Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species

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• 作者：Saemundur Sveinsson (12)
  Navdeep Gill (12)
  Nolan C Kane (13)
  Quentin Cronk (12)
  
• 关键词：Theobroma cacao ; Transposable elements ; Next generation sequencing ; Graph based clustering ; Retrotransposon
• 刊名：BMC Genomics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：14
• 期：1
• 全文大小：470KB
• 参考文献：1. Kumar A, Bennetzen JL: Plant retrotransposons. / Annu Rev Genet 1999, 33:479-32. CrossRef
  2. Feschotte C, Pritham EJ: DNA transposons and the evolution of eukaryotic genomes. / Annu Rev Genet 2007, 41:331-68. CrossRef
  3. Kelly LJ, Leitch IJ: Exploring giant plant genomes with next-generation sequencing technology. / Chromosome Res 2011, 19:1-5. CrossRef
  4. Sun C, Shepard DB, Chong RA, Arriaza JL, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. / Genome Biol Evol 2012, 4:168-83. CrossRef
  5. Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A: A transposon-induced epigenetic change leads to sex determination in melon. / Nature 2009, 461:1135-138. CrossRef
  6. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, Craig NL: Transposition of hAT elements links transposable elements and V (D) J recombination. / Nature 2004, 432:995-001. CrossRef
  7. Craig NL, Craigie R, Gellert M, Lambowitz AM: / Mobile DNA II. Washington, DC: Amer Society for Microbiology; 2002.
  8. Boeke JD, Corces VG: Transcription and reverse transcription of retrotransposons. / Annu Rev Microbiol 1989, 43:403-34. CrossRef
  9. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O: A unified classification system for eukaryotic transposable elements. / Nat Rev Genet 2007, 8:973-82. CrossRef
  10. Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S: The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. / Genome Biol Evol 2011, 3:1-4. CrossRef
  11. Vicient CM, Suoniemi A, Anamthawat-Jónsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH: Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. / Plant Cell Online 1999, 11:1769-784.
  12. Pearce SR, Knox M, Ellis TH, Flavell AJ, Kumar A: Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. / Mol Gen Genet 2000, 263:898-07. CrossRef
  13. Huang X, Lu G, Zhao Q, Liu X, Han B: Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. / Plant Physiol 2008, 148:25-0. CrossRef
  14. Kumar A, Hirochika H: Applications of retrotransposons as genetic tools in plant biology. / Trends Plant Sci 2001, 6:127-34. CrossRef
  15. Syed N, Sureshsundar S, Wilkinson M, Bhau B, Cavalcanti J, Flavell A: Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). / Theor Appl Genet 2005, 110:1195-202. CrossRef
  16. Schulman AH, Flavell AJ, Paux E, Ellis T: The application of LTR retrotransposons as molecular markers in plants. / Methods Mol Biol 2012, 859:115-53. CrossRef
  17. Flavell AJ, Smith DB, Kumar A: Extreme heterogeneity of Ty1-copia group retrotransposons in plants. / Mol Gen Genet 1992, 231:233-42.
  18. Wood GAR, Lass RA: / Cocoa. 4th edition. Blackwell, UK: Longman Group; 2001. CrossRef
  19. Motamayor JC, Lachenaud P, e Mota JWS, Loor R, Kuhn DN, Brown JS, Schnell RJ: Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). / PLoS One 2008, 3:e3311. CrossRef
  20. Cheesman EE: Notes on the nomenclature, classification and possible relationships of cocoa populations. / Trop Agric 1944, 21:144-59.
  21. Motamayor JC, Risterucci AM, Heath M, Lanaud C: Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. / Heredity 2003, 91:322-30. CrossRef
  22. Kane N, Sveinsson S, Dempewolf H, Yang JY, Zhang D, Engels JMM, Cronk Q: Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. / Am J Bot 2012, 99:320-29. CrossRef
  23. Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN: The genome of Theobroma cacao. / Nat Genet 2010, 43:101-08. CrossRef
  24. Chaparro C, Sabot F: Methods and software in NGS for TE analysis. / Methods Mol Biol 2012, 859:105-14. CrossRef
  25. Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J: Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. / Genome Biol Evol 2011, 3:219. CrossRef
  26. Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, Piegu B, Roulin A, Guiderdoni E, Delabastide M, McCombie R: Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. / Plant J 2011, 66:241-46. CrossRef
  27. Macas J, Neumann P, Navratilova 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. CrossRef
  28. Wicker T, Narechania A, Sabot F, Stein J, Vu G, Graner A, Ware D, Stein N: Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. / BMC Genomics 2008, 9:518. CrossRef
  29. Hribova E, Neumann P, Matsumoto T, Roux N, Macas J, Dole?el J: Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. / BMC Plant Biol 2010, 10:204. CrossRef
  30. Wessler SR: Transposable elements and the evolution of eukaryotic genomes. / Proc Natl Acad Sci 2006, 103:17600-7601. CrossRef
  31. Gabriel A, Willems M, Mules EH, Boeke JD: Replication infidelity during a single cycle of Ty1 retrotransposition. / Proc Natl Acad Sci 1996, 93:7767-771. CrossRef
  32. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH: Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. / Proc Natl Acad Sci 2000, 97:6603-607. CrossRef
  33. Figueira A, Janick J, Goldsbrough P: Genome size and DNA polymorphism in Theobroma cacao. / J Am Soc Hortic Sci 1992, 117:673-77.
  34. Marie D, Brown SC: A cytometric exercise in plant DNA histograms, with 2C values for 70 species. / Biological Cell 1993, 78:41-1. CrossRef
  35. Xu Z, Wang H: LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. / Nucleic Acids Res 2007, 35:W265-W268. CrossRef
  36. Ellinghaus D, Kurtz S, Willhoeft U: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. / BMC Bioinforma 2008, 9:18. CrossRef
  37. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase update, a database of eukaryotic repetitive elements. / Cytogenet Genome Res 2005, 110:462-67. CrossRef
  38. Li H, Durbin R: Fast and accurate short read alignment with Burrows–Wheeler transform. / Bioinformatics 2009, 25:1754-760. CrossRef
  39. Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. / Bioinformatics 2010, 26:841-42. CrossRef
  40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. / Bioinformatics 2009, 25:2078-079. CrossRef
  41. Steinbiss S, Willhoeft U, Gremme G, Kurtz S: Fine-grained annotation and classification of de novo predicted LTR retrotransposons. / Nucleic Acids Res 2009, 37:7002-013. CrossRef
  42. Kozik A, Matvienko M, Kozik I, Van Leeuwen H, Van Deynze A, Michelmore R: Eukaryotic ultra conserved orthologs and estimation of gene capture In EST libraries [abstract]. / Plant and Animal Genomes Conference 2008, 16:P6.
  43. Altschul SF, Madden TL, Sch?ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Res 1997, 25:3389-402. CrossRef
  44. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. / Bioinformatics 2009, 25:1972-973. CrossRef
  45. Smith SA, Dunn CW: Phyutility: a phyloinformatics tool for trees, alignments and molecular data. / Bioinformatics 2008, 24:715-16. CrossRef
  46. Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. / Bioinformatics 2006, 22:2688-690. CrossRef
  47. Liu L, Yu L, Pearl DK, Edwards SV: Estimating species phylogenies using coalescence times among sequences. / Syst Biol 2009, 58:468-77. CrossRef
  48. Liu L, Yu L: PHYBASE: an R package for phylogenetic analysis. / Bioinformatics 2010, 26:962-63. CrossRef
  49. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. / Syst Biol 2003, 52:696-04. CrossRef
  50. Posada D: jModelTest: phylogenetic model averaging. / Mol Biol Evol 2008, 25:1253-256. CrossRef
  51. Zwickl DJ: / Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis. University of Texas; 2006.
  52. Seo TK: Calculating bootstrap probabilities of phylogeny using multilocus sequence data. / Mol Biol Evol 2008, 25:960-71. CrossRef
  53. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. / Syst Biol 2010, 59:307-1. CrossRef
  54. Felsenstein J: / PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Seattle: Department of Genetics, University of Washington; 1993.
  55. Novak 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, 29:792-93. CrossRef
  56. Novák P, Neumann P, Macas J: Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. / BMC Bioinforma 2010, 11:378. CrossRef
  57. Blondel VD, Guillaume JL, Lambiotte R, Lefebvre E: Fast unfolding of communities in large networks. / Journal of Statistical Mechanics: Theory and Experiment 2008.,200(8): P10008 CrossRef
  58. Ihaka R, Gentleman R: R: a language for data analysis and graphics. / J Comp Graph Stat 1996, 5:299-14.
  
• 作者单位：Saemundur Sveinsson (12)
  Navdeep Gill (12)
  Nolan C Kane (13)
  Quentin Cronk (12)
  
  12. Department of Botany and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
  13. Department of Ecology & Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Ave, Boulder, CO, 80309, USA
  

文摘

Background Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. Results (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. Conclusions (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint-to identify and characterize cacao accessions.