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Identification and Annotation of Repetitive Sequences in Fungal Genomes

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Fungal Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 722))

Abstract

Advances in sequencing technologies have fundamentally changed the pace of genome sequencing projects and have contributed to the ever-increasing volume of genomic data. This has been paralleled by an increase in computational power and resources to process and translate raw sequence data into meaningful information. In addition to protein coding regions, an integral part of all the genomes studied so far has been the presence of repetitive sequences. Previously considered as “junk,” numerous studies have implicated repetitive sequences in important biological and structural roles in the genome. Therefore, the identification and characterization of these repetitive sequences has become an indispensable part of genome sequencing projects. Numerous similarity-based and de novo methods have been developed to search for and annotate repeats in the genome, many of which have been discussed in this chapter.

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References

  1. Hugenholtz, P., and Tyson, G. W. (2008) Metagenomics Nature 455, 481–3.

    Article  CAS  Google Scholar 

  2. Wolinsky, H. (2007) The thousand-dollar genome EMBO reports 8, 900–3.

    Article  CAS  Google Scholar 

  3. Thomas, C. A. (1971) The genetic organization of chromosomes Annu Rev Genet 5, 237–56.

    CAS  Google Scholar 

  4. Lynch, M., and Conery, J. S. (2003) The origins of genome complexity Science 302, 1401–4.

    CAS  Google Scholar 

  5. Walbot, V., and Petrov, D. A. (2001) Gene galaxies in the maize genome Proc Natl Acad Sci USA 98, 8163–4.

    Article  CAS  Google Scholar 

  6. Thomas, E. E. (2005) Short, local duplication in eukaryotic genomes Curr Op Genet Dev 15, 640–4.

    Google Scholar 

  7. Kim et al (2008) Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history Genome Res 18, 1865–74

    Google Scholar 

  8. Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., and Eichler, E. E. (2002) Recent segmental duplications in the human genome Science 297, 1003–7.

    CAS  Google Scholar 

  9. Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Paabo, S., Rocchi, M. and Eichler E. E. (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications Nature 437, 88–93.

    CAS  Google Scholar 

  10. Koszul, R. S., Caburet, B. D., and Fischer, G. (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments EMBO J 23, 234–43.

    CAS  Google Scholar 

  11. Zhang, J. (2003) Evolution by gene duplication: an update Trends Ecol Evol 18, 292–8.

    Google Scholar 

  12. Lespinet, O., Wolf, Y. I., Koonin, E. V., and Aravind, L. (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes Genome Res 12, 1048–59.

    CAS  Google Scholar 

  13. Gu, Z., Cavalcanti, A., Chen, F. C., Bouman, P., and Li, W. H. (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast Mol Biol Evol 19, 256–62.

    Google Scholar 

  14. Zhang, X., and Firestein, S. (2002) The olfactory receptor gene superfamily of the mouse Nat Neurosci 5, 124–33.

    CAS  Google Scholar 

  15. Rajashekar, B., Kohler, A., Johansson, T., Martin, F., Tunlid, A., and Ahrén, D. (2009) Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases New Phytol 183, 365–79.

    CAS  Google Scholar 

  16. Wilhelm, M., and Wilhelm, F. X. (2001) Reverse transcription of retroviruses and LTR retrotransposons Cell Mol Life Sci 58, 1246–62.

    CAS  Google Scholar 

  17. Kunze, R., and Weil, C.F. (2002) The hAT and CACTA superfamilies of plant transposons In Mobile DNA II (eds. Craig, N., Craigie, R., Gellert, M., and Lambowitz, A.) ASM Press, Washington, DC, 565–610.

    Google Scholar 

  18. Engels, W. R., Johnson-Schlitz, D. M., Eggleston, W. B., and Sved, J. (1990) High-frequency P-element loss in Drosophila is homolog dependent. Cell 62, 515–25.

    Article  PubMed  CAS  Google Scholar 

  19. Kapitonov, V. V., and Jurka, J. (2001) Rolling-circle transposons in eukaryotes Proc Natl Acad Sci USA 98, 8714–9.

    Article  CAS  Google Scholar 

  20. Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A., and Rafalski, A. (2005) Gene duplication and exon shuffling by Helitron-like transposons generate intraspecies diversity in maize Nat Genet 37, 997–1002.

    CAS  Google Scholar 

  21. Jiang, N., Feschotte, C., Zhang, X., and Wessler, S. R. (2004) Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs) Curr Op Plt Biol 7, 115–9.

    Google Scholar 

  22. Feschotte, C., and Wessler, S. R. (2001) Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes Proc Natl Acad Sci USA 98, 8923–4.

    CAS  Google Scholar 

  23. Orgel, L. E., and Crick, F. H. (1980) Selfish DNA: the ultimate parasite Nature 284, 604–7.

    CAS  Google Scholar 

  24. Cameron, J. R., Loh, E. Y., and Davis, R. W. (1979) Evidence for transposition of dispersed repetitive DNA families in yeast Cell 16, 739–51.

    CAS  Google Scholar 

  25. Kinsey, J. A., and Helber, J. (1989) Isolation of a transposable element from Neurospora crassa Proc Natl Acad Sci USA 86, 1929–33.

    CAS  Google Scholar 

  26. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S. G. (1996) Life with 6000 genes Science 274, 563–7.

    Google Scholar 

  27. Galagan, J. E., Calvo, S. E., Borkovich, K. A., Selker, E. U., Read, N. D., Jaffe, D., FitzHugh, W., Ma, L. J., Smirnov, S., Purcell, S., Rehman, B., Elkins, T., Engels, R., Wang, S., Nielsen, C. B., Butler, J., Endrizzi, M., Qui, D., Ianakiev, P., Bell-Pedersen, D., Nelson, M. A., Werner-Washburne, M., Selitrennikoff, C. P., Kinsey, J. A., Braun, E. L., Zelter, A., Schulte, U., Kothe, G. O., Jedd, G., Mewes, W., Staben, C., Marcotte, E., Greenberg, D., Roy, A., Foley, K., Naylor, J., Stange-Thomann, N., Barrett, R., Gnerre, S., Kamal, M., Kamvysselis, M., Mauceli, E., Bielke, C., Rudd, S., Frishman, D., Krystofova, S., Rasmussen, C., Metzenberg, RL., Perkins, DD., Kroken, S., Cogoni, C., Macino, G., Catcheside, D., Li, W., Pratt, R. J., Osmani, S. A., DeSouza, C. P., Glass, L., Orbach, M. J., Berglund, J. A., Voelker, R., Yarden, O., Plamann, M., Seiler, S., Dunlap, J., Radford, A., Aramayo, R., Natvig, D. O., Alex, L. A., Mannhaupt, G., Ebbole, D. J., Freitag, M., Paulsen, I., Sachs, M. S., Lander, E. S., Nusbaum, C., and Birren, B. (2003) The genome sequence of filamentous fungus Neurospora crassa Nature 422, 859–68.

    Google Scholar 

  28. Selker, E. U., Cambareri, E. B., Jensen, B. C., and Haack, K. R. (1987) Rearrangement of duplicated DNA in specialized cells of Neurospora Cell 51, 741–52.

    CAS  Google Scholar 

  29. Britten, R. J., Graham, D. E., and Neufeld, B. R. (1974) Analysis of repeating DNA by reassociation Methods Enzymol 29, 363–418.

    CAS  Google Scholar 

  30. Sambrook, J., and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual CSHL Press, Cold Spring Harbor, NY.

    Google Scholar 

  31. Zhong, X. B., Fransz, P. F., Wennekes-van, E. J., Zabel, P., van Kammen, A., and de Jong, J. H. (1996) High resolution mapping by fluorescence in situ hybridisation to pachytene chromosomes and extended DNA fibres Plant Mol Biol Rep 14, 232–42.

    CAS  Google Scholar 

  32. Yuan, J. S., Burris, J., Stewart, N. R., Mentewab, A., and Stewart, C. N. (2007) Statistical tools for transgene copy number estimation based on real-time P 33

    Google Scholar 

  33. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements Cytogenet Genome Res 110, 462–7.

    Google Scholar 

  34. Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. (1996) CENSOR-a program for identification and elimination of repetitive elements from DNA sequences Comput Chem 20, 119–21.

    CAS  Google Scholar 

  35. Kohany, O., Gentles, A. J., Hankus, L., and Jurka, J. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor BMC Bioinform 7, 474.

    Google Scholar 

  36. Smit, A. F. A., Hubley, R., and Green, P. (1996–2004) RepeatMasker Open-3.0. http://repeatmasker.org.

  37. Morgulis, A., Gertz, E. M., Schäffer, A. A., and Agarwala, R. (2006) WindowMasker: window-based masker for sequenced genomes Bioinformatics 22, 134–41.

    CAS  Google Scholar 

  38. Bedell, J. A., Korf, I., and Gish, W. (2000) MaskerAid: a performance enhancement to RepeatMasker Bioinformatics 16, 1040–1.

    CAS  Google Scholar 

  39. Green, P. (1994–1999) http://www.phrap.org/phredphrap/phrap.html.

  40. Bao, Z., and Eddy, S. R. (2002) Automated de novo identification of repeat sequence families in sequenced genomes Genome Res 12, 1269–76.

    CAS  Google Scholar 

  41. Price, A. L., Jones, N. C., and Pevzner, P. A. (2005) De novo identification of repeat families in large genomes Bioinformatics 21, Suppl 1, i351–8.

    Google Scholar 

  42. Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale Nucleic Acids Res 29, 4633–42.

    CAS  Google Scholar 

  43. Kurtz, S., and Schleiermacher, C. (1999) REPuter: fast computation of maximal repeats in complete genomes Bioinformatics 15, 426–7.

    CAS  Google Scholar 

  44. Volfovsky, N., Haas, B. J., and Salzberg, S. L. (2001) A clustering method for repeat analysis in DNA sequences Genome Biol 2, research0027.1–0027.11.

    Google Scholar 

  45. Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., and Salzberg, S. L. (1999) Alignment of whole genomes. Nucleic Acids Res 27, 2369–76.

    Article  PubMed  CAS  Google Scholar 

  46. Edgar, R. C., and Myers, E.W. (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21, Suppl 1, i152–8.

    Article  PubMed  CAS  Google Scholar 

  47. Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32, 1792–7.

    CAS  Google Scholar 

  48. Wootton, J. C., and Federhen, S. (1993) Statistics of local complexity in amino acid sequences and sequence databases Comput Chem 17, 149–63.

    CAS  Google Scholar 

  49. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res 27, 573–80.

    CAS  Google Scholar 

  50. Kurtz, S., Narechania, A., Stein, J. C., and Ware, D. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes BMC Genomics 9, 517.

    Google Scholar 

  51. Campagna, D., Romualdi, C., Vitulo, N., Favero, M. D., Lexa, M., Cannata, N., and Valle, G. (2005) RAP: a new computer program for de novo identification of repeated sequences in whole genomes Bioinformatics 21, 582–8.

    CAS  Google Scholar 

  52. Allauzen, C., Crochemore, M., and Raffinot, M. (1999) Factor oracle: a new structure for pattern matching In Pavelka, J., Tel, G., and Bartosek, M. (eds), SOFSEM ’99, Theory and Practice of Informatics, Lecture Notes in Computer Science, 1725, Springer, Milovy, Czech Republic, Berlin, pp. 291–306.

    Google Scholar 

  53. Lefebvre, A., Lecroq, T., Dauchel, H., and Alexandre, J. (2003) FORRepeats: detects repeats on entire chromosomes and between genomes Bioinformatics 19, 319–26.

    CAS  Google Scholar 

  54. Li, R., Ye, J., Li, S., Wang, J., Han, Y., Ye, C., Wang, J., Yang, H., Yu, J., Wong, G. K., and Wang, J. (2005) ReAS: Recovery of Ancestral Sequences for transposable elements from the unassembled reads of a whole genome shotgun PLoS Comput Biol 1, e43.

    Google Scholar 

  55. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P. and Schulman, A. H. (2007) A unified classification system for eukaryotic transposable elements Nat Rev Genet 8, 973–82.

    CAS  Google Scholar 

  56. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool J Mol Biol 215, 403–10.

    CAS  Google Scholar 

  57. McCarthy, E. M., and McDonald, J. F. (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons Bioinformatics 19, 362–7.

    Google Scholar 

  58. Xu, Z., and Wang, H. (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons Nucleic Acids Res 35, W265–8.

    Google Scholar 

  59. Ellinghaus, D., Kurtz, S., and Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9, 18.

    Article  PubMed  Google Scholar 

  60. Pereira, V. (2004) Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome Genome Biol 5, R79.

    Google Scholar 

  61. Kalyanaraman, A., and Aluru, S. (2006) Efficient algorithms and software for detection of full-length LTR retrotransposons. J Bioinform Comput Bio 4, 197–216.

    Article  CAS  Google Scholar 

  62. Rho, M., Choi, J. H., Kim, S., Lynch. M., and Tang, H. (2007) De novo identification of LTR retrotransposons in eukaryotic genomes BMC Genomics 8, 90.

    Google Scholar 

  63. Tu, Z. (2001) Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae Proc Natl Acad SciUSA 98, 1699–704.

    Article  CAS  Google Scholar 

  64. Yang, G., and Hall, T. C. (2003) MAK, a computational tool kit for automated MITE analysis Nucleic Acids Res 31, 3659–65.

    Google Scholar 

  65. Chen, Y., Zhou, F., Li, G., and Xu, Y. (2009) MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi Gene 436, 1–7s.

    CAS  Google Scholar 

  66. Yang, L., and Bennetzen, J. (2009) Structure-based discovery and description of plant and animal Helitrons Proc Natl Acad Sci USA 106, 12832–7.

    CAS  Google Scholar 

  67. Du, C., Caronna, J., He. L., and Dooner, H. K. (2008) Computational prediction and molecular confirmation of Helitron transposons in the maize genome BMC Genomics 9, 51.

    Google Scholar 

  68. Quesneville, H., Bergman, C. M., Andrieu, O., Autard, D., Nouaud, D., Ashburner, M., and Anxolabehere, D. (2005) Combined evidence annotation of transposable elements in genome sequences PLoS Comput Biol 1, 166–75.

    CAS  Google Scholar 

  69. Quesneville, H., Nouaud, D., and Anxolabehere, D. (2003) Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes J Mol Evol 57, S50–9.

    CAS  Google Scholar 

  70. Andrieu, O., Fiston, A. S., Anxolabehere, D., and Quesneville, H. (2004) Detection of transposable elements by their compositional bias BMC Bioinformatics 5, 94.

    Google Scholar 

  71. Lewis, S. E., Searle, S. M., Harris, N., Gibson, M., Iyer, V., Ricter, J., Wiel, C., Bayraktaroglu, L., Birney, E., Crosby, M. A., Kaminker, J. S., Matthews, B., Prochnik, S. E., Smith, C. D., Tupy, J. L., Rubin, G. M., Misra, S., Mungall, C. J., and Clamp, M. E. (2002) Apollo: A sequence annotation editor Genome Biol 3, Research0082.

    Google Scholar 

  72. Estill, J. C., and Bennetzen, J. L. (2009) The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes Plant Methods 5, 8.

    Google Scholar 

  73. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) Clustal W and Clustal X version 2.0 Bioinformatics, 23, 2947–8.

    Google Scholar 

  74. Richards, R., Holman, K., Yu, S., and Southerland, G. (1993) Fragile X syndrome unstable element, p(CCG)n, and other simple tandem repeat sequences are binding sites for specific nuclear proteins Hum Mol Genet 2, 1429–35.

    Google Scholar 

  75. Majewski, J., and Ott, J. (2000) GT repeats are associated with recombination on human chromosome 22 Genome Res 10, 1108–14.

    Google Scholar 

  76. Wells, R. D. (1996) Molecular basis of genetic instability of triplet repeats J Biol Chem 271, 2875–8.

    CAS  Google Scholar 

  77. Edwards, A., Hammond, H. A., Jin, L., Caskey, C. T., and Chakraborty, R. (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups Genomics 12, 241–53.

    CAS  Google Scholar 

  78. Sobreira, T. J., Durham, A. M., and Gruber, A. (2006) TRAP: automated classification, quantification and annotation of tandemly repeated sequences Bioinformatics 22, 361–2.

    Google Scholar 

  79. Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: The european molecular biology open software suite Trends Genet 16, 276–7.

    CAS  Google Scholar 

  80. Kolpakov, R., Bana. G., and Kucherov, G. (2003) mreps: Efficient and flexible detection of tandem repeats in DNA Nucleic Acids Res 31, 3672–8.

    Google Scholar 

  81. Castelo, A. T., Martins, W., and Gao, G. R. (2002) TROLL-tandem repeat occurrence locator Bioinformatics 18, 634–6.

    CAS  Google Scholar 

  82. Krishnan, A., and Tang, F. (2004) Exhaustive whole-genome tandem repeats search Bioinformatics 20, 2702–10.

    CAS  Google Scholar 

  83. Delgrange, O., and Rivals, E. (2004) STAR: an algorithm to Search for Tandem Approximate Repeats Bioinformatics 20, 2812–20.

    CAS  Google Scholar 

  84. Karaca, M., Bilgen, M., Onus, A. N., Ince, A. G., and Elmasulu, S. Y. (2005) Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining J Genet 84, 49–54.

    Google Scholar 

  85. Gelfand, Y., Rodriguez, A., and Benson, G. TRDB-the Tandem Repeats Database (2007) Nucleic Acids Res 35, D80–7.

    Article  PubMed  CAS  Google Scholar 

  86. Lupski, J. R. (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits Trends Genet 14, 417–22.

    CAS  Google Scholar 

  87. Eichler, E. E. (2001) Recent duplication, domain accretion and the dynamic mutation of the human genome Trends Genet 17, 661–9.

    Google Scholar 

  88. Jiang, Z., Hubley, R., Smit, A., and Eichler, E. E. (2008) DupMasker: A tool for annotating primate segmental duplications Genome Res 18, 1362–8.

    CAS  Google Scholar 

  89. Leh-Louis, V., Wirth, B., Potier, S., Souciet, J. L. and Despons, L. (2004) Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations Genetics 167, 1611–9.

    Google Scholar 

  90. Schacherer, J., Tourrette, Y., Souciet, J. L., Potier, S. and De Montigny, J. (2004) Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae Genome Res 14, 1291–7.

    CAS  Google Scholar 

  91. Korbel, J. O., Kim, P. M., Chen, X., Urban, A. E., Weissman, S., Snyder, M., and Gerstein, M. B. (2008) The current excitement about copy-number variation: How it relates to gene duplications and protein families Curr Op Struct Biol 18, 366–74.

    CAS  Google Scholar 

  92. Van Dongen, S. (2000) Graph clustering by flow simulation PhD Thesis University of Utrecht The Netherlands.

    Google Scholar 

  93. Li, L., Stoeckert Jr., C. J., and Roos, D. S. (2003) OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Genome Res 13, 2178–89.

    CAS  Google Scholar 

  94. Retief, J. D., Lynch, K. R., and Pearson, W. R. (1999) Panning for genes-A visual strategy for identifying novel gene orthologs and paralogs Genome Res 9, 373–82.

    CAS  Google Scholar 

  95. Dufayard, J. F., Duret, L., Penel, S., Gouy, M., Rechenmann, F., and Perrière G. (2005) Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases Bioinformatics 21, 2596–603.

    PubMed  CAS  Google Scholar 

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  1. USDA-ARS, Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN, USA

    Stephen B. Goodwin

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  1. Braham Dhillon
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  2. Stephen B. Goodwin
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  1. , Dept. of Botany and Plant Pathology, Purdue University, West State Street 915, West Lafayette, 47907, Indiana, USA

    Jin-Rong Xu

  2. Division of Agriculture, Department of Plant Pathology, University of Arkansas, North Campus Drive 495, Fayetteville, 72701, Arkansas, USA

    Burton H. Bluhm

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Dhillon, B., Goodwin, S.B. (2011). Identification and Annotation of Repetitive Sequences in Fungal Genomes. In: Xu, JR., Bluhm, B. (eds) Fungal Genomics. Methods in Molecular Biology, vol 722. Humana Press. https://doi.org/10.1007/978-1-61779-040-9_3

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  • DOI: https://doi.org/10.1007/978-1-61779-040-9_3

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