The maize genome as a model for efficient sequence analysis of large plant genomes

Current Opinion in Plant Biology

Volumn 9, Issue 2, 2006, Pages 149-156

  Rabinowicz, Pablo D ^a   Bennetzen, Jeffrey L ^b  

^a J CRAIG VENTER INSTITUTE   (United States)

^b Davison Life Sciences Complex ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

BIOLOGICAL MODEL; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; MAIZE; METHODOLOGY; REVIEW;

DNA, PLANT; GENOME, PLANT; GENOMICS; MODELS, BIOLOGICAL; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

ARABIDOPSIS; MAGNOLIOPHYTA; ZEA MAYS;

EID: 33344475536     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2006.01.015     Document Type: Review

References (68)

1. International Rice Genome Sequencing Project The map-based sequence of the rice genome Nature 436 2005 793 800 This paper provides a comprehensive and clear description of the degree of completion of the sequence of Oryza sativa ssp. japonica (cultivar Nipponbare), generated by a clone-by-clone sequencing approach. The paper includes a description of the most impressive sequence dataset yet for centromeres in any multicellular eukaryote. The authors predict 37 544 genes in rice, of which 2859 were not found in Arabidopsis.
2. The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 2000 796 815
3. J.L. Bennetzen, V.L. Chandler, and P. Schnable National Science Foundation - sponsored workshop report. Maize genome sequencing project Plant Physiol 127 2001 1572 1578
4. Z. Swigonova, J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J.L. Bennetzen, and J. Messing Close split of sorghum and maize genome progenitors Genome Res 14 2004 1916 1923 Using genes that were unambiguously identified as orthologs, the authors demonstrate that the parents that contributed diploid genomes to the tetraploid maize ancestor themselves diverged from a common ancestor about 11.9 mya. On the basis of a putative cross-ortholog conversion event, the authors argue that the polyploidy event itself must have occurred more than 4.8 mya.
5. J. Lai, J. Ma, Z. Swigonova, W. Ramakrishna, E. Linton, V. Llaca, B. Tanyolac, Y.J. Park, O.Y. Jeong, and J.L. Bennetzen Gene loss and movement in the maize genome Genome Res 14 2004 1924 1931
6. R.J. Langham, J. Walsh, M. Dunn, C. Ko, S.A. Goff, and M. Freeling Genomic duplication, fractionation and the origin of regulatory novelty Genetics 166 2004 935 945
7. K. Ilic, P.J. SanMiguel, and J.L. Bennetzen A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes Proc Natl Acad Sci USA 100 2003 12265 12270
8. J. Ma, K.M. Devos, and J.L. Bennetzen Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice Genome Res 14 2004 860 869 This study demonstrates that DNA can be very rapidly removed from a plant genome, primarily through small deletions caused by illegitimate recombination and unequal homologous recombination. The results indicate that more than 190 Mb of LTR-retrotransposon sequence have been removed from the rice genome by these processes in less than 8 million years, and that the half-life for retention of LTR-retrotransposon sequences in rice is less than 6 million years.
9. S. Hake, and V. Walbot The genome of Zea mays, its organization and homology to related grasses Chromosoma 79 1980 251 270
10. P. SanMiguel, B.S. Gaut, A. Tikhonov, Y. Nakajima, and J.L. Bennetzen The paleontology of intergene retrotransposons of maize Nat Genet 20 1998 43 45
11. P. SanMiguel, A. Tikhonov, Y.K. Jin, N. Motchoulskaia, D. Zakharov, A. Melake-Berhan, P.S. Springer, K.J. Edwards, M. Lee, and Z. Avramova Nested retrotransposons in the intergenic regions of the maize genome Science 274 1996 765 768
12. W. Ramakrishna, J. Emberton, M. Ogden, P. SanMiguel, and J.L. Bennetzen Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement Plant Cell 14 2002 3213 3223
13. B.C. Meyers, S.V. Tingey, and M. Morgante Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome Genome Res 11 2001 1660 1676
14. P. SanMiguel, and J.L. Bennetzen Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons Ann Bot 82 1998 37 44
15. Bennetzen JL, Ma J, Liu R, Pontaroli AC: Structure and evolution of the maize genome. Maydica 2005, in press.
16. P.M. Harrison, H. Hegyi, S. Balasubramanian, N.M. Luscombe, P. Bertone, N. Echols, T. Johnson, and M. Gerstein Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 Genome Res 12 2002 272 280
17. N. Jiang, Z. Bao, X. Zhang, S.R. Eddy, and S.R. Wessler Pack-MULE transposable elements mediate gene evolution in plants Nature 431 2004 569 573 The authors identify Mutator-like transposable elements (called Pack-MULEs) in rice that frequently acquire gene fragments. They found more than 3000 Pack-MULEs in rice, which contain fragments from more than 1000 different cellular genes. Many of these Pack-MULEs are transcribed and have processed introns, creating some cases in which fusion of different gene fragments can yield chimeric mRNAs and resultant proteins. This phenomenon suggests a rapid mechanism for the creation of sequences that could evolve into novel genes, and also explains many cases of the mis-annotation of transposons as non-colinear genes.
18. M. Morgante, S. Brunner, G. Pea, K. Fengler, A. Zuccolo, and A. Rafalski Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize Nat Genet 37 2005 997 1002 Careful annotation of BAC sequences from homologous regions in Mo17 and B73 inbreds of maize led to the observation that most of the apparent genic non-colinearities observed between these inbreds were actually caused by the presence of a new class of eukaryotic transposable elements, the Helitrons. The authors show that these elements often acquire several gene fragments from different loci, usually in the same transcriptional orientation, and that these fragments can lead to the production of chimeric mRNAs and proteins. As with Pack-MULEs, Helitrons may be a major mechanism for the creation of sequences that can evolve novel gene function.
19. J. Lai, Y. Li, J. Messing, and H.K. Dooner Gene movement by Helitron transposons contributes to the haplotype variability of maize Proc Natl Acad Sci USA 102 2005 9068 9073
20. V.V. Kapitonov, and J. Jurka Rolling-circle transposons in eukaryotes Proc Natl Acad Sci USA 98 2001 8714 8719
21. S.K. Lal, M.J. Giroux, V. Brendel, C.E. Vallejos, and L.C. Hannah The maize genome contains a helitron insertion Plant Cell 15 2003 381 391
22. V.V. Kapitonov, and J. Jurka Molecular paleontology of transposable elements in the Drosophila melanogaster genome Proc Natl Acad Sci USA 100 2003 6569 6574
23. R.T. Poulter, T.J. Goodwin, and M.I. Butler Vertebrate helentrons and other novel Helitrons Gene 313 2003 201 212
24. W. Gilbert Why genes in pieces? Nature 271 1978 501
25. H. Fu, and H.K. Dooner Intraspecific violation of genetic colinearity and its implications in maize Proc Natl Acad Sci USA 99 2002 9573 9578
26. S. Brunner, K. Fengler, M. Morgante, S. Tingey, and A. Rafalski Evolution of DNA sequence nonhomologies among maize inbreds Plant Cell 17 2005 343 360 This article determines that the observed lack of gene colinearity between maize inbreds is actually caused by truncated genes. Such non-colinear, truncated genes also lack colinearity with rice, whereas genes that are colinear between maize inbreds are also colinear with rice. The authors concluded that the non-colinear genes originated by an insertion mechanism.
27. S. Brunner, G. Pea, and A. Rafalski Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize Plant J 43 2005 799 810
28. S. Hirotsune, N. Yoshida, A. Chen, L. Garrett, F. Sugiyama, S. Takahashi, K. Yagami, A. Wynshaw-Boris, and A. Yoshiki An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene Nature 423 2003 91 96
29. S.A. Korneev, J.H. Park, and M. O'Shea Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene J Neurosci 19 1999 7711 7720
30. R. Song, V. Llaca, and J. Messing Mosaic organization of orthologous sequences in grass genomes Genome Res 12 2002 1549 1555
31. Z. Swigonova, J.L. Bennetzen, and J. Messing Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum Genetics 169 2005 891 906
32. S.J. Emrich, S. Aluru, Y. Fu, T.J. Wen, M. Narayanan, L. Guo, D.A. Ashlock, and P.S. Schnable A strategy for assembling the maize (Zea mays L.) genome Bioinformatics 20 2004 140 147
33. J.L. Bennetzen, K. Schrick, P.S. Springer, W.E. Brown, and P. SanMiguel Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA Genome 37 1994 565 576
34. C.P. Walsh, J.R. Chaillet, and T.H. Bestor Transcription of IAP endogenous retroviruses is constrained by cytosine methylation Nat Genet 20 1998 116 117
35. P.D. Rabinowicz, L.E. Palmer, B.P. May, M.T. Hemann, S.W. Lowe, W.R. McCombie, and R.A. Martienssen Genes and transposons are differentially methylated in plants, but not in mammals Genome Res 13 2003 2658 2664
36. A. Bird DNA methylation patterns and epigenetic memory Genes Dev 16 2002 6 21
37. G. Moore, K.M. Devos, Z. Wang, and M.D. Gale Cereal genome evolution. Grasses, line up and form a circle Curr Biol 5 1995 737 739
38. J.L. Bennetzen, and J. Ma The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis Curr Opin Plant Biol 6 2003 128 133
39. A.P. Tikhonov, P.J. SanMiguel, Y. Nakajima, N.M. Gorenstein, J.L. Bennetzen, and Z. Avramova Colinearity and its exceptions in orthologous adh regions of maize and sorghum Proc Natl Acad Sci USA 96 1999 7409 7414
40. W. Ramakrishna, J. Dubcovsky, Y.J. Park, C. Busso, J. Emberton, P. SanMiguel, and J.L. Bennetzen Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes Genetics 162 2002 1389 1400
41. W. Ramakrishna, J. Emberton, P. SanMiguel, M. Ogden, V. Llaca, J. Messing, and J.L. Bennetzen Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex Plant Physiol 130 2002 1728 1738
42. M. Chen, P. SanMiguel, A.C. de Oliveira, S.S. Woo, H. Zhang, R.A. Wing, and J.L. Bennetzen Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes Proc Natl Acad Sci USA 94 1997 3431 3435
43. C. Feuillet, and B. Keller High gene density is conserved at syntenic loci of small and large grass genomes Proc Natl Acad Sci USA 96 1999 8265 8270
44. J. Ma, P. Sanmiguel, J. Lai, J. Messing, and J.L. Bennetzen DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes Genetics 170 2005 1209 1220
45. M. Feldman, and A.A. Levy Allopolyploidy - a shaping force in the evolution of wheat genomes Cytogenet Genome Res 109 2005 250 258
46. P.D. Rabinowicz, R. Citek, M.A. Budiman, A. Nunberg, J.A. Bedell, N. Lakey, A.L. O'Shaughnessy, L.U. Nascimento, W.R. McCombie, and R.A. Martienssen Differential methylation of genes and repeats in land plants Genome Res 15 2005 1431 1440 A pilot analysis of several grasses, in addition to several dicot and non-angiosperm plants, shows that to some extent MF enriches for genes in all plants tested. In some cases, a large number of pseudogenes could account for the apparent low level of enrichment. Abundant unmethylated repeats can also explain the observation in some cases. Nevertheless, an expansion in the number of pseudogenes in recent polyploids or an abundance of tandem duplications seems to be part of the explanation for the lowest levels of gene enrichment by MF.
47. B.P. May, H. Liu, E. Vollbrecht, L. Senior, P.D. Rabinowicz, D. Roh, X. Pan, L. Stein, M. Freeling, and D. Alexander Maize-targeted mutagenesis: a knockout resource for maize Proc Natl Acad Sci USA 100 2003 11541 11546
48. B.J. Till, S.H. Reynolds, C. Weil, N. Springer, C. Burtner, K. Young, E. Bowers, C.A. Codomo, L.C. Enns, and A.R. Odden Discovery of induced point mutations in maize genes by TILLING BMC Plant Biol 4 2004 12
49. M.N. Raizada, G.L. Nan, and V. Walbot Somatic and germinal mobility of the RescueMu transposon in transgenic maize Plant Cell 13 2001 1587 1608
50. D.R. McCarty, A. Mark Settles, M. Suzuki, B.C. Tan, S. Latshaw, T. Porch, K. Robin, J. Baier, W. Avigne, and J. Lai Steady-state transposon mutagenesis in inbred maize Plant J 44 2005 52 61
51. B.R. Frame, H. Shou, R.K. Chikwamba, Z. Zhang, C. Xiang, T.M. Fonger, S.E. Pegg, B. Li, D.S. Nettleton, and D. Pei Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system Plant Physiol 129 2002 13 22
52. W.M. Nelson, A.K. Bharti, E. Butler, F. Wei, G. Fuks, H. Kim, R.A. Wing, J. Messing, and C. Soderlund Whole-genome validation of high-information-content fingerprinting Plant Physiol 139 2005 27 38
53. 2 population Genetics 134 1993 917 930
54. J. Messing, A.K. Bharti, W.M. Karlowski, H. Gundlach, H.R. Kim, Y. Yu, F. Wei, G. Fuks, C.A. Soderlund, and K.F. Mayer Sequence composition and genome organization of maize Proc Natl Acad Sci USA 101 2004 14349 14354
55. Y. Yuan, P.J. SanMiguel, and J.L. Bennetzen High-Cot sequence analysis of the maize genome Plant J 34 2003 249 255
56. P.D. Rabinowicz, K. Schutz, N. Dedhia, C. Yordan, L.D. Parnell, L. Stein, W.R. McCombie, and R.A. Martienssen Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome Nat Genet 23 1999 305 308
57. L.E. Palmer, P.D. Rabinowicz, A. O'Shaughnessy, V. Balija, L. Nascimento, S. Dike, M. de la Bastide, R.A. Martienssen, and W.R. McCombie Maize genome sequencing by methylation filtration Science 302 2003 2115 2117
58. C.A. Whitelaw, W.B. Barbazuk, G. Pertea, A.P. Chan, F. Cheung, Y. Lee, L. Zheng, S. van Heeringen, S. Karamycheva, and J.L. Bennetzen Enrichment of gene-coding sequences in maize by genome filtration Science 302 2003 2118 2120
59. A.P. Chan, G. Pertea, F. Cheung, D. Lee, L. Zheng, A.C. Pontaroli, P. SanMiguel, Y. Yuan, J.L. Bennetzen, and W.B. Barbazuk The TIGR maize database Nucleic Acids Res 34 Database issue 2006 D771 D776
60. N.M. Springer, X. Xu, and W.B. Barbazuk Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space Plant Physiol 136 2004 3023 3033 The authors analyze gene coverage by MF and HC maize sequences by comparing them to a set of maize ESTs. 95% of the ESTs were at least tagged by MF or HC reads, and 73% of the nucleotides were covered. Although the level of coverage of the gene space by MF and HC was too low to draw definitive conclusions, the authors propose that the two methods are complementary.
61. J. Emberton, J. Ma, Y. Yuan, P. SanMiguel, and J.L. Bennetzen Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries Genome Res 15 2005 1441 1446
62. Y. Yuan, P.J. SanMiguel, and J.L. Bennetzen Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays Genome Res 12 2002 1345 1349
63. C. Grunau, W. Hindermann, and A. Rosenthal Large-scale methylation analysis of human genomic DNA reveals tissue-specific differences between the methylation profiles of genes and pseudogenes Hum Mol Genet 9 2000 2651 2663
64. M.D. Bennett, I.J. Leitch, H.J. Price, and J.S. Johnston Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb Ann Bot 91 2003 547 557
65. T. Hosouchi, N. Kumekawa, H. Tsuruoka, and H. Kotani Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3 DNA Res 9 2002 117 121
66. J.R. Wortman, B.J. Haas, L.I. Hannick, R.K. Smith Jr., R. Maiti, C.M. Ronning, A.P. Chan, C. Yu, M. Ayele, and C.A. Whitelaw Annotation of the Arabidopsis genome Plant Physiol 132 2003 461 468
67. R.A. Gibbs, G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, and P.E. Burch Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 2004 493 521
68. H. Yao, L. Guo, Y. Fu, L.A. Borsuk, T.J. Wen, D.S. Skibbe, X. Cui, B.E. Scheffler, J. Cao, and S.J. Emrich Evaluation of five ab initio gene prediction programs for the discovery of maize genes Plant Mol Biol 57 2005 445 460