Abstract
The economic and agricultural importance of cereals and millets has motivated whole-genome sequencing of many grass (Poaceae) taxa, empowering vigorous comparative genomics research in this family. Initial analyses of sequenced genomes have already contributed to an understanding of the occurrence of polyploidizations, genome structural changes, biological pathway evolution, evolution of gene repertoire, and other important dimensions of evolution of the members of the grass family. In-depth analysis of the sequenced genomes, along with on-going sequencing and re-sequencing efforts, will help generate knowledge about genes in cereal models. It will also shed light on other Poaceae species with more complex genomes, and will help enhance fundamental knowledge, which can be effectively used for sustainable improvement of agricultural productivity.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218
Backstrom N, Ceplitis H et al (2005) Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome. Mol Biol Evol 22(10):1992–1999
Baucom RS, Estill JC et al (2009) Exceptional diversity, non-random distribution, and rapid evolution of retro-elements in the B73 maize genome. PLoS Genet 5(11):e1000732
Bennetzen JL, Schmutz J et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561
Bensen RJ, Johal GS et al (1995) Cloning and characterization of the maize An1 gene. Plant Cell 7(1):75–84
Bevan MW, Garvin DF et al (2010) Brachypodium distachyon genomics for sustainable food and fuel production. Curr Opin Biotechnol 21(2):211–217
Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16(7):1679–1691
Bomblies K, Lempe J et al (2007) Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol 5(9):e236
Bowers JE, Chapman BA et al (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422(6930):433–438
Bowers JE, Arias MA et al (2005) Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA A102(37):13206–13211
Bozza CG, Pawlowski WP (2008) The cytogenetics of homologous chromosome pairing in meiosis in plants. Cytogenet Genome Res 120(3–4):313–319
Brown J, Ersland D et al (1982) Molecular aspects of storage protein synthesis during seed development. In: Khan A (ed) The physiology and biochemistry of seed development, dormancy, and germination. Elsevier Biomedical Press, Amsterdam, pp 3–42
Brown NJ, Newell CA et al (2011) Independent and parallel recruitment of preexisting mechanisms underlying C photosynthesis. Science 331(6023):1436–1439
Buell CR (2009) Poaceae genomes: going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiol 149(1):111–116
Calderon-Urrea A, Dellaporta SL (1999) Cell death and cell protection genes determine the fate of pistils in maize. Development 126(3):435–441
Cannon SB, Kozik A, Chan B, Michelmore R, Young ND (2003) DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biology 4:R68
Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154(4):1819–1825
Cerling TE, Harris JM et al (1997) Global vegetation change through the Miocene/Pliocene boundary. Nature 389:153–158
Charlesworth B (2002) The evolution of chromosomal sex determination. Novartis Found Symp 244:207–219 (discussion 220–204, 253–207)
Chen F, Mackey AJ et al (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2(4):e383
Chittenden LM, Schertz KF et al (1994) A detailed RFLP map of Sorghum bicolor and S. propinquum suitable for high-density mapping suggests ancestral duplication of Sorghum chromosomes or chromosomal segments. Theor Appl Genet 87:925–933
Christin PA, Osborne CP et al (2011) C4 eudicots are not younger than C4 monocots. J Exp Bot 62(9) : 3171–3181
Christin PA, Besnard G et al (2008) Oligocene CO2 decline promoted C4 photosynthesis in grasses. Curr Biol 18(1):37–43
Christin PA, Salamin N et al (2009) Integrating phylogeny into studies of C4 variation in the grasses”. Plant Physiol 149(1):82–87
Datta A, Hendrix M et al (1997) Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proc Natl Acad Sci USA A94(18):9757–9762
DeLong A, Calderon-Urrea A et al (1993) Sex determination gene TASSELSEED2 of maize encodes a short-chain alcohol dehydrogenase required for stage-specific floral organ abortion. Cell 74(4):757–768
Devos KM (2010) Grass genome organization and evolution. Curr Opin Plant Biol 13(2):139–145
Devos KM, Pittaway TS et al (2000) Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theoret Appl Genet 100(2):190–198
Ding DQ, Yamamoto A et al (2004) Dynamics of homologous chromosome pairing during meiotic prophase in fission yeast. Dev Cell 6(3):329–341
Duret L, Galtier N (2009) Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10:285–311
Ehleringer JR, Bjorkman O (1978) A Comparison of Photosynthetic Characteristics of Encelia Species Possessing Glabrous and Pubescent Leaves. Plant Physiol 62(2):185–190
Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96(14):8265–8270
Freeling M (2001) Grasses as a single genetic system: reassessment 2001. Plant Physiol 125(3):1191–1197
Galtier N (2003) Gene conversion drives GC content evolution in mammalian histones. Trends Genet 19(2):65–68
Galtier N, Piganeau G et al (2001) GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159(2):907–911
Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94(13):6809–6814
Giussani LM, Cota-Sanchez JH et al (2001) A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. Am J Bot 88(11):1993–2012
Global Perspective Studies Unit, F a A O o t U N (2006) FAQ: World Agriculture: towards 2030/2050. Interim Report, Rome, Italy
Goff SA, Ricke D et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296(5565):92–100
Gojobori T, Li WH et al (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18(5):360–369
Haas BJ, Delcher AL et al (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31(19):5654–5666
Haldane JBS (1932) The causes of evolution. Cornell University Press, Ithaca
Hatch MD, Slack CR (1966) Photosynthesis by sugar-cane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem J 101(1):103–111
Hattersley PG (1983) The distribution of C3 and C4 grasses in Australia in relation to climate. Oecologia 57:113–128
Hilu KW (2004) Phylogenetics and chromosomal evolution in the Poaceae (grasses). Aust J Bot 52:10
The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800
Jaillon O, Aury JM et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467
Kadyk LC, Hartwell LH (1992) Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics 132(2):387–402
Kellogg EA (1999) Phylogenetic aspects of the evolution of C4 photosynthesis. In: Sage RF, Monson RK (eds) C4 plant biology. Academic Press, San Diego, CA, pp 411–444
Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125(3):1198–1205
Khakhlova O, Bock R (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46(1):85–94
Kim JC, Laparra H et al (2007) Cell cycle arrest of stamen initials in maize sex determination. Genetics 177(4):2547–2551
Kishimoto NHH, Abe K, Arai S, Saito A, Higo K (1994) Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor Appl Genet 88:722–726
Kudla G, Helwak A et al (2004) Gene conversion and GC-content evolution in mammalian Hsp70. Mol Biol Evol 21(7):1438–1444
Lahn BT, Page DC (1999) Four evolutionary strata on the human X chromosome. Science 286(5441):964–967
Lawson Handley LJ, Hammond RL et al (2006) Low Y chromosome variation in Saudi-Arabian hamadryas baboons (Papio hamadryas hamadryas). Heredity 96(4):298–303
Lescot M, Piffanelli P et al (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9:58
Li L, Stoeckert CJ et al (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189
Lin Y, Byrnes JK et al (2006) Codon usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc Natl Acad Sci USA 103:14412–14416
Lohithaswa HC, Feltus FA et al (2007) Leveraging the rice genome sequence for comparative genomics in monocots. Theor Appl Genet 115:237–243
Lynch M, Force AG (2000) The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156(6):590–605
Lyons E, Pedersen B et al (2008) Finding and comparing syntenic regions among arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148(4):1772–1781
Mayer KF, Martis M et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23(4):1249–1263
Ming R, Moore PH (2007) Genomics of sex chromosomes. Curr Opin Plant Biol 10(2):123–130
Monson RK (2003) Gene duplication, neofunctionalization, and the evolution of C4 photosynthesis. Int J Plant Sci 164(6920):S43–S54
Mulhaidat R, Sage RF et al (2007) Diversity of kranz anatomy and biochemistry in C4 eudicots. Am J Bot 94(3):20
Murat F, Xu JH et al (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20(11):1545–1557
Nagamura YIT, Antonio B, Shimano T, Kajiya H, Shomura A, Lin S, Kuboki Y, Kurata N et al (1995) Conservation of duplicated segments between rice chromosomes 11 and 12. Breed Sci 45:373–376
O’Brien KP, Remm M et al (2005) In paranoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33:D476–D480 (database issue)
Paterson AH (2005) Polyploidy, evolutionary opportunity and crop adaptation. Genetica 123(1–2):191–196
Paterson AH (2008) Paleopolyploidy and its Impact on the Structure and Function of Modern Plant Genomes. Genome Dyn 4:1–12
Paterson AH, Bowers JE et al (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101(26):9903–9908
Paterson AH, Chapman BA et al (2006) Convergent retention or loss of gene/domain families following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces, and Tetraodon. Trends Genet 22:597–602
Paterson AH, Bowers JE et al (2009a) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556
Paterson AH, Bowers JE et al (2009b) Comparative genomics of grasses promises a bountiful harvest. Plant Physiol 149(1):125–131
Pedersen BS, Tang H et al (2011) Gobe: an interactive, web-based tool for comparative genomic visualization. Bioinformatics 27(7):1015–1016
Puchta H, Dujon B et al (1996) Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci USA 93(10):5055–5060
Pyankov VI, Artyusheva EG et al (2001) Phylogenetic analysis of tribe Salsoleae (Chenopodiaceae) based on ribosomal ITS sequences: implications for the evolution of photosynthesis types. Am J Bot 88(7):1189–1198
Sage RF (2004) The evolution of C4 photosynthesis. New Phytol 161:341–370
Salse J, Abrouk M et al (2009) Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci USA 106(35):14908–14913
Schnable JC, Freeling M (2011) Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One 6(3):e17855
Schnable PS, Ware D et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115
Schnable JC, Springer NM et al (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci USA 108(10):4069–4074
Seemann JR, Sharkey TD et al (1987) Environmental effects on photosynthesis, nitrogen-use efficiency, and metabolite pools in leaves of sun and shade plants. Plant Physiol 84(3):796–802
Shi X, Wang X et al (2007) Evidence that natural selection is the primary cause of the GC content variation in rice genes. J Integr Plant Biol 49(9):1393–1399
Singh NK, Dalal V et al (2007) Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 7(1):17–35
Soderstrom TR, Hilu KW, Campbell CS, Barkworth MA (1987) Grass systematics and evolution. Smithsonian Institution Press, Washington, DC
Soltis PS (2005) Ancient and recent polyploidy in angiosperms. New Phytol 166(1):5–8
Storm CE, Sonnhammer EL (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13(10):2353–2362
Swigonova ZJ, Lai S et al (2004b) Close split of sorghum and maize genome progenitors. Genome Res 14(10A):1916–1923
Swigonova Z, Lai JS et al (2004a) On the tetraploid origin of the maize genome. Compa Funct Genomics 5(3):281–284
Tang HB, Wang XY et al (2008b) Unraveling ancient hexaploidy through multiply aligned angiosperm gene maps. Genome Res 18(12):1944–1954
Tang H, Bowers JE et al (2008a) Synteny and colinearity in plant genomes. Science 320:486–488
Tang H, Bowers JE et al (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci USA 107(1):472–477
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815
The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rice in disease resistance genes and recent gene duplications. BMC Biol 3:20
Thomas BC, Pedersen B et al (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homology leaving clusters enriched in dose-sensitive genes. Genome Res 16(7):934–946
Van de Peer Y (2004) Computational approaches to unveiling ancient genome duplications. Nat Rev Genet 5(10):752–763
Vandepoele K, Saeys Y et al (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res 12(11):1792–1801
Vandepoele K, Simillion C et al (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15(9):2192–2202
Vicentini A, Barber JC et al (2008) The age of the grasses and clusters of origins of C4 photosynthesis. Glob Change Biol 14:15
Wang HC, Singer GA et al (2004) Mutational bias affects protein evolution in flowering plants. Mol Biol Evol 21(1):90–96
Wang X, Shi X et al (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165(3):937–946
Wang X, Shi X et al (2006) Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinf 7(1):447
Wang X, Tang H et al (2007) Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics 177(3):1753–1763
Wang X, Gowik U et al (2009a) Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol 10(6):R68
Wang X, Tang H et al (2009b) Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res 19(6):1026–1032
Wang X, Tang H et al (2011) Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell 23(1):27–37
Watson L, Dallwitz MJ (1992) The grass genera of the world. CAB International, Wallingford
Werth CR, Windham MD (1991) A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137(4):515–526
Wicker T, Mayer KF et al (2011) frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23(5): 1706–1718
Winkler RG, Freeling M (1994) Physiological genetics of the dominant gibberellin-nonresponsive maize dwarfs, dwarf-8 and dwarf-9. Planta 193(3):341–348
Wong GK, Wang J et al (2002) Compositional gradients in Gramineae genes. Genome Res 12(6):851–856
Woodhouse MR, Schnable JC et al (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 8(6):e1000409
Yin T, Difazio SP et al (2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 18(3):422–430
Youens-Clark K, Buckler E et al (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094 (database issue)
Yu J, Hu S et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92
Yu J, Wang J et al (2005) The genomes of Oryza sativa: a history of duplications. Plos Biol 3(2):266–281
Zhang G, Liu X et al (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30(6):549–554
Zhou T, Wang Y et al (2004) Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 271(4):402–415
Zmasek CM, Eddy SR (2002) RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinf 3:14
Acknowledgments
We are grateful to members in Paterson lab for useful discussion and collaboration in publishing many high-impact papers in comparative genomics. We appreciate financial support from the US National Science Foundation (MCB-1021718) and the J. S. Guggenheim Foundation to AHP, and from the China National Science Foundation (30971611, 31170212), and Hebei Natural Science Foundation distinguished young scholorship project China-Hebei New Century 100 Creative Talents Project to XW.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Wang, XY., Paterson, A.H. (2013). Genome Sequencing and Comparative Genomics in Cereals. In: Gupta, P., Varshney, R. (eds) Cereal Genomics II. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6401-9_5
Download citation
DOI: https://doi.org/10.1007/978-94-007-6401-9_5
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-6400-2
Online ISBN: 978-94-007-6401-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)