Characteristics and evolution of satellite DNA sequences in bivalve mollusks

References

• Bao W, Kojima KK, Kohany O. 2015. Repbase update, a database of repetitive elements in eukaryotic genomes. Mobile DNA 6: 11. DOI: 10.1186/s13100-015-0041-9.
   PubMed Web of Science ®Google Scholar
• Bieler R, Mikkelsen PM, Collins T, Glover E, González V, Graf D, Harper EM, Healy J, Kawauchi GY, Sharma PP, Staubach S, Strong EE, Taylor JD, Tëmkin I, Zardus JD, Clark S, Guzmán A, McIntyre E, Sharp P, Giribet G. 2014. Investigating the bivalve tree of life – An exemplar-based approach combining molecular and novel morphological characters. Invertebrate Systematics 28:32–115. http://www.bioone.org/doi/abs/10.1071/IS13010. DOI: 10.1071/IS13010.
   Web of Science ®Google Scholar
• Biscotti MA, Canapa A, Olmo E, Barucca M, Teo CH, Schwarzacher T, Dennerlein S, Richter R, Heslop-Harrison JSP. 2007. Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus). Gene 406:91–98. DOI: 10.1016/j.gene.2007.06.027.
   Web of Science ®Google Scholar
• Biscotti MA, Olmo E, Heslop-Harrison JS. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23:415–420. DOI: 10.1007/s10577-015-9499-z.
   Web of Science ®Google Scholar
• Canapa A, Barucca M, Cerioni PN, Olmo E. 2000. A satellite DNA containing CENP-B box-like motifs is present in the antarctic scallop Adamussium colbecki. Gene 247:175–180. DOI:10.1016/S0378-1119(00)00101-3.
   PubMed Web of Science ®Google Scholar
• Clabby C, Goswami U, Flavin F, Wilkins NP, Houghton JA, Powell R. 1996. Cloning, characterization and chromosomal location of a satellite DNA from the pacific oyster, Crassostrea-gigas. Gene 168:205–209. DOI:10.1016/0378-1119(95)00749-0.
   PubMed Web of Science ®Google Scholar
• Gaffney PM, Pierce JC, Mackinley AG, Titchen DA, Glenn WK. 2003. Pearl, a novel family of putative transposable elements in bivalve mollusks. Journal of Molecular Evolution 56:308–316. DOI: 10.1007/s00239-002-2402-5.
   Web of Science ®Google Scholar
• García-Souto D, Mravinac B, Šatović E, Plohl M, Morán P, Pasantes JJ. 2017. Methylation profile of a satellite DNA constituting the intercalary G+C-rich heterochromatin of the cut trough shell Spisula subtruncata (Bivalvia, Mactridae). Scientific Reports 7:6930. DOI: 10.1038/s41598-017-07231-7.
   Web of Science ®Google Scholar
• Garrido-Ramos MA. 2017. Satellite DNA: An evolving topic. Genes 8:9. DOI: 10.3390/genes8090230.
   Web of Science ®Google Scholar
• Gosling E. 2003. Bivalve molluscs: Biology, ecology and culture. Oxford: Fishing News Books.
   Google Scholar
• Henikoff S, Ahmad K, Malik HS. 2001. The centromere paradox: Stable inheritance with rapidly evolving DNA. Science 293:1098–1102. DOI: 10.1126/science.1062939.
   PubMed Web of Science ®Google Scholar
• Heslop-Harrison JSP, Schwarzacher T 2013. Nucleosomes and centromeric DNA packaging. Proceedings of the National Academy of Sciences of the United States of America 110:19974–19975. DOI: 10.1073/pnas.1319945110
   Google Scholar
• Jurka J. 2012. Satellite DNA from the Pacific oyster genome SAT-1_CGi. Repbase Reports 12:2722.
   Google Scholar
• Kipling D, Warburton PE. 1997. Centromeres, CENP-B and tigger too. Trends in Genetics 13:1–5. DOI: 10.1016/S0168-9525(97)01098-6.
   Web of Science ®Google Scholar
• Kourtidis A, Drosopoulou E, Pantzartzi CN, Chintiroglou CC, Scouras ZG. 2006. Three new satellite sequences and a mobile element found inside HSP70 introns of the Mediterranean mussel (Mytilus galloprovincialis). Genome 49:1451–1458. DOI: 10.1139/g06-111.
   Web of Science ®Google Scholar
• Kuhn GCS, Teo CH, Schwarzacher T, Heslop-Harrison JS. 2009. Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species. Heredity 102:453–464. DOI: 10.1038/hdy.2009.9.
   Web of Science ®Google Scholar
• López-Flores I, de la Herrán R, Garrido-Ramos MA, Boudry P, Ruiz-Rejón C, Ruiz-Rejón M. 2004. The molecular phylogeny of oysters based on a satellite DNA related to transposons. Gene 339:181–188. DOI: 10.1016/j.gene.2004.06.049.
   PubMed Web of Science ®Google Scholar
• López-Flores I, Garrido-Ramos MA. 2012. The repetitive DNA content of eukaryotic genomes. In: Garrido-Ramos MA, editor. Repetitive DNA. Genome dynamics. Vol. 7: Basel: Karger. pp. 1–28. DOI: 10.1159/000337118.
   Google Scholar
• López-Flores I, Ruiz-Rejón C, Cross I, Rebordinos L, Robles F, Navajas-Pérez R, de la Herrán R. 2010. Molecular characterization and evolution of an interspersed repetitive DNA family of oysters. Genetica 138:1211–1219. DOI: 10.1007/s10709-010-9517-1.
   Web of Science ®Google Scholar
• Martínez-Lage A, Rodríguez F, González-Tizón A, Prats E, Cornudella L, Méndez J. 2002. Comparative analysis of different satellite DNAs in four Mytilus species. Genome 45:922–929. DOI:10.1139/g02-056.
   PubMed Web of Science ®Google Scholar
• Martínez-Lage A, Rodríguez-Fariña F, González-Tizón A, Méndez J. 2005. Origin and evolution of Mytilus mussel satellite DNAs. Genome 48:247–256. DOI: 10.1139/G04-115.
   Web of Science ®Google Scholar
• Masumoto H, Masukata H, Muro Y, Nozaki N, Okazaki T. 1989. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. The Journal of Cell Biology 109:1963–1973. DOI:10.1083/jcb.109.5.1963.
   PubMed Web of Science ®Google Scholar
• Meštrović N, Mravinac B, Pavlek M, Vojvoda-Zeljko T, Šatović E, Plohl M. 2015. Structural and functional liaisons between transposable elements and satellite DNAs. Chromosome Research 23:583–596. DOI: 10.1007/s10577-015-9483-7.
   Web of Science ®Google Scholar
• Meštrović N, Pavlek M, Car A, Castagnone-Sereno P, Abad P, Plohl M. 2013. Conserved DNA motifs, including the CENP-B Box-like, are possible promoters of satellite DNA array rearrangements in Nematodes. PLoS ONE 8:e67328. DOI: 10.1371/journal.pone.0067328.
   Web of Science ®Google Scholar
• Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C. 2016. A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialis. PloS One 11:1–22. DOI: 10.1371/journal.pone.0151561.
   Web of Science ®Google Scholar
• Odierna G, Aprea G, Barucca M, Canapa A, Capriglione T, Olmo E. 2006. Karyology of the Antarctic scallop Adamussium colbecki, with some comments on the karyological evolution of pectinids. Genetica 127:341–349. DOI: 10.1007/s10709-005-5366-8.
   Web of Science ®Google Scholar
• Passamonti M, Mantovani B, Scali V. 1998. Characterization of a highly repeated DNA family in tapetinae species (Mollusca Bivalvia: Veneridae). Zoological Science 15:599–605. DOI: 10.2108/0289-0003(1998)15[599:COAHRD]2.0.CO;2.
   Web of Science ®Google Scholar
• Petraccioli A, Odierna G, Capriglione T, Barucca M, Forconi M, Olmo E, Biscotti MA. 2015. A novel satellite DNA isolated in Pecten jacobaeus shows high sequence similarity among molluscs. Molecular Genetics and Genomics 290:1717–1725. DOI: 10.1007/s00438-015-1036-4.
   Web of Science ®Google Scholar
• Petrović V, Pérez-García C, Pasantes JJ, Šatović E, Prats E, Plohl M. 2009. A GC-rich satellite DNA and karyology of the bivalve mollusk Donax trunculus: A dominance of GC-rich heterochromatin. Cytogenetic and Genome Research 124:63–71. DOI: 10.1159/000200089.
   Web of Science ®Google Scholar
• Petrović V, Plohl M. 2005. Sequence divergence and conservation in organizationally distinct subfamilies of Donax trunculus satellite DNA. Gene 362:37–43. DOI: 10.1016/j.gene.2005.06.044.
   PubMed Web of Science ®Google Scholar
• Pita S, Panzera F, Mora P, Vela J, Cuadrado Á, Sánchez A, Palomeque T, Lorite P. 2017. Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease. PloS One 12:e0181635. DOI: 10.1371/journal.pone.0181635.
   Web of Science ®Google Scholar
• Plohl M, Cornudella L. 1996. Characterization of a complex satellite DNA in the mollusc Donax trunculus: Analysis of sequence variations and divergence. Gene 169:157–164. DOI:10.1016/0378-1119(95)00734-2.
   PubMed Web of Science ®Google Scholar
• Plohl M, Cornudella L. 1997. Characterization of interrelated sequence motifs in four satellite DNAs and their distribution in the genome of the mollusc Donax trunculus. Journal of Molecular Evolution 44:189–198. DOI:10.1007/PL00006135.
   Web of Science ®Google Scholar
• Plohl M, Luchetti A, Meštrović N, Mantovani B. 2008. Satellite DNAs between selfishness and functionality: Structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409:72–82. DOI:10.1016/j.gene.2007.11.013.
   PubMed Web of Science ®Google Scholar
• Plohl M, Meštrović N, Mravinac B. 2012. Satellite DNA evolution. In: Garrido- Ramos MA, editor. Genome dynamics. Vol. 7: Basel: Karger. pp. 126–152. DOI: 10.1159/000337122.
   Google Scholar
• Plohl M, Petrović V, Luchetti A, Ricci A, Šatović E, Passamonti M, Mantovani B. 2010. Long-term conservation vs high sequence divergence: The case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity 104:543–551. DOI: 10.1038/hdy.2009.141.
   Web of Science ®Google Scholar
• Plohl M, Prats E, Martinez-Lage A, Gonzalez-Tizon A, Mendez J, Cornudella L. 2002. Telomeric localization of the vertebrate-type hexamer repeat, (TTAGGG)n, in the wedgeshell clam Donax trunculus and other marine invertebrate genomes. The Journal of Biological Chemistry 277:19839–19846. DOI: 10.1074/jbc.M201032200.
   PubMed Web of Science ®Google Scholar
• Ruiz-Lara S, Prats E, Sainz J, Cornudella L. 1992. Cloning and characterization of a highly conserved satellite DNA from the mollusc Mytilus edulis. Gene 117:237–242.
   Web of Science ®Google Scholar
• Ruiz-Ruano FJ, López-León MD, Cabrero J, Camacho JPM. 2016. High-throughput analysis of the satellitome illuminates satellite DNA evolution. Scientific Reports 6:28333. DOI: 10.1038/srep28333.
   PubMed Web of Science ®Google Scholar
• Saavedra C, Bachère E. 2006. Bivalve genomics. Aquaculture 256:1–14. DOI:10.1016/j.aquaculture.2006.02.023.
   Web of Science ®Google Scholar
• Šatović E, Plohl M. In press. Distribution of DTHS3 satellite DNA across 12 bivalve species. Journal Od Genetics.
   Google Scholar
• Šatović E, Vojvoda Zeljko T, Luchetti A, Mantovani B, Plohl M. 2016. Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements. BMC Genomics 17:997. DOI: 10.1186/s12864-016-3347-1.
   Web of Science ®Google Scholar
• Silva DMZDA, Utsunomia R, Ruiz-Ruano FJ, Daniel SN, Porto-Foresti F, Hashimoto DT, Oliveira C, Porto-Foresti F, Foresti F. 2017. High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. Scientific Reports 7:12726. DOI: 10.1038/s41598-017-12939-7.
   Web of Science ®Google Scholar
• Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, et al. 2012. Draft genome of the pearl oyster Pinctada fucata: A platform for understanding bivalve biology. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes 19:117–130. DOI: 10.1093/dnares/dss005.
   PubMed Web of Science ®Google Scholar
• Thomas J, Pritham EJ. 2015. Helitrons, the Eukaryotic rolling-circle transposable elements. Microbiology Spectrum 3:1–32. DOI: 10.1128/microbiolspec.MDNA3-0049-2014.
   Web of Science ®Google Scholar
• Wang X, Li Q, Lian J, Li L, Jin L, Cai H, Xu F, Qi H, Zhang L, Wu F, Meng J, Que H, Fang X, Guo X, Zhang G. 2014. Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation. BMC Genomics 15:1119. DOI: 10.1186/1471-2164-15-1119.
   Web of Science ®Google Scholar
• Wang Y, Xu Z, Guo X. 2001. A centromeric satellite sequence in the Pacific oyster (Crassostrea gigas Thunberg) identified by fluorescence in situ hybridization. Marine Biotechnology 3:486–492. DOI: 10.1007/s10126-001-0063-3.
   Web of Science ®Google Scholar
• Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, et al. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490:49–54. DOI: 10.1038/nature11413.
   PubMed Web of Science ®Google Scholar