Sequencing genes and gene islands by gene enrichment

Handbook of Maize: Genetics and Genomics

Volumn , Issue , 2009, Pages 673-689

  Rabinowicz, Pablo D ^a   Barbazuk, W Brad ^b  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954110229     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-77863-1_34     Document Type: Chapter

References (95)

1. Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M., Polymeropoulos, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Moreno, R. F. et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651-1656.
2. Bai, L., Singh, M., Pitt, L., Sweeney, M., and Brutnell, T. P. (2007) Generating novel allelic variation through activator insertional mutagenesis in maize. Genetics 175:981-992.
3. 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 297:1003-1007.
4. Bainbridge, M. N., Warren, R. L., Hirst, M., Romanuik, T., Zeng, T., Go, A., Delaney, A., Griffith, M., Hickenbotham, M., Magrini, V. et al. (2006) Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7:246.
5. Barbazuk, W. B., Bedell, J. A., and Rabinowicz, P. D. (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27:839-848.
6. Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., and Schnable, P. S. (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910-918.
7. Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823-837.
8. Batzoglou, S., Jaffe, D. B., Stanley, K., Butler, J., Gnerre, S., Mauceli, E., Berger, B., Mesirov, J. P., and Lander, E. S. (2002) ARACHNE: a whole-genome shotgun assembler. Genome Res. 12:177-189.
9. Bennetzen, J. L., Chandler, V. L., and Schnable, P. (2001) National Science Foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol. 127:1572-1578.
10. Bennetzen, J. L., C. Coleman, J. Ma, R. Liu and W. Ramakrishna (2004) Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7:732-736.
11. Bentley, D. R. (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16:545-552.
12. Berezikov, E., Thuemmler, F., Van Laake, L. W., Kondova, I., Bontrop, R., Cuppen, E., and Plasterk, R. H. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38:1375-1377.
13. Bonaldo, M. F., Lennon, G., and Soares, M. B. (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6:791-806.
14. Bortiri, E., Jackson, D., and Hake, S. (2006) Advances in maize genomics: the emergence of positional cloning. Curr Opin Plant Biol 9:164-171.
15. Bruggmann, R., Bharti, A. K., Gundlach, H., Lai, J., Young, S., Pontaroli, A. C., Wei, F., Haberer, G., Fuks, G., Du, C. et al. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16:1241-1251.
16. Burr, B., Burr, F. A., Thompson, K. H., Albertson, M. C., and Stuber, C. W. (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519-526.
17. Childs, K. L., Hamilton, J. P., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P. D., Town, C. D., Buell, C. R., and Chan, A. P. (2006) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res.
18. Clifton, S. W., Minx, P., Fauron, C. M., Gibson, M., Allen, J. O., Sun, H., Thompson, M., Barbazuk, W. B., Kanuganti, S., Tayloe, C. et al. (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136:3486-3503.
19. Colasanti, J., Tremblay, R., Wong, A. Y., Coneva, V., Kozaki, A., and Mable, B. K. (2006) The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants. BMC Genomics 7:158.
20. Dean, F. B., Hosono, S., Fang, L., Wu, X., Faruqi, A. F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J. et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99:5261-5266.
21. Dila, D., Sutherland, E., Moran, L., Slatko, B., and Raleigh, E. A. (1990) Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12. J. Bacteriol. 172:4888-4900.
22. Dong, Q., Lawrence, C. J., Schlueter, S. D., Wilkerson, M. D., Kurtz, S., Lushbough, C., and Brendel, V. (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol. 139:610-618.
23. Emberton, J., Ma, J., Yuan, Y., San Miguel, P., and Bennetzen, J. L. (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 15:1441-1446.
24. Emrich, S. J., Aluru, S., Fu, Y., Wen, T. J., Narayanan, M., Guo, L., Ashlock, D. A., and Schnable, P. S. (2004) A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics 20:140-147.
25. Emrich, S. J., Barbazuk, W. B., Li, L., and Schnable, P. S. (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17:69-73.
26. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
27. Fojtova, M., Kovarik, A., and Matyasek, R. (2001) Cytosine methylation of plastid genome in higher plants. Fact or artefact? Plant Sci 160:585-593.
28. Fu, Y., Wen, T. J., Ronin, Y. I., Chen, H. D., Guo, L., Mester, D. I., Yang, Y. Lee, M., Korol, A. B., Ashlock, D. A. et al. (2006) Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174:1671-1683.
29. Gardiner, J. M., Buell, C. R., Elumalai, R., Galbraith, D. W., Henderson, D. A., Iniguez, A. L., Kaeppler, S. M., Kim, J. J., Liu, J., Smith, A. et al. (2005) Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica 50:425-435.
30. Gaut, B. S. and Doebley, J. F. (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94:6809-6814.
31. Gibbs, R. A. Weinstock, G. M. Metzker, M. L. Muzny, D. M. Sodergren, E. J. Scherer, S. Scott, G. Steffen, D. Worley, K. C. Burch, P. E. et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.
32. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M. et al. (1996) Life with 6000 genes. Science 274:546-567.
33. Haberer, G., Young, S., Bharti, A. K., Gundlach, H., Raymond, C., Fuks, G., Butler, E., Wing, R. A., Rounsley, S., Birren, B. et al. (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612-1624.
34. Hake, S. and Walbot, V. (1980) The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79:251-270.
35. Hanley, S., Edwards, D., Stevenson, D., Haines, S., Hegarty, M., Schuch, W., and Edwards, K. J. (2000) Identification of transposon-tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. Plant J. 23:557-566.
36. Henderson, I. R., Zhang, X., Lu, C., Johnson, L., Meyers, B. C., Green, P. J., and Jacobsen, S. E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38:721-725.
37. Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res. 9:868-877.
38. Ilic, K., San Miguel, P. J., and Bennetzen, J. L. (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. U. S. A. 100:12265-12270.
39. Jaffe, D. B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J. P., Zody, M. C., and Lander, E. S. (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13:91-96.
40. Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L., and Jones, C. D. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics.
41. Jin, Y. Wang, M., Fu, J., Xuan, N., Zhu, Y., Lian, Y. Jia, Z., Zheng, J., and Wang, G. (2007) Phylogenetic and expression analysis of ZnF-AN1 genes in plants. Genomics 90:265-275.
42. Johnson, D. S., Mortazavi, A., Myers, R. M., and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502.
43. Kalyanaraman, A., Aluru, S., and Schnable, P. S. (2006) Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons. Comput Syst Bioinformatics Conf: 167-178.
44. Lai, J., Ma, J., Swigonova, Z., Ramakrishna, W., Linton, E., Llaca, V. Tanyolac, B., Park, Y. J., Jeong, O. Y., Bennetzen, J. L. et al. (2004) Gene loss and movement in the maize genome. Genome Res. 14:1924-1931.
45. Lander, E. S. and Weinberg, R. A. (2000) Genomics: journey to the center of biology. Science 287:1777-1782.
46. Langham, R. J., Walsh, J., Dunn, M., Ko, C., Goff, S. A., and Freeling, M. (2004) Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166:935-945.
47. Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R., Antonescu, V., Chan, A., Cheung, F., and Quackenbush, J. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33:D71-74.
48. Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476.
49. Luo, M. C., Thomas, C., You, F. M., Hsiao, J., Ouyang, S., Buell, C. R., Malandro, M., McGuire, P. E., Anderson, O. D., and Dvorak, J. (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378-389.
50. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y. J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
51. Marra, M., Kucaba, T., Sekhon, M., Hillier, L., Martienssen, R., Chinwalla, A., Crockett, J., Fedele, J., Grover, H., Gund, C. et al. (1999) zA map for sequence analysis of the Arabidopsis thaliana genome. Nat. Genet. 22:265-270.
52. May, B. P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P. D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D. et al. (2003) Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. U. S. A. 100:11541-11546.
53. McCarty, D. R., Settles, A. M., Suzuki, M., Tan, B. C., Latshaw, S., Porch, T., Robin, K., Baier, J., Avigne, W., Lai, J. et al. (2005) Steady-state transposon mutagenesis in inbred maize. Plant J. 44:52-61.
54. McCullough, A. J., Kangasjarvi, J., Gengenbach, B. G., and Jones, R. J. (1992) Plastid DNA in Developing Maize Endosperm: Genome Structure, Methylation, and Transcript Accumulation Patterns. Plant Physiol 100:958-964.
55. Meyers, B. C., Tingey, S. V., and Morgante, M. (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11:1660-1676.
56. Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T. K., Koche, R. P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560.
57. Miura, A., Yonebayashi, S., Watanabe, K., Toyama, T., Shimada, H., and Kakutani, T. (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212-214.
58. Mouse Genome Sequencing Consortium. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
59. Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K. H., Remington, K. A. et al. (2000) A whole-genome assembly of Drosophila. Science 287:2196-2204.
60. Palmer, L. E., Rabinowicz, P. D., O'Shaughnessy, A. L., Balija, V. S., Nascimento, L. U., Dike, S., De La Bastide, M., Martienssen, R. A., and McCombie, W. R. (2003) Maize genome sequencing by methylation filtration. Science 302:2115-2117.
61. Patanjali, S. R., Parimoo, S., and Weissman, S. M. (1991) Construction of a uniform-abundance (normalized) cDNA library. Proc. Natl. Acad. Sci. U. S. A. 88:1943-1947.
62. Pertea, G., Huang, X., Liang, F., Antonescu, V. Sultana, R., Karamycheva, S., Lee, Y. White, J., Cheung, F., Parvizi, B. et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651-652.
63. Peterson, D. G., Schulze, S. R., Sciara, E. B., Lee, S. A., Bowers, J. E., Nagel, A., Jiang, N., Tibbitts, D. C., Wessler, S. R., and Paterson, A. H. (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 12:795-807.
64. Rabinowicz, P. D. (2007) Plant genomic sequencing using gene-enriched libraries. Chem Rev 107:3377-3390.
65. Rabinowicz, P. D. and Bennetzen, J. L. (2006) The maize genome as a model for efficient sequence analysis of large plant genomes. Curr. Opin. Plant Biol. 9:149-156.
66. Rabinowicz, P. D., Citek, R., Budiman, M. A., Nunberg, A., Bedell, J. A., Lakey, N., O'Shaughnessy, A. L., Nascimento, L. U., McCombie, W. R., and Martienssen, R. A. (2005) Differential methylation of genes and repeats in land plants. Genome Res. 15:1431-1440.
67. Rabinowicz, P. D., Palmer, L. E., May, B. P., Hemann, M. T., Lowe, S. W., McCombie, W. R., and Martienssen, R. A. (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res. 13:2658-2664.
68. Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., and Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat. Genet. 23:305-308.
69. Raizada, M. N., Nan, G. L., and Walbot, V. (2001) Somatic and germinal mobility of the RescueMu transposon in transgenic maize. Plant Cell 13:1587-1608.
70. Raleigh, E. A. and Wilson, G. (1986) Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc. Natl. Acad. Sci. U. S. A. 83:9070-9074.
71. Rayburn, A. L., Biradar, D. P., Bullock, D. G., and McMurphy, L. M. (1993) Nuclear DNA content in F1 hybrids of maize. Heredity 70:294-300.
72. San Miguel, P., and J. L. Bennetzen (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals Bot. 82:37-44.
73. San Miguel, P., Tikhonov, A., Jin, Y. K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P. S., Edwards, K. J., Lee, M., Avramova, Z. et al. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768.
74. Sasaki, T. and Burr, B. (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr. Opin. Plant Biol. 3:138-141.
75. Singer, T., Yordan, C., and Martienssen, R. A. (2001) Robertson's Mutator transposons in A.thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev. 15:591-602.
76. Soares, M. B., Bonaldo, M. F., Jelene, P., Su, L., Lawton, L., and Efstratiadis, A. (1994) Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. U. S. A. 91:9228-9232.
77. Soderlund, C., Humphray, S., Dunham, A., and French, L. (2000) Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10:1772-1787.
78. Soderlund, C., Longden, I., and Mott, R. (1997) FPC: a system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13:523-535.
79. Springer, N. M. and Kaeppler, S. M. (2005) Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiol 138:92-104.
80. Springer, N. M., Xu, X., and Barbazuk, W. B. (2004) Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol. 136:3023-3033.
81. Sutherland, E., Coe, L., and Raleigh, E. A. (1992) McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225:327-348.
82. Sutton, G., White, O., Adams, M., and Kerlavage, A. R. (1995) TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Tech. 1:9-19.
83. Swigonova, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J. L., and Messing, J. (2004) Close split of sorghum and maize genome progenitors. Genome Res 14:1916-1923.
84. Tang, H. (2007) Genome assembly, rearrangement, and repeats. Chem Rev 107:3391-3406.
85. The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
86. The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C.elegans: a platform for investigating biology. Science 282:2012-2018.
87. Vaughn, M. W., Tanurd Ic, M., Lippman, Z., Jiang, H., Carrasquillo, R., Rabinowicz, P. D., Dedhia, N., McCombie, W. R., Agier, N., Bulski, A. et al. (2007) Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Biol 5:e174.
88. Warren, R. L., Sutton, G. G., Jones, S. J., and Holt, R. A. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500-501.
89. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., Dicuccio, M., Edgar, R., Federhen, S. et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res.
90. Whitelaw, C. A., Barbazuk, W. B., Pertea, G., Chan, A. P., Cheung, F., Lee, Y. Zheng, L., Van Heeringen, S., Karamycheva, S., Bennetzen, J. L. et al. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118-2120.
91. Yu C. and Li, Z. (2006) Construction of methylation-sensitive partial restriction bacterial artificial chromosome libraries in maize. Anal. Biochem. 359:141-143.
92. Yuan, Y. San Miguel, P. J., and Bennetzen, J. L. (2002) Methylation-Spanning Linker Libraries Link Gene-Rich Regions and Identify Epigenetic Boundaries in Zea mays. Genome Res. 12:1345-1349.
93. Yuan, Y., San Miguel, P. J., and Bennetzen, J. L. (2003) High-Cot sequence analysis of the maize genome. Plant J. 34:249-255.
94. Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S. W., Chen, H., Henderson, I. R., Shinn, P., Pellegrini, M., Jacobsen, S. E. et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126:1189-1201.
95. Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., and Henikoff, S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61-69.