Allium telomeres unmasked: The unusual telomeric sequence (CTCGGTTATGGG)n is synthesized by telomerase

Plant Journal

Volumn 85, Issue 3, 2016, Pages 337-347

  Fajkus, Petr ^a,b   Peška, Vratislav ^b   Sitová, Zdeňka ^a   Fulnečková, Jana ^b   Dvořáčková, Martina ^a,b   Gogela, Roman ^a   Sýkorová, Eva ^b   Hapala, Jan ^a   Fajkus, Jiří ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

^b INSTITUTE OF MATHEMATICS   (Czech Republic)

Author keywords

Allium; evolution; genome sequencing; onion; telomerase; TERT; unusual telomere

Indexed keywords

BIOINFORMATICS; BIOLOGY; CHROMOSOMES; FLUORESCENCE MICROSCOPY; GENES; PLANTS (BOTANY);

ALLIUM; EVOLUTION; GENOME SEQUENCING; ONION; TELOMERASE; TELOMERES; TERT;

IN SITU PROCESSING;

TELOMERASE; TRANSCRIPTOME;

ALLIUM; BIOLOGY; DNA SEQUENCE; ENZYMOLOGY; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GENOMICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT CHROMOSOME; TELOMERE;

ALLIUM; BASE SEQUENCE; CHROMOSOMES, PLANT; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOMICS; IN SITU HYBRIDIZATION, FLUORESCENCE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TELOMERASE; TELOMERE; TRANSCRIPTOME;

EID: 84956733763     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.13115     Document Type: Article

References (47)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and, Lipman, D.J., (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Baranyi, M., and, Greilhuber, J., (1999) Genome size in Allium: in quest of reproducible data. Ann. Bot., 83, 687-695.
3. Benson, G., (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
4. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and, Taylor, J., (2010) Galaxy: a web-based genome analysis tool for experimentalists. Current protocols in molecular biology, 2010, 1-21.
5. Bremer, B., Bremer, K., Chase, M.W., et al. (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc., 161, 105-121.
6. Bryan, T.M., and, Reddel, R.R., (1997) Telomere dynamics and telomerase activity in in vitro immortalised human cells. Eur. J. Cancer, 33, 767-773.
7. Bryan, T.M., Englezou, A., DallaPozza, L., Dunham, M.A., and, Reddel, R.R., (1997) Evidence for an alternative mechanism for maintaining telomere length in human tumors and tumor-derived cell lines. Nat. Med., 3, 1271-1274.
8. Chester, M., Sykorova, E., Fajkus, J., and, Leitch, A.R., (2010) Single integration and spread of a Copia-like sequence nested in rDNA intergenic spacers of Allium cernuum (Alliaceae). Cytogenet Genome Res, 129, 35-46.
9. Dellaporta, S., Wood, J., and, Hicks, J., (1983) A plant DNA minipreparation: version II. Plant Mol. Biol. Rep., 1, 19-21.
10. Fajkus, J., Kovarik, A., and, Kralovics, R., (1996) Telomerase activity in plant cells. FEBS Lett., 391, 307-309.
11. Fajkus, J., Fulneckova, J., Hulanova, M., Berkova, K., Riha, K., and, Matyasek, R., (1998) Plant cells express telomerase activity upon transfer to callus culture, without extensively changing telomere lengths. Mol. Gen. Genet., 260, 470-474.
12. Fajkus, J., Sykorova, E., and, Leitch, A.R., (2005a) Techniques in plant telomere biology. Biotechniques, 38, 233-243.
13. Fajkus, J., Sykorova, E., and, Leitch, A.R., (2005b) Telomeres in evolution and evolution of telomeres. Chromosome Res., 13, 469-479.
14. Fitzgerald, M.S., McKnight, T.D., and, Shippen, D.E., (1996) Characterization and developmental patterns of telomerase expression in plants. Proc. Natl Acad. Sci. USA, 93, 14422-14427.
15. Friesen, N., Fritsch, R.M., and, Blattner, F.R., (2006) Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso, 22, 372-395.
16. Fuchs, J., Brandes, A., and, Schubert, I., (1995) Telomere sequence localization and karyotype evolution in higher plants. Plant Syst. Evol., 196, 227-241.
17. Giardine, B., Riemer, C., Hardison, R.C., et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
18. Goecks, J., Nekrutenko, A., Taylor, J., and, Galaxy, T., (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
19. Grant, J.D., Broccoli, D., Muquit, M., Manion, F.J., Tisdall, J., and, Ochs, M.F., (2001) Telometric: a tool providing simplified, reproducible measurements of telomeric DNA from constant field agarose gels. Biotechniques, 31 (1314-1316), 1318.
20. n generated by PCR. Nucleic Acids Res., 19, 4780.
21. Jain, D., Hebden, A.K., Nakamura, T.M., Miller, K.M., and, Cooper, J.P., (2010) HAATI survivors replace canonical telomeres with blocks of generic heterochromatin. Nature, 467, 223-227.
22. Katoh, K., Misawa, K., Kuma, K., and, Miyata, T., (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
23. Kumar, A., Pearce, S.R., McLean, K., Harrison, G., Heslop-Harrison, J.S., Waugh, R., and, Flavell, A.J., (1997) The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica, 100, 205-217.
24. Li, Q.Q., Zhou, S.D., He, X.J., Yu, Y., Zhang, Y.C., and, Wei, X.Q., (2010) Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann. Bot., 106, 709-733.
25. - senescence. Cell, 73, 347-360.
26. Mandakova, T., and, Lysak, M.A., (2008) Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell, 20, 2559-2570.
27. Martin, M., (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17, 10-12.
28. Muchova, V., Amiard, S., Mozgova, I., Dvorackova, M., Gallego, M.E., White, C., and, Fajkus, J., (2015) Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants. Plant Journal, 81, 198-209.
29. Novak, P., Neumann, P., Pech, J., Steinhaisl, J., and, Macas, J., (2013) RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics, 29, 792-793.
30. Orlov, Y.L., and, Potapov, V.N., (2004) Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Res., 32, W628-W633.
31. n in the plant Cestrum elegans (Solanaceae), a species with a large genome. Plant journal, 82, 644-654.
32. Pich, U., and, Schubert, I., (1998) Terminal heterochromatin and alternative telomeric sequences in Allium cepa. Chromosome Res., 6, 315-321.
33. Pich, U., Fuchs, J., and, Schubert, I., (1996) How do Alliaceae stabilize their chromosome ends in the absence of TTTAGGG sequences? Chromosome Res., 4, 207-213.
34. Reddel, R.R., Bryan, T.M., and, Murnane, J.P., (1997) Immortalized cells with no detectable telomerase activity. A review. Biochemistry, 62, 1254-1262.
35. Richards, E.J., and, Ausubel, F.M., (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell, 53, 127-136.
36. Roth, C.W., Kobeski, F., Walter, M.F., and, Biessmann, H., (1997) Chromosome end elongation by recombination in the mosquito Anopheles gambiae. Mol. Cell. Biol., 17, 5176-5183.
37. Ruckova, E., Friml, J., Schrumpfova, P.P., and, Fajkus, J., (2008) Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Mol. Biol., 66, 637-646.
38. Saitou, N., and, Nei, M., (1987) The neighbor-joining method-a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
39. Siroky, J., Zluvova, J., Riha, K., Shippen, D.E., and, Vyskot, B., (2003) Rearrangements of ribosomal DNA clusters in late generation telomerase-deficient Arabidopsis. Chromosoma, 112, 116-123.
40. Sykorova, E., and, Fajkus, J., (2009) Structure-function relationships in telomerase genes. Biol. Cell, 101, 375-392.
41. Sykorova, E., Lim, K.Y., Kunicka, Z., Chase, M.W., Bennett, M.D., Fajkus, J., and, Leitch, A.R., (2003) Telomere variability in the monocotyledonous plant order Asparagales. Proc Biol Sci, 270, 1893-1904.
42. Sykorova, E., Fajkus, J., Meznikova, M., Lim, K.Y., Neplechova, K., Blattner, F.R., Chase, M.W., and, Leitch, A.R., (2006a) Minisatellite telomeres occur in the family Alliaceae but are lost in Allium. Am. J. Bot., 93, 814-823.
43. Sykorova, E., Leitch, A.R., and, Fajkus, J., (2006b) Asparagales telomerases which synthesize the human type of telomeres. Plant Mol. Biol., 60, 633-646.
44. Trifonov, E.N., (1990) Making sense of the human genome. In Structure and Methods: human Genome Initiative and DNA Recombination (, Sarma, R.H., and, Saram, M.H., eds). Schenectady, NY: Adenine Press, pp. 69-78.
45. Weiss, H., and, Scherthan, H., (2002) Aloe spp.-plants with vertebrate-like telomeric sequences. Chromosome Res., 10, 155-164.
46. Yu, W., Yau, Y.Y., and, Birchler, J.A., (2016) Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnol. J., doi: 10.1111/pbi.12466.
47. Zhang, H.Q., Li, Y.Q., Kuras, M., Bednara, J., and, Cresti, M., (1996) Influence of hydroxyurea on cell divisions and microtubular cytoskeleton in Allium cepa root meristem. Acta Soc Bot Pol, 65, 179-185.