Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008-2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687-2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.

Biology Centre of the Czech Academy of Sciences Institute of Plant Molecular Biology České Budějovice 37005 Czech Republic

Leibniz Institute of Plant Genetics and Crop Plant Research 06466 Gatersleben Stadt Seeland Germany

University of South Bohemia Faculty of Science České Budějovice 37005 Czech Republic

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Macas J, Mészáros T, Nouzová M. PlantSat: a specialized database for plant satellite repeats. Bioinformatics. 2002;18:28–35. doi: 10.1093/bioinformatics/18.1.28. PubMed DOI

Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004;5:435–445. doi: 10.1038/nrg1348. PubMed DOI

Gong Z, et al. Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell. 2012;24:3559–74. doi: 10.1105/tpc.112.100511. PubMed DOI PMC

Garcia, S., Garnatje, T. & Kovařík, A. Plant rDNA database: ribosomal DNA loci information goes online. Chromosoma121, 389–394 (2012). PubMed

Chan SRWL, Blackburn EH. Telomeres and telomerase. Philos. Trans. R. Soc. B Biol. Sci. 2004;359:109–122. doi: 10.1098/rstb.2003.1370. PubMed DOI PMC

Garrido-Ramos, M. A. Satellite DNA in plants: more than just rubbish. Cytogenet. Genome Res. 146, 153–70 (2015). PubMed

Feliciello, I., Akrap, I. & Ugarković, Đ. Satellite DNA modulates gene expression in the beetle Tribolium castaneum after heat stress. PLoS Genet.11, e1005466 (2015). PubMed PMC

Plohl M, Meštrović N, Mravinac B. Centromere identity from the DNA point of view. Chromosoma. 2014;123:313–325. doi: 10.1007/s00412-014-0462-0. PubMed DOI PMC

Tolomeo D, et al. Epigenetic origin of evolutionary novel centromeres. Sci. Rep. 2017;7:41980. doi: 10.1038/srep41980. PubMed DOI PMC

Smith, G. P. Evolution of repeated DNA sequences by unequal crossover. Science191, 528–535 (1976). PubMed

Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 1987;4:203–221. PubMed

Fieldhouse D, Golding B. A source of small repeats in genomic DNA. Genetics. 1991;129:563–572. PubMed PMC

Nikolov I, Taddei A. Linking replication stress with heterochromatin formation. Chromosoma. 2016;125:523–533. doi: 10.1007/s00412-015-0545-6. PubMed DOI PMC

Mazurczyk M, Rybaczek D. Replication and re-replication: Different implications of the same mechanism. Biochimie. 2015;108:25–32. doi: 10.1016/j.biochi.2014.10.026. PubMed DOI

Kuzminov A. Chromosomal replication complexity: a novel DNA metrics and genome instability factor. PLoS Genet. 2016;12:e1006229. doi: 10.1371/journal.pgen.1006229. PubMed DOI PMC

Macas J, Navrátilová A, Mészáros T. Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes. Chromosoma. 2003;112:152–8. doi: 10.1007/s00412-003-0255-3. PubMed DOI

Macas J, Koblízková A, Navrátilová A, Neumann P. Hypervariable 3′ UTR region of plant LTR-retrotransposons as a source of novel satellite repeats. Gene. 2009;448:198–206. doi: 10.1016/j.gene.2009.06.014. PubMed DOI

Dover G. Molecular drive: a cohesive mode of species evolution. Nature. 1982;299:111–7. doi: 10.1038/299111a0. PubMed DOI

Kuhn GCS, Heinrich K, Moreira-Filho O, Heslop-Harrison JS. The 1.688 repetitive DNA of Drosophila: concerted evolution at different genomic scales and association with genes. Mol. Biol. Evol. 2012;29:7–11. doi: 10.1093/molbev/msr173. PubMed DOI

Liao D. Concerted evolution: molecular mechanism and biological implications. Am. J. Hum. Genet. 1999;64:24–30. doi: 10.1086/302221. PubMed DOI PMC

Cohen S, Houben A, Segal D. Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants. Plant J. 2008;53:1027–1034. doi: 10.1111/j.1365-313X.2007.03394.x. PubMed DOI

Navrátilová, A., Koblížková, A. & Macas, J. Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC Plant Biol.8, 90 (2008). PubMed PMC

Ma J, Jackson SA. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res. 2006;16:251–259. doi: 10.1101/gr.4583106. PubMed DOI PMC

Kit, S. Equilibrium sedimentation in density gradients of DNA preparations from animal tissues. J. Mol. Biol.3, 711–716 (1961). PubMed

Hemleben V, Kovařík A, Torres-Ruiz RA, Volkov RA, Beridze T. Plant highly repeated satellite DNA: Molecular evolution, distribution and use for identification of hybrids. Syst. Biodivers. 2007;5:277–289. doi: 10.1017/S147720000700240X. DOI

Novák P, Neumann P, Macas J. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics. 2010;11:378. doi: 10.1186/1471-2105-11-378. PubMed DOI PMC

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;29:792–793. doi: 10.1093/bioinformatics/btt054. PubMed DOI

Novák, P. et al. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res. 45, e111 (2017). PubMed PMC

Ruiz-Ruano FJ, López-León MD, Cabrero J, Camacho JPM. High-throughput analysis of the satellitome illuminates satellite DNA evolution. Sci. Rep. 2016;6:28333. doi: 10.1038/srep28333. PubMed DOI PMC

Heckmann S, et al. The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. Plant J. 2013;73:555–565. doi: 10.1111/tpj.12054. PubMed DOI

Macas, J. et al. In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe Fabeae. PLoS One10, e0143424 (2015). PubMed PMC

Döbel P, Schubert I, Rieger R. Distribution of heterochromatin in a reconstructed karyotype of Vicia faba as identified by banding- and DNA-late replication patterns. Chromosoma. 1978;69:193–209. doi: 10.1007/BF00329918. DOI

Fuchs J, Pich U, Meister A, Schubert I. Differentiation of field bean heterochromatin byin situ hybridization with a repeated FokI sequence. Chromosom. Res. 1994;2:25–28. doi: 10.1007/BF01539450. PubMed DOI

Schubert I, Rieger R. Asymmetric banding of Vicia faba chromosomes after BrdU incorporation. Chromosoma. 1979;70:385–391. doi: 10.1007/BF00328774. DOI

Fuchs J, Strehl S, Brandes A, Schweizer D, Schubert I. Molecular-cytogenetic characterization of the Vicia faba genome- heterochromatin differentiation, replication patterns and sequence localization. Chromosom. Res. 1998;6:219–30. doi: 10.1023/A:1009215802737. PubMed DOI

Fuchs, J. & Schubert, I. Chromosomal distribution and functional interpretation of epigenetic histone marks in plants. In Plant Cytogenetics (eds. Bass, H. W. & Birchler, J. A.) 231–253 (Springer Science + Business Media, LLC, 2012).

Kato, A., Yakura, K. & Tanifuji, S. Sequence analysis of Vicia faba repeated DNA, the FokI repeat element. Nucleic Acids Res. 12, 6415–6426 (1984). PubMed PMC

Maggini F, et al. Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba. Chromosoma. 1991;100:229–234. doi: 10.1007/BF00344156. PubMed DOI

Houben A, Brandes A, Pich U, Manteuffel R, Schubert I. Molecular-cytogenetic characterization of a higher plant centromere/kinetochore complex. Theor. Appl. Genet. 1996;93:477–484. doi: 10.1007/BF00417938. PubMed DOI

Nouzová M, et al. Cloning and characterization of new repetitive sequences in field bean (Vicia faba L.) Ann. Bot. 1999;83:535–541. doi: 10.1006/anbo.1999.0853. DOI

Neumann P, et al. Stretching the rules: monocentric chromosomes with multiple centromere domains. PLoS Genet. 2012;8:e1002777. doi: 10.1371/journal.pgen.1002777. PubMed DOI PMC

Puterova J, et al. Satellite DNA and transposable elements in Seabuckthorn (Hippophae rhamnoides), a dioecious plant with small Y and large x chromosomes. Genome Biol. Evol. 2017;9:197–212. PubMed PMC

Emadzade K, et al. Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae) Ann. Bot. 2014;114:1597–608. doi: 10.1093/aob/mcu178. PubMed DOI PMC

Macas J, Požárková D, Navrátilová A, Nouzová M, Neumann P. Two new families of tandem repeats isolated from genus Vicia using genomic self-priming PCR. Mol. Gen. Genet. 2000;263:741–51. doi: 10.1007/s004380000245. PubMed DOI

Klemme S, et al. High-copy sequences reveal distinct evolution of the rye B chromosome. New Phytol. 2013;199:550–558. doi: 10.1111/nph.12289. PubMed DOI

Langdon T, et al. De novo evolution of satellite DNA on the rye B chromosome. Genetics. 2000;154:869–84. PubMed PMC

Martis MM, et al. Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc. Natl. Acad. Sci. USA. 2012;109:13343–13346. doi: 10.1073/pnas.1204237109. PubMed DOI PMC

Tek AL, Song J, Macas J, Jiang J. Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences. Genetics. 2005;170:1231–8. doi: 10.1534/genetics.105.041087. PubMed DOI PMC

Zhang H, et al. Boom-bust turnovers of megabase-sized centromeric DNA in Solanum species: rapid evolution of DNA sequences associated with centromeres. Plant Cell. 2014;26:1436–1447. doi: 10.1105/tpc.114.123877. PubMed DOI PMC

McKinley KL, Cheeseman IM. The molecular basis for centromere identity and function. Nat Rev Mol Cell Biol. 2016;17:16–29. doi: 10.1038/nrm.2015.5. PubMed DOI PMC

Comai L, Maheshwari S, Marimuthu MPA. Plant centromeres. Curr. Opin. Plant Biol. 2017;36:158–167. doi: 10.1016/j.pbi.2017.03.003. PubMed DOI

Catania S, Pidoux AL, Allshire RC. Sequence features and transcriptional stalling within centromere DNA promote establishment of CENP-A chromatin. PLOS Genet. 2015;11:e1004986. doi: 10.1371/journal.pgen.1004986. PubMed DOI PMC

McFarlane RJ, Humphrey TC. A role for recombination in centromere function. Trends Genet. 2010;26:209–13. doi: 10.1016/j.tig.2010.02.005. PubMed DOI

Wang G, Zhang X, Jin W. An overview of plant centromeres. J. Genet. Genomics. 2009;36:529–537. doi: 10.1016/S1673-8527(08)60144-7. PubMed DOI

Malik HS, Henikoff S. Major evolutionary transitions in centromere complexity. Cell. 2009;138:1067–82. doi: 10.1016/j.cell.2009.08.036. PubMed DOI

Neumann P, et al. Centromeres off the hook: massive changes in centromere size and structure following duplication of CenH3 gene in Fabeae species. Mol. Biol. Evol. 2015;32:1862–1879. doi: 10.1093/molbev/msv070. PubMed DOI PMC

Wear, E. E. et al. Genomic analysis of the DNA replication timing program during mitotic S phase in maize (Zea mays L.) root tips. Plant Cell. 29, 2126–2149 (2017). PubMed PMC

Lee, T. J. et al. Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genet.6, e1000982 (2010). PubMed PMC

Rieger MA, Schubert I, Dobel P, Jank H-W. Non-random intrachromosomal distribution of chromatid aberrations induced by X-rays, alkylating agents and ethanol in Vicia faba. Mutat. Res. 1975;27:69–79. doi: 10.1016/0027-5107(75)90274-2. DOI

Rieger R, Michaelis A, Schubert I, Kaina B. Effects of chromosome repatterning in Vicia faba L. Biol. Zent. Bl. 1977;96:161–182.

Schubert I, et al. DNA damage processing and aberration formation in plants. Cytogenet. Genome Res. 2004;104:104–108. doi: 10.1159/000077473. PubMed DOI

Schubert I, Rieger R, Fuchs J, Pich U. Sequence organization and the mechanism of interstitial deletion clustering in a plant genome (Vicia faba) Mutat. Res. 1994;325:1–5. doi: 10.1016/0165-7992(94)90020-5. PubMed DOI

Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Mol. Biol. Report. 1983;1:19–21. doi: 10.1007/BF02712670. DOI

Burge C, Campbell AM, Karlin S. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. 1992;89:1358–1362. doi: 10.1073/pnas.89.4.1358. PubMed DOI PMC

Neumann, P., Požárková, D., Vrána, J., Doležel, J. & Macas, J. Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.). Chromosom. Res.10, 63–71 (2002). PubMed

Kato, A., Albert, P. S., Vega, J. M. & Birchler, J. A. Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech. Histochem. 81, 71–78 (2006). PubMed

Macas J, Neumann P, Navrátilová A. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics. 2007;8:427. doi: 10.1186/1471-2164-8-427. PubMed DOI PMC

Altschul SF, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402. doi: 10.1093/nar/25.17.3389. PubMed DOI PMC

Evans HJ, Scott D. Influence of DNA synthesis on the production of chromatid aberrations. Genetics. 1964;49:17–38. PubMed PMC

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