":"Willard","year":"1985","journal-title":"Am. J. Hum. Genet."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/BF02100014","article-title":"Chromosome-specific subsets of human alpha satellite DNA: Analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat","volume":"25","author":"Willard","year":"1987","journal-title":"J. Mol. Evol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2209","DOI":"10.1093\/nar\/21.9.2209","article-title":"Definition of a new alpha satellite suprachromosomal family characterized by monomeric organization","volume":"21","author":"AIexandrov","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.gdata.2015.05.035","article-title":"Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly","volume":"5","author":"Shepelev","year":"2015","journal-title":"Genom. Data"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1083\/jcb.116.3.585","article-title":"Centromere protein B assembles human centromeric alpha-satellite DNA at the 17-bp sequence, CENP-B box","volume":"116","author":"Muro","year":"1992","journal-title":"J. Cell Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1007\/BF00337514","article-title":"CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins","volume":"100","author":"Sullivan","year":"1991","journal-title":"Chromosoma"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.devcel.2015.03.020","article-title":"DNA sequence-specific binding of CENP-B enhances the fidelity of human centromere function","volume":"33","author":"Fachinetti","year":"2015","journal-title":"Dev. Cell"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1159\/000132229","article-title":"Two subsets of human alphoid repetitive DNA show distinct preferential localization in the pericentric regions of chromosomes 13, 18, and 21","volume":"41","author":"Devilee","year":"1986","journal-title":"Cytogenet. Genome Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/nar\/19.6.1179","article-title":"A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence","volume":"19","author":"Choo","year":"1991","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1080\/19491034.2017.1308989","article-title":"\u03b1 satellite DNA variation and function of the human centromere","volume":"8","author":"Sullivan","year":"2017","journal-title":"Nucleus"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Sullivan, L.L., and Sullivan, B.A. (2020). Genomic and functional variation of human centromeres. Exp. Cell Res., 111896.","DOI":"10.1016\/j.yexcr.2020.111896"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1128\/MCB.01198-12","article-title":"Sequences associated with centromere competency in the human genome","volume":"33","author":"Hayden","year":"2013","journal-title":"Mol. Cell. Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e1400234","DOI":"10.1126\/sciadv.1400234","article-title":"A unique chromatin complex occupies young \u03b1-satellite arrays of human centromeres","volume":"1","author":"Henikoff","year":"2015","journal-title":"Sci. Adv."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"7549","DOI":"10.1093\/nar\/15.18.7549","article-title":"Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: A survey of alphoid sequences from different human chromosomes","volume":"15","author":"Waye","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"10563","DOI":"10.1073\/pnas.0503346102","article-title":"Progressive proximal expansion of the primate X chromosome centromere","volume":"102","author":"Schueler","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Logsdon, G.A., Vollger, M.R., Hsieh, P., Mao, Y., Liskovykh, M.A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P.C., and Rhie, A. (2021). The structure, function and evolution of a complete human chromosome 8. Nature, 1\u20137.","DOI":"10.1101\/2020.09.08.285395"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Shepelev, V.A., Alexandrov, A.A., Yurov, Y.B., and Alexandrov, I.A. (2009). The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet, 5.","DOI":"10.1371\/journal.pgen.1000641"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/BF00352318","article-title":"Chromosome localization and orientation of the simple sequence repeat of human satellite I DNA","volume":"103","author":"Meyne","year":"1994","journal-title":"Chromosoma"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1006\/geno.1993.1147","article-title":"A chromosome 13-specific human satellite I DNA subfamily with minor presence on chromosome 21: Further studies on Robertsonian translocations","volume":"16","author":"Kalitsis","year":"1993","journal-title":"Genomics"},{"key":"ref_75","first-page":"163","article-title":"Human satellites 2 and 3","volume":"37","author":"Jeanpierre","year":"1994","journal-title":"Ann. De Genet."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/0888-7543(89)90331-5","article-title":"The distribution of interspersed repetitive DNA sequences in the human genome","volume":"4","author":"Moyzis","year":"1989","journal-title":"Genomics"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1159\/000132547","article-title":"Characterization of human heterochromatin by in situ hybridization with satellite DNA clones","volume":"47","author":"Cram","year":"1988","journal-title":"Cytogenet. Cell Genet."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"7569","DOI":"10.1093\/nar\/14.19.7569","article-title":"A human Y-chromosome specific repeated DNA family (DYZ1) consists of a tandem array of pentanucleotides","volume":"14","author":"Nakahori","year":"1986","journal-title":"Nucleic Acids Res."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Choo, K.A. (1997). The Centromere, Oxford University Press.","DOI":"10.1093\/oso\/9780198577812.001.0001"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1038\/262182a0","article-title":"Repeated sequence specific to human males","volume":"262","author":"Cooke","year":"1976","journal-title":"Nature"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1126\/science.1257744","article-title":"Human Y-chromosome-specific reiterated DNA","volume":"191","author":"Kunkel","year":"1976","journal-title":"Science"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"5641","DOI":"10.1093\/nar\/18.19.5641","article-title":"A homologous subfamily of satellite III DNA on human chromosomes 14 and 22","volume":"18","author":"Choo","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"ref_83","first-page":"706","article-title":"A chromosome 14-specific human satellite III DNA subfamily that shows variable presence on different chromosomes 14","volume":"50","author":"Choo","year":"1992","journal-title":"Am. J. Hum. Genet."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1023\/A:1016648404388","article-title":"Identification and characterization of satellite III subfamilies to the acrocentric chromosomes","volume":"9","author":"Bandyopadhyay","year":"2001","journal-title":"Chromosome Res."},{"key":"ref_85","first-page":"717","article-title":"Identification of DNA sequences flanking the breakpoint of human t (14q21q) Robertsonian translocations","volume":"50","author":"Earle","year":"1992","journal-title":"Am. J. Hum. Genet."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/0022-2836(85)90123-8","article-title":"Identification of a human clustered G+ C-rich DNA family of repeats (Sau3A family)","volume":"186","author":"Meneveri","year":"1985","journal-title":"J. Mol. Biol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"6250","DOI":"10.1073\/pnas.86.16.6250","article-title":"Human beta satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA","volume":"86","author":"Waye","year":"1989","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/0378-1119(93)90128-P","article-title":"Molecular organization and chromosomal location of human GC-rich heterochromatic blocks","volume":"123","author":"Meneveri","year":"1993","journal-title":"Gene"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1101\/gr.8.8.791","article-title":"Complex \u03b2-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12","volume":"8","author":"Eichler","year":"1998","journal-title":"Genome Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/molbev\/msh190","article-title":"Evolution of beta satellite DNA sequences: Evidence for duplication-mediated repeat amplification and spreading","volume":"21","author":"Cardone","year":"2004","journal-title":"Mol. Biol. Evol."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Yang, J., Yuan, B., Wu, Y., Li, M., Li, J., Xu, D., Gao, Z.-h., Ma, G., Zhou, Y., and Zuo, Y. (2020). The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes. Genomics.","DOI":"10.1101\/772921"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/BF00661276","article-title":"Isolation and identification of a novel tandemly repeated DNA sequence in the centromeric region of human chromosome 8","volume":"102","author":"Lin","year":"1993","journal-title":"Chromosoma"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/BF00347692","article-title":"Human gamma X satellite DNA: An X chromosome specific centromeric DNA sequence","volume":"104","author":"Lee","year":"1995","journal-title":"Chromosoma"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1101\/gr.086496.108","article-title":"Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing","volume":"19","author":"Kim","year":"2009","journal-title":"Genome Res."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1007\/978-3-319-58592-5_12","article-title":"The Promises and Challenges of Genomic Studies of Human Centromeres","volume":"56","author":"Miga","year":"2017","journal-title":"Prog. Mol. Subcell. Biol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nbt.4109","article-title":"Linear assembly of a human centromere on the Y chromosome","volume":"36","author":"Jain","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/s10577-015-9488-2","article-title":"Completing the human genome: The progress and challenge of satellite DNA assembly","volume":"23","author":"Miga","year":"2015","journal-title":"Chromosome Res. Int. J. Mol. Supramol. Evol. Asp. Chromosome Biol."},{"key":"ref_98","first-page":"243","article-title":"Satellite DNA sequences in the human acrocentric chromosomes: Information from translocations and heteromorphisms","volume":"33","author":"Gosden","year":"1981","journal-title":"Am. J. Hum. Genet."},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., and Denisov, G. (2007). The diploid genome sequence of an individual human. PLoS Biol., 5.","DOI":"10.1371\/journal.pbio.0050254"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/314067a0","article-title":"Hypervariable \u2018minisatellite\u2019regions in human DNA","volume":"314","author":"Jeffreys","year":"1985","journal-title":"Nature"},{"key":"ref_101","first-page":"397","article-title":"A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene","volume":"44","author":"Litt","year":"1989","journal-title":"Am. J. Hum. Genet."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1159\/000437008","article-title":"Satellite DNA in Plants: More than Just Rubbish","volume":"146","year":"2015","journal-title":"Cytogenet Genome Res"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Black, E.M., and Giunta, S. (2018). Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases. Genes, 9.","DOI":"10.3390\/genes9120615"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nature01626","article-title":"A vision for the future of genomics research","volume":"422","author":"Collins","year":"2003","journal-title":"Nature"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nrg1322","article-title":"An assessment of the sequence gaps: Unfinished business in a finished human genome","volume":"5","author":"Eichler","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"ref_106","unstructured":"Phillippy, A. (2021, April 20). The (Near) Complete Sequence of a Human Genome. Available online: https:\/\/genomeinformatics.github.io\/CHM13v1\/."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: A program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s13059-019-1667-6","article-title":"Tandem-genotypes: Robust detection of tandem repeat expansions from long DNA reads","volume":"20","author":"Mitsuhashi","year":"2019","journal-title":"Genome Biol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s10038-019-0671-8","article-title":"Long-read sequencing for rare human genetic diseases","volume":"65","author":"Mitsuhashi","year":"2020","journal-title":"J. Hum. Genet."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Louzada, S., Lopes, M., Ferreira, D., Adega, F., Escudeiro, A., Gama-Carvalho, M., and Chaves, R. (2020). Decoding the Role of Satellite DNA in Genome Architecture and Plasticity\u2014An Evolutionary and Clinical Affair. Genes, 11.","DOI":"10.3390\/genes11010072"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.1093\/bioinformatics\/btu356","article-title":"Toward better understanding of artifacts in variant calling from high-coverage samples","volume":"30","author":"Li","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.tibtech.2018.07.013","article-title":"Single-molecule sequencing: Towards clinical applications","volume":"37","author":"Ameur","year":"2018","journal-title":"Trends Biotechnol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"14515","DOI":"10.1038\/ncomms14515","article-title":"Scaffolding and completing genome assemblies in real-time with nanopore sequencing","volume":"8","author":"Cao","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Miga, K.H. (2020). Centromere studies in the era of \u2018telomere-to-telomere\u2019genomics. Exp. Cell Res., 112127.","DOI":"10.1016\/j.yexcr.2020.112127"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/bfgp\/elr035","article-title":"Comparison of the two major classes of assembly algorithms: Overlap\u2013layout\u2013consensus and de-bruijn-graph","volume":"11","author":"Li","year":"2012","journal-title":"Brief. Funct. Genom."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1534\/genetics.106.060467","article-title":"Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation\u2013polymerase chain reaction","volume":"174","author":"Luce","year":"2006","journal-title":"Genetics"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.ygeno.2010.03.001","article-title":"Assembly algorithms for next-generation sequencing data","volume":"95","author":"Miller","year":"2010","journal-title":"Genomics"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"Schneider","year":"2017","journal-title":"Genome Res."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ygeno.2017.01.005","article-title":"Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis","volume":"109","author":"Guo","year":"2017","journal-title":"Genomics"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/s41586-020-2547-7","article-title":"Telomere-to-telomere assembly of a complete human X chromosome","volume":"585","author":"Miga","year":"2020","journal-title":"Nature"},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Suzuki, Y., Myers, G., and Morishita, S. (2019). Long-read Data Revealed Structural Diversity in Human Centromere Sequences. BioRxiv, 784785.","DOI":"10.1101\/784785"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/0888-7543(90)90206-A","article-title":"Pulsed-field gel analysis of \u03b1-satellite DNA at the human X chromosome centromere: High-frequency polymorphisms and array size estimate","volume":"7","author":"Mahtani","year":"1990","journal-title":"Genomics"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1101\/gr.451502","article-title":"Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous \u03b1-satellite DNA array","volume":"12","author":"Schindelhauer","year":"2002","journal-title":"Genome Res."},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Miga, K.H. (2021). Breaking through the Unknowns of the Human Reference Genome, Nature Publishing Group.","DOI":"10.1038\/d41586-021-00293-8"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ygeno.2015.11.003","article-title":"The sequence of sequencers: The history of sequencing DNA","volume":"107","author":"Heather","year":"2016","journal-title":"Genomics"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/265687a0","article-title":"Nucleotide sequence of bacteriophage \u03c6X174 DNA","volume":"265","author":"Sanger","year":"1977","journal-title":"Nature"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","author":"Venter","year":"2001","journal-title":"Science"},{"key":"ref_129","unstructured":"Janitz, M. (2011). Next-Generation Genome Sequencing: Towards Personalized Medicine, John Wiley & Sons."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"4593","DOI":"10.1093\/nar\/15.11.4593","article-title":"Automated DNA sequencing: Ultrasensitive detection of fluorescent bands during electrophoresis","volume":"15","author":"Ansorge","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"4417","DOI":"10.1093\/nar\/18.15.4417","article-title":"High speed DNA sequencing by capillary electrophoresis","volume":"18","author":"Luckey","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1093\/nar\/13.7.2399","article-title":"The synthesis of oligonucleotides containing an aliphatic amino group at the 5\u2032 terminus: Synthesis of fluorescent DNA primers for use in DNA sequence analysis","volume":"13","author":"Smith","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1093\/nar\/18.6.1415","article-title":"Capillary gel electrophoresis for rapid, high resolution DNA sequencing","volume":"18","author":"Swerdlow","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"3015","DOI":"10.1093\/nar\/9.13.3015","article-title":"Shotgun DNA sequencing using cloned DNase I-generated fragments","volume":"9","author":"Anderson","year":"1981","journal-title":"Nucleic Acids Res."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1093\/nar\/6.7.2601","article-title":"A strategy of DNA sequencing employing computer programs","volume":"6","author":"Staden","year":"1979","journal-title":"Nucleic Acids Res."},{"key":"ref_136","first-page":"1023","article-title":"The long reads ahead: De novo genome assembly using the MinION","volume":"6","author":"Risse","year":"2017","journal-title":"F1000Research"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: Ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature24286","article-title":"DNA sequencing at 40: Past, present and future","volume":"550","author":"Shendure","year":"2017","journal-title":"Nature"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nprot.2016.182","article-title":"DNA sequencing technologies: 2006\u20132016","volume":"12","author":"Mardis","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"449","DOI":"10.3389\/fgene.2014.00449","article-title":"The evolution of nanopore sequencing","volume":"5","author":"Wang","year":"2015","journal-title":"Front. Genet."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"4809","DOI":"10.1093\/bioinformatics\/btz484","article-title":"Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data","volume":"35","author":"Harris","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Cacheux, L., Ponger, L., Gerbault-Seureau, M., Richard, F.A., and Escud\u00e9, C. (2016). Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus. BMC Genom., 17.","DOI":"10.1186\/s12864-016-3246-5"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41576-020-0236-x","article-title":"Long-read human genome sequencing and its applications","volume":"21","author":"Logsdon","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Amarasinghe, S.L., Su, S., Dong, X., Zappia, L., Ritchie, M.E., and Gouil, Q. (2020). Opportunities and challenges in long-read sequencing data analysis. Genome Biol., 21.","DOI":"10.1186\/s13059-020-1935-5"},{"key":"ref_146","unstructured":"(2021, March 21). ONT. At NCM, Announcements Include Single-Read Accuracy of 99.1% on New Chemistry and Sequencing a Record 10 Tb in a Single PromethION Run, Available online: https:\/\/nanoporetech.com\/about-us\/news\/ncm-announcements-include-single-read-accuracy-991-new-chemistry-and-sequencing."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"Kraft, F., and Kurth, I. (2020). Long-read sequencing to understand genome biology and cell function. Int. J. Biochem. Cell Biol., 105799.","DOI":"10.1016\/j.biocel.2020.105799"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-019-1856-3","article-title":"NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION","volume":"20","author":"Bossaerts","year":"2019","journal-title":"Genome Biol."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Nurk, S., Walenz, B.P., Rhie, A., Vollger, M.R., Logsdon, G.A., Grothe, R., Miga, K.H., Eichler, E.E., Phillippy, A.M., and Koren, S. (2020). HiCanu: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. BioRxiv.","DOI":"10.1101\/2020.03.14.992248"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/ahg.12364","article-title":"Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads","volume":"84","author":"Vollger","year":"2020","journal-title":"Ann. Hum. Genet."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.tig.2018.06.002","article-title":"Strategies to annotate and characterize long noncoding RNAs: Advantages and pitfalls","volume":"34","author":"Cao","year":"2018","journal-title":"Trends Genet."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1002\/1873-3468.13085","article-title":"Interactions between short and long noncoding RNAs","volume":"592","author":"Ulitsky","year":"2018","journal-title":"FEBS Lett."},{"key":"ref_154","doi-asserted-by":"crossref","unstructured":"Saksouk, N., Simboeck, E., and D\u00e9jardin, J. (2015). Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin, 8.","DOI":"10.1186\/1756-8935-8-3"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"Smith, A.M., Jain, M., Mulroney, L., Garalde, D.R., and Akeson, M. (2019). Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0216709"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: The teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1111\/dgd.12608","article-title":"Nanopore sequencing: Review of potential applications in functional genomics","volume":"61","author":"Kono","year":"2019","journal-title":"Dev. Growth Differ."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1038\/s41592-019-0617-2","article-title":"Nanopore native RNA sequencing of a human poly (A) transcriptome","volume":"16","author":"Workman","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"100","DOI":"10.12688\/f1000research.10571.2","article-title":"Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis","volume":"6","author":"Weirather","year":"2017","journal-title":"F1000Res"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/nrg3933","article-title":"Genetic variation and the de novo assembly of human genomes","volume":"16","author":"Chaisson","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1093\/bioinformatics\/btw101","article-title":"Alpha-CENTAURI: Assessing novel centromeric repeat sequence variation with long read sequencing","volume":"32","author":"Sevim","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_163","doi-asserted-by":"crossref","unstructured":"McCombie, W.R., McPherson, J.D., and Mardis, E.R. (2019). Next-Generation Sequencing Technologies. Cold Spring Harb. Perspect. Med., 9.","DOI":"10.1101\/cshperspect.a036798"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1055\/s-0039-1688446","article-title":"Next-generation sequencing and emerging technologies","volume":"45","author":"Kumar","year":"2019","journal-title":"Semin. Thromb. Hemost."},{"key":"ref_165","doi-asserted-by":"crossref","unstructured":"Miller, J.R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B.P., Liu, J., Stupar, R.M., and Denny, R. (2017). Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3927-8"},{"key":"ref_166","doi-asserted-by":"crossref","unstructured":"Minei, R., Hoshina, R., and Ogura, A. (2018). De novo assembly of middle-sized genome using MinION and Illumina sequencers. BMC Genom., 19.","DOI":"10.1186\/s12864-018-5067-1"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1101\/gr.215095.116","article-title":"Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications","volume":"27","author":"Weissensteiner","year":"2017","journal-title":"Genome Res."},{"key":"ref_168","doi-asserted-by":"crossref","unstructured":"Louzada, S., Komatsu, J., and Yang, F. (2017). Fluorescence in situ hybridization onto DNA fibres generated using molecular combing. Fluorescence In Situ Hybridization (FISH), Springer.","DOI":"10.1007\/978-3-662-52959-1_31"},{"key":"ref_169","doi-asserted-by":"crossref","unstructured":"Deschamps, S., Zhang, Y., Llaca, V., Ye, L., Sanyal, A., King, M., May, G., and Lin, H. (2018). A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. Nat. Commun., 9.","DOI":"10.1038\/s41467-018-07271-1"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"giaa045","DOI":"10.1093\/gigascience\/giaa045","article-title":"Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal","volume":"9","author":"Etherington","year":"2020","journal-title":"GigaScience"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41587-018-0004-z","article-title":"Errors in long-read assemblies can critically affect protein prediction","volume":"37","author":"Watson","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/bioinformatics\/btx675","article-title":"ARCS: Scaffolding genome drafts with linked reads","volume":"34","author":"Yeo","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_173","doi-asserted-by":"crossref","unstructured":"Hu, J., Fan, J., Sun, Z., and Liu, S. NextPolish: A fast and efficient genome polishing tool for long read assembly. Bioinformatics, 2020.","DOI":"10.1093\/bioinformatics\/btz891"},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"Deakin, J.E., Potter, S., O\u2019Neill, R., Ruiz-Herrera, A., Cioffi, M.B., Eldridge, M.D., Fukui, K., Marshall Graves, J.A., Griffin, D., and Grutzner, F. (2019). Chromosomics: Bridging the gap between genomes and chromosomes. Genes, 10.","DOI":"10.3390\/genes10080627"},{"key":"ref_175","doi-asserted-by":"crossref","unstructured":"Ma, L., Li, W., and Song, Q. (2017). Chromosome-range whole-genome high-throughput experimental haplotyping by single-chromosome microdissection. Haplotyping, Springer.","DOI":"10.1007\/978-1-4939-6750-6_9"},{"key":"ref_176","doi-asserted-by":"crossref","unstructured":"Seifertova, E., Zimmerman, L.B., Gilchrist, M.J., Macha, J., Kubickova, S., Cernohorska, H., Zarsky, V., Owens, N.D., Sesay, A.K., and Tlapakova, T. (2013). Efficient high-throughput sequencing of a laser microdissected chromosome arm. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-357"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1007\/s10577-013-9376-6","article-title":"High-throughput sequencing of a single chromosome: A moth W chromosome","volume":"21","author":"Traut","year":"2013","journal-title":"Chromosome Res."},{"key":"ref_178","doi-asserted-by":"crossref","unstructured":"Makunin, A.I., Kichigin, I.G., Larkin, D.M., O\u2019Brien, P.C., Ferguson-Smith, M.A., Yang, F., Proskuryakova, A.A., Vorobieva, N.V., Chernyaeva, E.N., and O\u2019Brien, S.J. (2016). Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing. BMC Genom., 17.","DOI":"10.1186\/s12864-016-2933-6"},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1101\/gr.193474.115","article-title":"Chromosome-scale shotgun assembly using an in vitro method for long-range linkage","volume":"26","author":"Putnam","year":"2016","journal-title":"Genome Res."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"9436","DOI":"10.1038\/s41598-018-27819-x","article-title":"Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads","volume":"8","author":"Santiago","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_182","doi-asserted-by":"crossref","unstructured":"Kuderna, L.F., Lizano, E., Juli\u00e0, E., Gomez-Garrido, J., Serres-Armero, A., Kuhlwilm, M., Alandes, R.A., Alvarez-Estape, M., Juan, D., and Simon, H. (2019). Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nat. Commun., 10.","DOI":"10.1038\/s41467-018-07885-5"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/s41576-018-0003-4","article-title":"Piercing the dark matter: Bioinformatics of long-range sequencing and mapping","volume":"19","author":"Sedlazeck","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S0074-7696(08)61789-1","article-title":"Highly repeated sequences in mammalian genomes","volume":"Volume 76","author":"Singer","year":"1982","journal-title":"International Review of Cytology"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.ymeth.2015.11.026","article-title":"The origin of in situ hybridization\u2013a personal history","volume":"98","author":"Gall","year":"2016","journal-title":"Methods"},{"key":"ref_186","unstructured":"Schwarzacher, T., and Heslop-Harrison, P. (2000). Practical In Situ Hybridization, BIOS Scientific Publishers Ltd."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"10630","DOI":"10.1073\/pnas.1410372111","article-title":"Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel","volume":"111","author":"Kim","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"28333","DOI":"10.1038\/srep28333","article-title":"High-throughput analysis of the satellitome illuminates satellite DNA evolution","volume":"6","author":"Cabrero","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_189","doi-asserted-by":"crossref","unstructured":"Ebert, P., Audano, P.A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., and Mari, R.S. (2021). Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 372.","DOI":"10.1126\/science.abf7117"},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0022-2836(67)80130-X","article-title":"A satellite DNA isolated from human tissues","volume":"23","author":"Corneo","year":"1967","journal-title":"J. Mol. Biol."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/0022-2836(68)90301-X","article-title":"Isolation of the complementary strands of a human satellite DNA","volume":"33","author":"Corneo","year":"1968","journal-title":"J. Mol. Biol."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/0022-2836(70)90163-4","article-title":"Repeated sequences in human DNA","volume":"48","author":"Corneo","year":"1970","journal-title":"J. Mol. Biol."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/0005-2787(71)90689-7","article-title":"Renaturation properties and localization in heterochromatin of human satellite DNA\u2019s","volume":"247","author":"Corneo","year":"1971","journal-title":"Biochim. Et Biophys. Acta (Bba)-Nucleic Acids Protein Synth."},{"key":"ref_194","doi-asserted-by":"crossref","unstructured":"Mikheenko, A., Bzikadze, A.V., Gurevich, A., Miga, K.H., and Pevzner, P.A. (2019). TandemMapper and TandemQUAST: Mapping long reads and assessing\/improving assembly quality in extra-long tandem repeats. BioRxiv.","DOI":"10.1101\/2019.12.23.887158"},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"i75","DOI":"10.1093\/bioinformatics\/btaa440","article-title":"TandemTools: Mapping long reads and assessing\/improving assembly quality in extra-long tandem repeats","volume":"36","author":"Mikheenko","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"e111","DOI":"10.1093\/nar\/gkx257","article-title":"TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads","volume":"45","author":"Neumann","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_197","doi-asserted-by":"crossref","unstructured":"Nov\u00e1k, P., Neumann, P., and Macas, J. (2010). Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-378"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1093\/bioinformatics\/btt054","article-title":"RepeatExplorer: A Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads","volume":"29","author":"Novak","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1093\/nar\/7.2.417","article-title":"Nucleotide sequence of a highly repetitive component of rat DNA","volume":"7","author":"Pech","year":"1979","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/9\/4707\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:55:09Z","timestamp":1760162109000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/9\/4707"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,29]]},"references-count":199,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2021,5]]}},"alternative-id":["ijms22094707"],"URL":"https:\/\/doi.org\/10.3390\/ijms22094707","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,29]]}}}