Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

Annals of Botany

Volumn 107, Issue 2, 2011, Pages 255-268

  Ambrožová, Kateřina ^a   Mandáková, Terezie ^a   Bureš, Petr ^a   Neumann, Pavel ^b   Leitch, Ilia J ^c   Koblížková, Andrea ^b   Macas, Jiří ^b   Lysak, Martin A ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

^b INSTITUTE OF PLANT MOLECULAR BIOLOGY   (Czech Republic)

^c JODRELL LABORATORY   (United Kingdom)

Author keywords

chromosomes; Fritillaria; genome size variation; heterochromatin; Liliaceae; repetitive DNA; retrotransposon; satellite repeats; transposable elements

Indexed keywords

SATELLITE DNA;

CHROMOSOME; GENOME; MITOCHONDRIAL DNA; MONOCOTYLEDON; PHYLOGENETICS; PHYLOGEOGRAPHY;

ARTICLE; AT RICH SEQUENCE; DNA SEQUENCE; FRITILLARIA; GENETIC VARIABILITY; GENETICS; HETEROCHROMATIN; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENOME; RETROPOSON;

AT RICH SEQUENCE; BASE SEQUENCE; DNA, SATELLITE; EVOLUTION, MOLECULAR; FRITILLARIA; GENETIC VARIATION; GENOME, PLANT; HETEROCHROMATIN; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TERMINAL REPEAT SEQUENCES;

FRITILLARIA (ANGIOSPERM); FRITILLARIA AFFINIS; FRITILLARIA IMPERIALIS; LILIACEAE;

EID: 79551534165     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcq235     Document Type: Article

References (51)

1. Altschul SF, Madden TL, Schaffer AA, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
2. Bakhshi Khaniki G. 2004. Giemsa C-banding and karyological studies in species of Rhinopetalum (Liliaceae). National Academy of Science Letters 27: 399-411.
3. Bennett MD, Leitch IJ. 2005. Plant DNA C-values database (release 4.0, October 2005).
4. Bennett MD, Smith JB. 1976. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society of London. B, Biological Sciences 274: 227-274.
5. Darlington CD. 1935. The internal mechanics of the chromosomes I.-The nuclear cycle in Fritillaria. Proceedings of the Royal Society of London-Series B 118: 33-59.
6. Darlington CD. 1937. Recent Advances in Cytology. London: Churchill.
7. Darlington CD, La Cour LF. 1941. The detection of inert genes. Journal of Heredity 32: 115-121.
8. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113-113.
9. Frankel OH. 1940. The causal sequence of meiosis. I. Chiasma formation and the order of pairing in Fritillaria. Journal of Genetics 41: 9-34.
10. Grandbastien MA, Spielmann A, Caboche M. 1989. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376-380.
11. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 16: 1252-1261.
12. Hawkins JS, Hu G, Rapp RA, Grafenberg JL, Wendel JF. 2008. Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium. Genome 51: 11-18.
13. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110: 462-467.
14. Kentner EK, Arnold ML, Wessler SR. 2003. Characterization of high-copy-number retrotransposons from the large genomes of the Louisiana iris species and their use as molecular markers. Genetics 164: 685-697.
15. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474. doi:10.1186/1471-2105-7-474.
16. La Cour LF. 1951. Heterochromatin and the organization of nucleoli in plants. Heredity 5: 37-50.
17. La Cour LF. 1978. The constitutive heterochromatin in chromosomes of Fritillaria sp., as revealed by Giemsa Banding. Philosophical Transactions of the Royal Society of London Series B 285: 61-71.
18. Leeton PR, Smyth DR. 1993. An abundant LINE-like element amplified in the genome of Lilium speciosum. Molecular and General Genetics 237: 97-104.
19. Leitch IJ, Beaulieu JM, Cheung K, Hanson L, Lysak MA, Fay MF. 2007. Punctuated genome size evolution in Liliaceae. Journal of Evolutionary Biology 20: 2296-2308.
20. Li R, Shang Z. 1989. The chromosome observation on five species of rare plants of China. Journal of Wuhan Botanical Research 7: 217-220.
21. Llorens C, Fares MA, Moya A. 2008. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evolutionary Biology 8: 276. doi:10.1186/ 1471-2148-8-276
22. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964.
23. Macas J, Neumann P, Navrátilova A. 2007. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 8: 427. doi:10.1186/1471-2164-8-427.
24. Mandáková T, Lysak MA. 2008. Chromosomal phylogeny and karyotype evolution in x7 crucifer species (Brassicaceae). Plant Cell 20: 2559-2570.
25. Marchant CJ, Macfarlane RM. 1980. Chromosome polymorphism in triploid populations of Fritillaria lanceolata Pursh (Liliaceae) in California. Botanical Journal of the Linnean Society 81: 135-154.
26. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, et al. 2003. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research 31: 383-387.
27. Moisy C, Garrison KE, Meredith CP, Pelsy F. 2008. Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome. BMC Genomics 9: 469. doi:10.1186/1471-2164-9-469.
28. Neumann P, Koblizkova A, Navratilova A, Macas J. 2006. Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics 173: 1047-1056.
29. Noda S. 1964. Cytology in the genus Fritillaria. I. Variations in karyotypes and B-chromosomes in F. amabilis. Bulletin of the Osaka Gakuin University 2: 125-132.
30. Noda S. 1968. Cytology in the genus Fritillaria. II. Karyotypes and B-chromosomes in F. japonica var. japonica and var. koidzumiana. Bulletin of the Osaka Gakuin University 10: 127-141.
31. Patterson TB, Givnish TJ. 2002. Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data. Evolution 56: 233-252.
32. Pellicer J, Fay MF, Leitch IJ. 2010. The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society 164: 10-15.
33. Peruzzi L, Leitch IJ, Caparelli KF. 2009. Chromosome diversity and evolution in Liliaceae. Annals of Botany 103: 459-475.
34. Pfosser M, Amon A, Lelley T, Heberle-Bors E. 1995. Evaluation of sensitivity of flow cytometry in detecting aneuploidy in wheat using disomic and ditelosomic wheat-rye addition lines. Cytometry 21: 387-393.
35. Rix EM. 2001. Fritillaria. A revised classification. The Fritillaria Group of the Alpine Garden Society, UK.
36. Rønsted N, Law S, Thornton H, Fay MF, Chase MW. 2005. Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria. Molecular Phylogenetics and Evolution 35: 509-527.
37. SanMiguel P, Tikhonov A, Jin YK, et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
38. Sentry JW, Smyth DR. 1989. An element with long terminal repeats and its variant arrangements in the genome of Lilium henryi. Molecular and General Genetics 215: 349-354.
39. Smyth DR, Kalitsis P, Joseph JL, Sentry JW. 1989. Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila. The Proceedings of the National Academy of Sciences USA 86: 5015-5019.
40. Sonnhammer EL, Durbin R. 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: 1-10.
41. Staden R. 1996. The Staden sequence analysis package. Molecular Biotechnology 5: 233-241.
42. Sun HY, Dai HY, Zhao GL, et al. 2008. Genome-wide characterization of long terminal repeat-retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons. Journal of Integrative Plant Biology 50: 1130-1139.
43. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
44. Vant Hof J. 1965. Relationships between mitotic cycle duration, S period duration and the average rate of DNA synthesis in the root meristem cells of several plants. Experimental Cell Research 39: 48-58.
45. Vinnersten A, Bremer K. 2001. Age and biogeography of major clades in Liliales. American Journal of Botany 88: 1695-1703.
46. Vitte C, Bennetzen JL. 2006. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. The Proceedings of the National Academy of Sciences USA 103: 17638-17643.
47. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B. 2001. Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. The Plant Journal 26: 307-316.
48. Wicker T, Sabot F, Hua-Van A, et al. 2007. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973-982.
49. Zonneveld BJM. 2010. New record holders for maximum genome size in eudicots and monocots. Journal of Botany 2010: 527357. doi:10.1155/ 2010/527357.
50. Zonneveld BJM, Leitch IJ, Bennett MD. 2005. First nuclear DNA amounts in more than 300 angiosperms. Annals of Botany 96: 229-244.
51. Zuccolo A, Sebastian A, Talag J, et al. 2007. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evolutionary Biology 7: 152. doi:10.1186/ 1471-2148-7-152