Detailed analysis of a contiguous 22-Mb region of the maize genome

PLoS Genetics

Volumn 5, Issue 11, 2009, Pages

  Wei, Fusheng ^a   Stein, Joshua C ^b   Liang, Chengzhi ^b   Zhang, Jianwei ^a   Fulton, Robert S ^c   Baucom, Regina S ^d   De Paoli, Emanuele ^e   Zhou, Shiguo ^f   Yang, Lixing ^d   Han, Yujun ^g   Pasternak, Shiran ^b   Narechania, Apurva ^b   Zhang, Lifang ^b   Yeh, Cheng Ting ^h   Ying, Kai ^h   Nagel, Dawn H ^g   Collura, Kristi ^a   Kudrna, David ^a   Currie, Jennifer ^a   Lin, Jinke ^a   Kim, HyeRan ^a   Angelova, Angelina ^a   Scara, Gabriel ^a   Wissotski, Marina ^a   Golser, Wolfgang ^a   Courtney, Laura ^c   Kruchowski, Scott ^c   Graves, Tina A ^c   Rock, Susan M ^c   Adams, Stephanie ^c   Fulton, Lucinda A ^c   Fronick, Catrina ^c   Courtney, William ^c   Kramer, Melissa ^b   Spiegel, Lori ^b   Nascimento, Lydia ^b   Kalyanaraman, Ananth ⁱ   Chaparro, Cristian ^j   Deragon, Jean Marc ^j   Miguel, Phillip San ^k   Jiang, Ning ^l   Wessler, Susan R ^g   Green, Pamela J ^e   Yu, Yeisoo ^a   Schwartz, David C ^f   Meyers, Blake C ^e   Bennetzen, Jeffrey L ^d   Martienssen, Robert A ^b   McCombie, W Richard ^b   Aluru, Srinivas ^m   Clifton, Sandra W ^c   Schnable, Patrick S ^h   Ware, Doreen ^b   Wilson, Richard K ^c   Wing, Rod A ^a   more..

^a University of Arizona   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d University of Georgia ^*  (United States)

^e UNIVERSITY OF DELAWARE   (United States)

^f UNIVERSITY OF WISCONSIN MADISON   (United States)

^g UNIVERSITY OF GEORGIA   (United States)

^h IOWA STATE UNIVERSITY   (United States)

ⁱ Washington State University   (United States)

^j UNIVERSITÉ DE PERPIGNAN   (France)

^k PURDUE UNIVERSITY   (United States)

^l MICHIGAN STATE UNIVERSITY   (United States)

^m Iowa State University of Science and Technology   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; MICRORNA; PLANT RNA;

ARTICLE; CHROMOSOME 4; COMPARATIVE GENE MAPPING; CONTIG MAPPING; CONTROLLED STUDY; GENE DUPLICATION; GENE IDENTIFICATION; GENE MUTATION; GENE REARRANGEMENT; GENETIC ANALYSIS; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; PLANT GENOME; RICE; SORGHUM; SYNTENY; TRANSPOSON; BASE PAIRING; CHROMOSOME MAP; GENE LOCUS; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; OPEN READING FRAME; PLANT GENE; SEQUENCE HOMOLOGY;

POACEAE; ZEA MAYS;

BASE PAIRING; BASE SEQUENCE; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE REARRANGEMENT; GENES, PLANT; GENETIC LOCI; GENOME, PLANT; MOLECULAR SEQUENCE DATA; MUTATION; OPEN READING FRAMES; ORYZA SATIVA; PHYSICAL CHROMOSOME MAPPING; RNA, PLANT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SORGHUM; SYNTENY; ZEA MAYS;

EID: 73649144195     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000728     Document Type: Article

References (115)

1. Duvick DN (1984) Genetic contributions to yield gains of U.S. hybrid maize, 1930-1980. In: Fehr WR, ed (1984) Genetic contributions to yield gains of five major crop plants. MadisonWI: Crop Science Soc of America Special Publ No 7.
2. Bennetzen JL, Hake S (2009) The maize handbook; Volumes 1 and II. New York: Springer.
3. McClintock B (1948) Mutable loci in maize. Carnegie Inst Wash Year Book 47: 155-169.
4. SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, et al. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
5. SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals Bot 82: 37-44.
6. Meyers B, Tingey S, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11: 1660-1676.
7. Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, et al. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120.
8. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, et al. (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101: 14349-14354.
9. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Annals Bot 95: 127-132.
10. Vitte Cm, Bennetzen JL (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103: 17638-17643.
11. McClintock B (1953) Induction of instability at selected loci in maize. Genetics 38: 579-599.
12. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, et al. (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96: 7409-7414.
13. Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99: 9573-9578.
14. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, et al. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37: 997-1002.
15. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101: 9903-9908.
16. Gale M, Devos K (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974.
17. Kellogg E (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 95: 2005-2010.
18. Vandepoele K, Simillion C, Van de Peer Y (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15: 2192-2202.
19. Gaut B, Doebley J (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94: 6809-6814.
20. Gaut B (2001) Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res 11: 55-66.
21. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, et al. (2004) Close split of sorghum and maize genome progenitors. Genome Res 14: 1916-1923.
22. Wei F, Zhang J, Zhou S, He R, Schaeffer M, et al. (2009) The physical and genetic framework of the maize B73 genome. PLoS Genet 5: e715. doi:10.1371/journal.pgen.1000715.
23. Schnable PS, Ware D, Fulton R, Stein J, Wei F, et al. (2009) The B73 maize genome: complexity, diversity and dynamics Science in press.
24. Wei F, Coe E, Nelson W, Bharti AK, Engler F, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123. 10.1371/journal.pgen.0030123.
25. Austin D, Lee M (1996) Genetic resolution and verification of quantitative trait loci for flowering and plant height with recombinant inbred lines of maize. Genome 39: 957-968.
26. Austin D, Lee M (1996) Comparative mapping in F-2:3 and F-6:7 generations of quantitative trait loci for grain yield and yield components in maize. Theor Appl Genet 92: 817-826.
27. Beavis W, Grant D, Albertsen M, Fincher R (1991) Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci. Theor Appl Genet 83: 141-145.
28. Bohn M, Khairallah M, Gonzalez de Leon D, Hoisington D, Utz H, et al. (1996) QTL mapping in tropical maize .1. Genomic regions affecting leaf feeding resistance to sugarcane borer and other traits. Crop Sci 36: 1352-1361.
29. Bohn M, Khairallah M, Jiang C, Gonzalez de Leon D, Hoisington D, et al. (1997) QTL mapping in tropical maize .2. Comparison of genomic regions for resistance to Diatraea spp. Crop Sci 37: 1892-1902.
30. Bubeck D, Goodman M, Beavis W, Grant D (1993) Quantitative trait loci controlling resistance to gray leaf spot in maize. Crop Sci 33: 838-847.
31. Byrne P, McMullen M, Wiseman B, Snook M, Musket T, et al. (1998) Maize silk maysin concentration and corn earworm antibiosis: QTLs and genetic mechanisms. Crop Sci 38: 461-471.
32. Goldman I, Rocheford T, Dudley J (1993) Quantitative trait loci influencing protein and starch concentration in the Illinois long term selection maize strains. Theor Appl Genet 87: 217-224.
33. Goldman I, Rocheford T, Dudley J (1994) Molecular markers associated with maize kernel oil concentration in an Illinois high protein x Illinois low protein cross. Crop Sci 34: 908-915.
34. Veldboom L, Lee M (1996) Genetic mapping of quantitative trait loci in maize in stress and nonstress environments .1. Grain yield and yield components. Crop Sci 36: 1310-1319.
35. Lahners K, Kramer V, Back E, Privalle L, Rothstein S (1988) Molecular cloning of complementary DNA encoding maize nitrite reductase: molecular analysis and nitrate induction. Plant Physiol 88: 741-746.
36. Liu F, Schnable PS (2002) Functional specialization of maize mitochondrial aldehyde dehydrogenases. Plant Physiol 130: 1657-1674.
37. Liu S, Dietrich CR, Schnable P (2009) DLA-based strategies for cloning insertion mutants: cloning the gl4 locus of maize using Mu transposon tagged alleles. Genetics;doi: 10.1534/genetics.109.108936.
38. Soderlund C, Humphray S, Dunham A, French L (2000) Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 10: 1772-1787.
39. Kurtz S, Narechania A, Stein J, Ware D (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9: 517.
40. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, et al. (2009) A single molecule scaffold of the maize genome. PLoS Genet 5: e711. doi:10.1371/journal. pgen.1000711.
41. Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, et al. (2009) A first generation haplotype map of maize Science 326: doi:1126/science.1178534.
42. Springer N, Ying K, Fu Y, Ji T, Yeh C-T, et al. (2009) Maize inbreds exhibit high levels of CNV and presence/absence differences in genome content. PLoS Genet 5: e734. doi: 10.1371/journal.pgen.1000734.
43. Bennetzen JL, Coleman C, Liu R, Ma J, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7: 732-736.
44. Spannagl M, Noubibou O, Haase D, Yang L, Gundlach H, et al. (2007) MIPSPlantsDB - plant database resource for integrative and comparative plant genome research. Nucleic Acids Res 35: D834-840.
45. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi J, et al. (2009) Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome. PLoS Genet 5: e732. doi: 10.1371/journal.pgen.1000732.
46. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, et al. (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26: 307-316.
47. Ramakrishna W, Dubcovsky J, Park Y-J, Busso C, Emberton J, et al. (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162: 1389-1400.
48. Rostoks N, Park Y-J, Ramakrishna W, Ma J, Druka A, et al. (2002) Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Functional & Integrative Genomics 2: 51-59.
49. Wei F, Wing RA, Wise RP (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14: 1903-1917.
50. Edwards KJ, Veuskens J, Rawles H, Daly A, Bennetzen JL (1996) Characterization of four dispersed repetitive DNA sequences in Zea mays and their use in constructing contiguous DNA fragments using YAC clones. Genome 39: 811-817.
51. Liu R, Vitte C, Ma J, Mahama AA, Dhliwayo T, et al. (2007) A GeneTrek analysis of the maize genome. Proc Natl Acad Sci USA 104: 11844-11849.
52. Gao X, Hou Y, Ebina H, Levin HL, Voytas DF (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res 18: 359-369.
53. Malik HS, Eickbush TH (1999) Modular Evolution of the Integrase Domain in the Ty3/Gypsy Class of LTR Retrotransposons. J Virol 73: 5186-5190.
54. Fu H, Zheng Z, Dooner HK (2002) Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc Natl Acad Sci USA 99: 1082-1087.
55. Yao H, Zhou Q, Li J, Smith H, Yandeau M, et al. (2002) Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize. Proc Natl Acad Sci USA 99: 6157-6162.
56. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
57. Jin YK, Bennetzen JL (1994) Integration and Nonrandom Mutation of a Plasma Membrane Proton ATPase Gene Fragment within the Bs1 Retroelement of Maize. Plant Cell 6: 1177-1186.
58. Takahashi S, Inagaki Y, Satoh H, Hoshino A, Iida S (1999) Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory. Molecular and General Genetics 261: 447-451.
59. Li Q, Li L, Dai JR, Li JS, Yan JB (2009) Identification and characterization of CACTA transposable elements capturing gene fragments in maize. Chinese Science Bulletin 54: 642-651.
60. Zabala G, Vodkin LO (2005) The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell 17: 2619-2632.
61. Gilbert W (1978) Why genes in pieces? Nature 271: 501.
62. Volff JN (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. BioEssays 28: 913-922.
63. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
64. Jia Y, Lisch D, Ohtsu K, Scanlon M, Nettleton D, et al. (2009) Loss of RNA-dependent RNA Polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons and genes in maize shoot apical meristems. PLoS Genet 5: e737. doi: 10.1371/journal.pgen.1000737.
65. Allen E, Xie ZX, Gustafson AM, Sung GH, Spatafora JW, et al. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36: 1282-1290.
66. Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, et al. (2004) The Ensembl Automatic Gene Annotation System. Genome Res 14: 942-950.
67. Liang C, Mao L, Ware D, Stein L (2009) Evidence-based gene predictions in plant genomes. Genome Res 19: 1912-1923.
68. Alexandrov N, Brover V, Freidin S, Troukhan M, Tatarinova T, et al. (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69: 179-194.
69. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, et al. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res 16: 1241-1251.
70. Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, et al. (2005) Structure and architecture of the maize genome. Plant Physiol 139: 1612-1624.
71. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
72. Cui X, Hsia A-P, Liu F, Ashlock DA, Wise RP, et al. (2003) Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics 163: 685-698.
73. Esen A, Bandaranayake H (1998) Insertional polymorphism in introns 4 and 10 of the maize beta-glucosidase gene glu1. Genome 41: 597-604.
74. Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, et al. (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5: e716. doi: 10.1371/journal.pgen.1000716.
75. Ahn S, Tanksley S (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984.
76. Paterson AH, Lin Y-R, Li Z, Schertz KF, Doebley JF, et al. (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714-1718.
77. Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, et al. (1999) Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153: 453-473.
78. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12: 1021-1030.
79. Chen M, SanMiguel P, deOliveira AC, Woo SS, Zhang H, et al. (1997) Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 94: 3431-3435.
80. Hulbert SH, Richter TE, Axtell JD, Bennetzen JL (1990) Genetic-mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci USA 87: 4251-4255.
81. Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, et al. (2004) Gene loss and movement in the maize genome. Genome Res. pp 1924-1931.
82. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-Mouse alignments with BLASTZ. Genome Res 13: 103-107.
83. Soderlund C, Nelson W, Shoemaker A, Paterson A (2006) SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res 16: 1159-1168.
84. Ilic K, SanMiguel PJ, Bennetzen JL (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100: 12265-12270.
85. AGI TAGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
86. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
87. Zhou Q, Zhang GJ, Zhang Y, Xu SY, Zhao RP, et al. (2008) On the origin of new genes in Drosophila. Genome Res 18: 1446-1455.
88. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98: 8714-8719.
89. Mann HB, Whitney DR (1947) On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18: 50-60.
90. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217: 624-626.
91. Kimura M (1983) Diffusion model of intergroup selection, with special reference to evolution of an altruistic character. Proc Natl Acad Sci USA 80: 6317-6321.
92. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, et al. (2008) Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 105: 14958-14963.
93. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, et al. (2006) An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442: 295-298.
94. Woodhouse MR, Freeling M, Lisch D (2006) Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol 4: e339. doi:10.1371/journal.pbio.0040339.
95. Martienssen RA (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nat Genet 35: 213-214.
96. Lisch D, Carey CC, Dorweiler JE, Chandler VL (2002) A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing. Proc Natl Acad Sci USA 99: 6130-6135.
97. Wang XF, Elling AA, Li XY, Li N, Peng ZY, et al. (2009) Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize. Plant Cell 21: 1053-1069.
98. Lin XY, Kaul SS, Rounsley S, Shea TP, Benito MI, et al. (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761-768.
99. McCarthy EM, McDonald JF (2003) LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
100. Kalyanaraman A, Aluru S (2006) Efficient algorithms and software for detection of full-length LTR retrotransposons. J Bioinform Comput Biol 4: 197-216.
101. Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
102. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869.
103. Smit A, Hubley R, Green P (1996-2004) RepeatMasker Open-3.0.
104. Kronmiller BA, Wise RP (2008) TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol 146: 45-59.
105. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, et al. (2002) Apollo: a sequence annotation editor. Genome Biol 3: research0082.0081 - 0082.0014.
106. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-288.
107. Yang L, Bennetzen JL (2009) Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA 106: 12832-12837.
108. Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, et al. (2009) Sequencing, mapping and analysis of 27,455 maize full-length cDNAs. PLoS Genet 5: e740. doi: 10.1371/journal.pgen.1000740.
109. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522.
110. Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33: W451-454.
111. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Res 35: D883-D887.
112. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100: 11484-11489.
113. 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 Res 22: 4673-4680.
114. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
115. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.