Genome evolution in Maize: From genomes back to genes

Annual Review of Plant Biology

Volumn 66, Issue , 2015, Pages 329-343

  Schnable, James C ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

Comparative genomics; Gene content; Genome evolution; Maize; Poaceae

Indexed keywords

POACEAE; TRITICUM AESTIVUM; ZEA MAYS;

GENETICS; MAIZE; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT GENE; PLANT GENOME; POACEAE; SYNTENY;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; PHENOTYPE; POACEAE; SYNTENY; ZEA MAYS;

EID: 84928887792     PISSN: 15435008     EISSN: 15452123     Source Type: Book Series    
DOI: 10.1146/annurev-arplant-043014-115604     Document Type: Article

References (108)

1. Arabidopsis Genome Initiat. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
2. Barbaglia AM, Klusman KM, Higgins J, Shaw JR, Hannah LC, Lal SK. 2012. Gene capture by helitron transposons reshuffles the transcriptome of maize. Genetics 190:965-75
3. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, et al. 2009. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLOS Genet. 5:e1000732
4. BekaertM, Edger PP, Pires JC, Conant GC. 2011. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23:1719-28
5. Bennetzen JL, Buckler E, Chandler V, Doebley J, Dorweiler J, et al. 2001. Genetic evidence and the origin of maize. Lat. Am. Antiq. 12:84-86
6. 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. 7:732-36
7. Bennetzen JL, Freeling M. 1993. Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet. 9:259-61
8. Bennetzen JL, Freeling M. 1997. The unified grass genome: synergy in synteny. Genome Res. 7:301-6
9. Bennetzen JL,Ma J, Devos KM. 2005. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95:127-32
10. Berhan AM, Hulbert SH, Butler LG, Bennetzen JL. 1993. Structure and evolution of the genomes of Sorghum bicolor and Zea mays. Theor. Appl. Genet. 86:598-604
11. Birchler JA, Riddle NC, Auger DL, Veitia RA. 2005. Dosage balance in gene regulation: biological implications. Trends Genet. 21:219-26
12. Birchler JA, Veitia RA. 2007. The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19:395-402
13. Birchler JA, Veitia RA. 2010. The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol. 186:54-62
14. Birchler JA, YaoH,Chudalayandi S. 2007. Biological consequences of dosage dependent gene regulatory systems. Biochim. Biophys. Acta 1769:422-28
15. Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-78
16. Bolot S, Abrouk M, Masood-Quraishi U, SteinN,Messing J, et al. 2009. The "inner circle" of the cereal genomes. Curr. Opin. Plant Biol. 12:119-25
17. Bomblies K, Doebley JF. 2005. Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae). Mol. Biol. Evol. 22:1082-94
18. Bomblies K, Wang R-L, Ambrose BA, Schmidt RJ, Meeley RB, Doebley J. 2003. Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize. Development 130:2385-95
19. Bouché N, Bouchez D. 2001. Arabidopsis gene knockout: phenotypes wanted. Curr. Opin. Plant Biol. 4:111-17
20. Chia J-M, Song C, Bradbury PJ, Costich D, de Leon N, et al. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44:803-7
21. Christin P-A, Spriggs E, Osborne CP, Strömberg CAE, Salamin N, Edwards EJ. 2014. Molecular dating, evolutionary rates, and the age of the grasses. Syst. Biol. 63:153-65
22. ClarkLG, ZhangW,Wendel JF. 1995.Aphylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst. Bot. 20:436-60
23. Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B, et al. 2012. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 71:492-502
24. Dewey CN. 2011. Positional orthology: putting genomic evolutionary relationships into context. Brief. Bioinform. 12:401-12
25. Doebley JF, Gaut BS, Smith BD. 2006. The molecular genetics of crop domestication. Cell 127:1309-21
26. Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, et al. 2011. Heritable epigenetic variation among maize inbreds. PLOS Genet. 7:e1002372
27. Emrich SJ,LiL,Wen T-J, Yandeau-NelsonMD,FuY, et al. 2007. Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution. Genetics 175:429-39
28. Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, et al. 2014. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum. Mol. Genet. 23:5866-78
29. Ferguson AA, Zhao D, JiangN. 2013. Selective acquisition and retention of genomic sequences by packmutator-like elements based on guanine-cytosine content and the breadth of expression. Plant Physiol. 163:1419-32
30. FitchWM. 1970. Distinguishing homologous from analogous proteins. Syst. Biol. 19:99-113
31. Foster T, Yamaguchi J, Wong BC, Veit B, Hake S. 1999. Gnarley1 is a dominant mutation in the knox4 homeobox gene affecting cell shape and identity. Plant Cell 11:1239-52
32. Franken P, Niesbach-Klösgen U,Weydemann U, Maréchal-Drouard L, Saedler H,Wienand U. 1991. The duplicated chalcone synthase genes C2 and Whp (white pollen) of Zea mays are independently regulated; evidence for translational control of Whp expression by the anthocyanin intensifying gene in. EMBO J. 10:2605-12
33. Freeling M. 2009. Bias in plant gene content following different sorts of duplication: tandem, wholegenome, segmental, or by transposition. Annu. Rev. Plant Biol. 60:433-53
34. Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18:1924-37
35. Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. 2012. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15:131-39
36. Fu H, Dooner HK. 2002. Intraspecific violation of genetic colinearity and its implications in maize. PNAS 99:9573-78
37. Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. PNAS 94:6809-14
38. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, et al. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Res. 17:669-81
39. Goff SA, Ricke D, Lan T-H, Presting G, Wang R, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100
40. Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, et al. 2009. A first-generation haplotype map of maize. Science 326:1115-17
41. Grass Phylogeny Work. Group. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Mo. Bot. Gard. 88:373-457
42. Grass Phylogeny Work. Group. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol. 193:304-12
43. Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK. 2005. A novel class of helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol. Biol. 57:115-27
44. Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE,Waterston RH. 2005. Genomics in C. elegans: so many genes, such a little worm. Genome Res. 15:1651-60
45. Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, et al. 2014. Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26:121-35
46. Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J. 2013. The genomic signature of crop-wild introgression in maize. PLOS Genet. 9:e1003477
47. Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS. 2009. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLOS Genet. 5:e1000737
48. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-73
49. Kawabe A, Hansson B, Hagenblad J, Forrest A, Charlesworth D. 2006. Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana. Genetics 173:1613-19
50. Kellogg EA. 2000. The grasses: A case study in macroevolution. Annu. Rev. Ecol. Syst. 31:217-38
51. Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, et al. 2006. A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J. 47:640-51
52. Lai J, Li R, Xu X, Jin W, Xu M, et al. 2010. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat. Genet. 42:1027-30
53. Lai J, Li Y, Messing J, Dooner HK. 2005. Gene movement by helitron transposons contributes to the haplotype variability of maize. PNAS 102:9068-73
54. Lisch D. 2013. How important are transposons for plant evolution? Nat. Rev. Genet. 14:49-61
55. Longley AE. 1941. Chromosome morphology in maize and its relatives. Bot. Rev. 7:263-89
56. LynchM,Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-55
57. Lyons E, Pedersen B, Kane J, FreelingM. 2008. The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Trop. Plant Biol. 1:181-90
58. Maeda I,Kohara Y, YamamotoM, Sugimoto A. 2001. Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11:171-76
59. Mangelsdorf PC, Reeves RG. 1931. Hybridization of maize, Tripsacum, and Euchlaena. J. Hered. 22:329-43
60. Mano Y, Omori F, Kindiger B, Takahashi H. 2008. A linkage map of maize × teosinte Zea luxurians and identification of QTLs controlling root aerenchyma formation. Mol. Breed. 21:327-37
61. Mathews S, Spangler RE, Mason-Gamer RJ, Kellogg EA. 2002. Phylogeny of Andropogoneae inferred from phytochrome B, GBSSI, and ndhF. Int. J. Plant Sci. 163:441-50
62. Mauro-Herrera M, Wang X, BarbierH, Brutnell TP, Devos KM, Doust AN. 2013. Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae). G3 3:283-95
63. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, et al. 2004. Sequence composition and genome organization of maize. PNAS 101:14349-54
64. Mikel MA, Dudley JW. 2006. Evolution of North American dent corn from public to proprietary germplasm. Crop Sci. 46:1193
65. Moore G, Devos KM, Wang Z, Gale MD. 1995. Cereal genome evolution. Grasses, line up and form a circle. Curr. Biol. 5:737-39
66. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A. 2005. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37:997-1002
67. Murat F, Xu J-H,Tannier E, Abrouk M, Guilhot N, et al. 2010. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res. 20:1545-57
68. Nardmann J, Ji J, Werr W, Scanlon MJ. 2004. The maize duplicate genes narrow sheath1 and narrow sheath2 encode a conserved homeobox gene function in a lateral domain of shoot apical meristems. Development 131:2827-39
69. O'Malley RC, Ecker JR. 2010. Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 61:928-40
70. Ouyang S, ZhuW, Hamilton J, Lin H, Campbell M, et al. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 35:D883-87
71. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-56
72. Pennisi E. 2003. A low number wins the GeneSweep pool. Science 300:1484
73. Prasad V, Strömberg CAE, Leaché AD, Samant B, Patnaik R, et al. 2011. Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae. Nat. Commun. 2:480
74. Reeves RG, Mangelsdorf PC. 1942. A proposed taxonomic change in the tribe Maydeae (family Gramineae). Am. J. Bot. 29:815-17
75. Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, et al. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413-18
76. Russell WA. 1972. Registration of B70 and B73 parental lines of maize (reg. nos. PL16 and PL17). Crop Sci. 12:721
77. Sakai H, Lee SS, Tanaka T, Numa H, Kim J, et al. 2013. Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54:e6
78. Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, et al. 2009. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. PNAS 106:14908-13
79. Salse J, Píegu B, Cooke R, Delseny M. 2004. New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J. 38:396-409
80. Scannell DR, Byrne KP,Gordon JL,Wong S,Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-45
81. Schnable JC, Freeling M. 2011. Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLOS ONE 6:e17855
82. Schnable JC, FreelingM, Lyons E. 2012. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol. Evol. 4:265-77
83. Schnable JC, Pedersen BS, Subramaniam S, Freeling M. 2011. Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses. Front. Plant Genet. Plant Genomics 2:2
84. Schnable JC, Springer NM, Freeling M. 2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. PNAS 108:4069-74
85. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-15
86. Sémon M, Wolfe KH. 2007. Reciprocal gene loss between tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet. 23:108-12
87. Song R, Llaca V, Linton E, Messing J. 2001. Sequence, regulation, and evolution of the maize 22-kD zein gene family. Genome Res. 11:1817-25
88. Springer NM, Ying K, Fu Y, JiT, Yeh C-T, et al. 2009. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLOS Genet. 5:e1000734
89. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, et al. 2010. Pervasive gene content variation and copy number variation inmaize and its undomesticated progenitor. Genome Res. 20:1689-99
90. Swidan F, Rocha EPC, Shmoish M, Pinter RY. 2006. An integrative method for accurate comparative genome mapping. PLOS Comput. Biol. 2:e75
91. Swigo nová Z, Lai J, Ma J, Ramakrishna W, Llaca V, et al. 2004. Close split of sorghum and maize genome progenitors. Genome Res. 14:1916-23
92. Talbert LE, Doebley JF, Larson S, Chandler VL. 1990. Tripsacum andersonii is a natural hybrid involving Zea and Tripsacum: molecular evidence. Am. J. Bot. 77:722-26
93. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. 2011. Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinform. 12:102
94. TenaillonMI, HuffordMB, Gaut BS,Ross-Ibarra J. 2011. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol. Evol. 3:219-29
95. Tiffin P,Moeller DA. 2006. Molecular evolution of plant immune system genes. Trends Genet. 22:662-70
96. van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, et al. 2011. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. PNAS 108:1088-92
97. Wang H, Bennetzen JL. 2012. Centromere retention and loss during the descent of maize from a tetraploid ancestor. PNAS 109:21004-9
98. Wang W, ZhengH, Fan C, Li J, Shi J, et al. 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791-802
99. Wang X, GowikU, TangH, Bowers JE, Westhoff P, Paterson AH. 2009. Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol. 10:R68
100. 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
101. 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:e1000715
102. Whitkus R, Doebley J, Lee M. 1992. Comparative genome mapping of sorghum and maize. Genetics 132:1119-30
103. Woodhouse MR, Pedersen B, Freeling M. 2010. Transposed genes in Arabidopsis are often associated with flanking repeats. PLOS Genet. 6:e1000949
104. Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, et al. 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLOS Biol. 8:e1000409
105. Xu X, Liu X, Ge S, Jensen JD, Hu F, et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30:105-11
106. Zhang P, Chopra S, Peterson T. 2000. A segmental gene duplication generated differentially expressed myb-homologous genes in maize. Plant Cell 12:2311-22
107. Zhou L, HuangB,MengX,WangG,WangF, et al. 2010. The amplification and evolution of orthologous 22-kDa?-prolamin tandemly arrayed genes in coix, sorghum andmaize genomes. PlantMol. Biol. 74:631-43
108. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, et al. 2009. A single molecule scaffold for the maize genome. PLOS Genet. 5:e1000711