Advertisement

Synteny with Allied and Model Genomes

  • P. Rajendrakumar
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Analysis of synteny is an integral part of comparative genomics inasmuch as it helps us to understand the structures and functions of genes in the related genomes in relation to genome evolution and their roles in gene expression. The identification of synteny blocks, the basic unit of genome synteny, may provide insights into the gene structure and regulation that are essential for biological processes. During earlier days, synteny blocks were identified through ad hoc methods that were slow, lacked reproducibility, ignored the conservation of gene order and orientation, and were not suitable for general applications. However, during the last decade, concerted efforts by several researchers have led to the development of a large volume of genomic data as well as computational resources that allow comparative genomic analysis between genomes of interest with high resolution. Comparative analysis of map-based genomic sequences led to the identification of shared intragenomic duplications, which provide important clues on the evolution of crop genomes from common ancestors. Recent studies in synteny analysis involve transcriptomic synteny to understand the functional conservation of orthologous genes and paleogenomic synteny to understand the role of whole-genome duplications on genome evolution. This chapter discusses the role of synteny analysis in comparative genomics; various computational tools employed for synteny analysis; synteny of sorghum with allied and model genomes with reference to molecular maps, markers, and the whole genome; emerging trends in synteny analysis; and future prospects.

Keywords

Genome Comparative genomics Synteny Transcriptomics Phylogeny 

References

  1. Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J (2010) Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci 15(9):479–487PubMedCrossRefGoogle Scholar
  2. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135–141PubMedCrossRefGoogle Scholar
  3. Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J (2014) Comparative mapping in the Poaceae family reveals translocations in the complex polyploidy genome of sugarcane. BMC Plant Biol 14:190PubMedPubMedCentralCrossRefGoogle Scholar
  4. Ben-Israel I, Kilian B, Nida H, Fridman E (2012) Heterotic trait locus (HTL) mapping identifies intra-locus interactions that underlie reproductive hybrid vigor in Sorghum bicolor. PLoS ONE 7(6):e38993PubMedPubMedCentralCrossRefGoogle Scholar
  5. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomics: microcolinearity and its many exceptions. Plant Cell 12:1021–1029PubMedPubMedCentralCrossRefGoogle Scholar
  6. Bennetzen JLH, Sarah C (2009) Handbook of maize, genetics and genomics. XII:800–894Google Scholar
  7. Binelli G, Gianfranceschi L, Pe ME, Taramino G, Busso C, Stenhouse J, Ottaviano E (1992) Similarity of maize and sorghum genomes as revealed by maize RFLP probes. Theor Appl Genet 84:10–16PubMedCrossRefGoogle Scholar
  8. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678PubMedPubMedCentralCrossRefGoogle Scholar
  9. Blom J, Albaum S, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinform 10:154CrossRefGoogle Scholar
  10. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422(6930):433–438PubMedCrossRefGoogle Scholar
  11. Bowers JE, Arias MA, Asher R, Avise JA, Ball RT, Brewer GA, Buss RW, Chen AH, Edwards TM, Estill JC, Exum HE, Goff VH, Herrick KL, James Steele CL, Karunakaran S, Lafayette GK, Lemke C, Marler BS, Masters SL, McMillan JM, Nelson LK, Newsome GA, Nwakanma CC, Odeh RN, Phelps CA, Rarick EA, Rogers CJ, Ryan SP, Slaughter KA, Soderlund CA, Tang H, Wing RA, Paterson AH (2005) Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA 102(37):13206–13211PubMedPubMedCentralCrossRefGoogle Scholar
  12. Brendel V, Kurtz S, Pan X (2007) Visualization of syntenic relationships with SynBrowse. Methods Mol Biol 396:153–163PubMedCrossRefGoogle Scholar
  13. Cai B, Yang X, Tuskan GA, Cheng ZM (2011) MicroSyn: a user friendly tool for detection of microsynteny in a gene family. BMC Bioinform 12:79CrossRefGoogle Scholar
  14. Cardoso-Silva CB, Costa EA, Mancini MC, Balsalobre TW, Canesin LE, Pinto LR, Carneiro MS, Garcia AA, de Souza AP, Vicentini R (2014) De Novo assembly and transcriptome analysis of contrasting sugarcane varieties. PLoS ONE 9(2):e88462PubMedPubMedCentralCrossRefGoogle Scholar
  15. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21(16):3422–3423PubMedCrossRefGoogle Scholar
  16. Cheng ZK, Buell CR, Wing RA, Gu MH, Jiang JM (2001) Toward a cytological characterization of the rice genome. Genome Res 11:2133–2141PubMedPubMedCentralCrossRefGoogle Scholar
  17. Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463–1502PubMedPubMedCentralCrossRefGoogle Scholar
  18. Costa V, Angelini C, De Feis I, Ciccodicola A (2010) Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010:853916PubMedPubMedCentralCrossRefGoogle Scholar
  19. Crabtree J, Angiuoli SV, Wortman JR, White OR (2007) Sybil: methods and software for multiple genome comparison and visualization. Methods Mol Biol 408:93–108PubMedCrossRefGoogle Scholar
  20. Davidson RM, Hansey CN, Gowda M, Childs KL, Lin H, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Jiang N, Robin Buell C (2011) Utility of RNA sequencing for analysis of maize reproductive transcriptomes. Plant Genome 4:191–203CrossRefGoogle Scholar
  21. Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B, Shiu SH, Jiang N, Robin Buell C (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J 71:492–502PubMedGoogle Scholar
  22. de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GM, Del Bem LE, Vicentini R, Nogueira FT, Campos RA, Nunes SL, Turrini PC, Vieira AP, Ochoa Cruz EA, Corrêa TC, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY Jr, Cardoso-Silva CB, Scortecci KC, Garcia AA, Carneiro MS, Kim C, Paterson AH, Bergès H, D’Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA (2014) Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genom 15:540CrossRefGoogle Scholar
  23. Derrien T, Andre C, Galibert F, Hitte C (2007) AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics 23(4):498–499PubMedCrossRefGoogle Scholar
  24. Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35:3–15PubMedCrossRefGoogle Scholar
  25. D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217PubMedCrossRefGoogle Scholar
  26. Drillon G, Carbone A, Fischer G (2014) SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS ONE 9(3):e92621PubMedPubMedCentralCrossRefGoogle Scholar
  27. Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218CrossRefGoogle Scholar
  28. Dufour P, Grivet L, D’Hont A, Deu M, Trouche G, Glaszmann JC, Hamon P (1996) Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane. Theor Appl Genet 92:1024–1030PubMedCrossRefGoogle Scholar
  29. Fawcett JA, Maere S, Van de Peer Y (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA 106:5737–5742PubMedPubMedCentralCrossRefGoogle Scholar
  30. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14:1812–1819PubMedPubMedCentralCrossRefGoogle Scholar
  31. Fernandez AC, Galeano CH, Cichy K, Blair MW (2012) MapSynteny: creating images of synteny. In: Proceedings of international plant and animal genome conference XX, 14–18 January 2012, San Diego, CA, USAGoogle Scholar
  32. Figueira TRS, Okura V, da Silva FR, da Silva MJ, Kudrna D, Ammiraju JSS, Talag J, Wing R, Arruda P (2012) A BAC library of the SP80–3280 sugarcane variety (Saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Res Notes 5:185Google Scholar
  33. Freeling M, Thomas BC (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16:805–814PubMedCrossRefGoogle Scholar
  34. Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol 60:433–453PubMedCrossRefGoogle Scholar
  35. Freeling M, Subramaniam S (2009) Conserved noncoding sequences (CNSs) in higher plants. Curr Opin Plant Biol 12:126–132PubMedCrossRefGoogle Scholar
  36. Gaut BS, Clark LG, Wendel JF, Muse SV (1997) Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol Biol Evol 14(7):769–777PubMedCrossRefGoogle Scholar
  37. Ghiurcuta CG, Moret BME (2014) Evaluating synteny for improved comparative studies. Bioinformatics 30:i9–i18PubMedPubMedCentralCrossRefGoogle Scholar
  38. Goel A, Taj G, Pandey D, Gupta S, Kumar A (2011) Genome-wide comparative in silico analysis of calcium transporters of rice and sorghum. Genom Proteom Bioinform 9(4–5):138–150CrossRefGoogle Scholar
  39. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  40. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR (2002) A physical map of the mouse genome. Nature 418:743–750PubMedCrossRefGoogle Scholar
  41. Gui YJ, Zhou Y, Wang Y, Wang S, Wang SY, Hu Y, Bo SP, Chen H, Zhou CP, Ma NX, Zhang TZ, Fan LJ (2010) Insights into the bamboo genome: syntenic relationships to rice and sorghum. J Integr Plant Biol 52(11):1008–1015PubMedCrossRefGoogle Scholar
  42. Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20(18):3643–3646PubMedCrossRefGoogle Scholar
  43. Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624PubMedPubMedCentralCrossRefGoogle Scholar
  44. 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 87:4251–4255PubMedPubMedCentralCrossRefGoogle Scholar
  45. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793800Google Scholar
  46. Jean G, Nikolski M (2011) SyDiG: uncovering synteny in distant genomes. Int J Bioinform Res Appl 7(1):43–62PubMedCrossRefGoogle Scholar
  47. Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome level regulation of transcription. Plant Cell 17:1641–1657PubMedPubMedCentralCrossRefGoogle Scholar
  48. Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125:1198–1205PubMedPubMedCentralCrossRefGoogle Scholar
  49. Kishimoto N, Higo H, Abe K, Arai S, Saito A, Higo K (1994) Identification of duplicated segment in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known function. Theor Appl Genet 88:722–726PubMedCrossRefGoogle Scholar
  50. Klein PE, Klein RR, Vrebalov J, Mullet JE (2003) Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and major chromosomal re-arrangement. Plant J 34:605–621PubMedCrossRefGoogle Scholar
  51. Kong W, Guo H, Goff VH, Lee TH, Kim C, Paterson AH (2014) Genetic analysis of vegetative branching in sorghum. Theor Appl Genet 127(11):2387–2403PubMedCrossRefGoogle Scholar
  52. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645PubMedPubMedCentralCrossRefGoogle Scholar
  53. Ku HM, Liu J, Doganlarand S, Tanksley SD (2001) Exploitation of Arabidopsis-tomato synteny to construct a high resolution map of the ovate-containing region in tomato chromosome 2. Genome 44:470–475PubMedCrossRefGoogle Scholar
  54. Kumar S, Mohan A, Balyan HS, Gupta PK (2009) Orthology between genomes of Brachypodium, wheat and rice. BMC Res Notes 2:93PubMedPubMedCentralCrossRefGoogle Scholar
  55. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D, Prasad M (2013) Development of e-SSR markers in Setaria italica and their applicability in studying genetic diversity, cross transferability and comparative mapping in millet and non-millet species. PLoS ONE 8(6):e67742PubMedPubMedCentralCrossRefGoogle Scholar
  56. Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106:15780–15785PubMedPubMedCentralCrossRefGoogle Scholar
  57. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155PubMedCrossRefGoogle Scholar
  58. Lyons E, Pedersen B, Kane J, Freeling M (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates rosids. Trop Plant Biol 1(3–4):181–190CrossRefGoogle Scholar
  59. Magalhaes JV, Garvin DF, Wang Y, Sorrells ME, Klein PE, Schaffert RE, Li L, Kochian LV (2004) Comparative mapping of a major aluminum tolerance gene in sorghum and other species in the poaceae. Genetics 167(4):1905–1914PubMedPubMedCentralCrossRefGoogle Scholar
  60. Mahalakshmi V, Ortiz R (2001) Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery. Elec J Biotechnol 4(3):1–10Google Scholar
  61. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517PubMedPubMedCentralCrossRefGoogle Scholar
  62. McClean PE, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genom 11:184CrossRefGoogle Scholar
  63. McIntyre CL, Casu RE, Drenth J, Knight D, Whan VA, Croft BJ, Jordan DR, Manners JM (2005) Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance. Genome 48(3):391–400PubMedCrossRefGoogle Scholar
  64. Melake-Berhan A, Hulbert SH, Butler LG, Bennetzen JL (1993) Structure and evolution of the genomes of Sorghum bicolour and Zea mays. Theor Appl Genet 86:598–604CrossRefGoogle Scholar
  65. Meyer M, Munzner T, Pfister H (2009) MizBee: a multiscale synteny browser. IEEE Trans Vis Comput Graph 15(6):897–904PubMedCrossRefGoogle Scholar
  66. Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15:809–834PubMedPubMedCentralCrossRefGoogle Scholar
  67. Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of Saccharum and Sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682PubMedPubMedCentralGoogle Scholar
  68. Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 5:37–739CrossRefGoogle Scholar
  69. Murat F, Xu JH, Tannier E, Abrouk M, Guihot N, Pont C, Messing J, Salse J (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545–1557Google Scholar
  70. Nadeau J, Taylor B (1984) Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci USA 81:814–818PubMedPubMedCentralCrossRefGoogle Scholar
  71. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349PubMedPubMedCentralCrossRefGoogle Scholar
  72. Nagamura Y, Inoue T, Antonio BA, Shimano T, Kajiya H, Shomura A, Lin SY, Kuboki Y, Harushima Y, Kurata N, Minobe Y, Yano M, Sasaki T (1995) Conservation of duplicated segments between rice chromosome 11 and chromosome 12. Breed Sci 45:373–376Google Scholar
  73. Nussbaumer T (2014) CrowsNest: a tool to visualize synteny between plant genomes including recently published cereal genomes of Aegilops tauschii and Hordeum vulgare. In: Proceedings of the international plant and animal genome conference XXII, 11–15 January 2014, San Diego, CA, USAGoogle Scholar
  74. Ohno S (1970) Evolution by gene duplication. Springer, New YorkCrossRefGoogle Scholar
  75. Palmer LE, Rabinowicz PD, O’Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtration. Science 302(5653):2115–2117PubMedCrossRefGoogle Scholar
  76. Pan X, Stein L, Brendel V (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 21(17):3461–3468PubMedCrossRefGoogle Scholar
  77. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20:197–207PubMedPubMedCentralCrossRefGoogle Scholar
  78. Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SRM, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–1718PubMedCrossRefGoogle Scholar
  79. 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(26):9903–9908PubMedPubMedCentralCrossRefGoogle Scholar
  80. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556PubMedCrossRefGoogle Scholar
  81. Paterson AH, Freeling M, Tang H, Wang X (2010) Insights from the comparison of plant genome sequences. Annu Rev Plant Biol 61:349–372PubMedCrossRefGoogle Scholar
  82. Peng Y, Schertz KF, Cartinhour S, Hart GE (1999) Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines. Plant Breed 118:225–235CrossRefGoogle Scholar
  83. Pereira MG, Lee M, Bramel-Cox P, Woodman W, Doebley J, Whitkus R (1994) Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 37(2):236–243PubMedCrossRefGoogle Scholar
  84. Ramu P, Kassahun B, Senthilvel S, Kumar CA, Jayashree B, Folkertsma RT, Reddy LA, Kuruvinashetti MS, Haussmann BIG, Hash CT (2009) Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map. Theor Appl Genet 119:1193–1204PubMedCrossRefGoogle Scholar
  85. Renwick JH (1971) The mapping of human chromosomes. Ann Rev Gen 5:81–120CrossRefGoogle Scholar
  86. Revanna KV, Chiu CC, Bierschank E, Dong Q (2011) GSV: a web-based genome synteny viewer for customized data. BMC Bioinformatics 12:316PubMedPubMedCentralCrossRefGoogle Scholar
  87. Richter DC, Schuster SC, Huson DH (2007) OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics 23:1573–1579PubMedCrossRefGoogle Scholar
  88. Ritter KB (2007) An investigation into the genetics and physiology of sugar accumulation in sweet sorghum as a potential model for sugarcane. PhD Thesis, School of Land, Crop and Food Sciences, University of Queensland, AustraliaGoogle Scholar
  89. Salse J, Piegu B, Cooke R, Delseny M (2002) Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in ongoing rice genome sequencing project. Nucleic Acids Res 30:2316–2328PubMedPubMedCentralCrossRefGoogle Scholar
  90. Salse J, Piegu 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 38:396–409PubMedCrossRefGoogle Scholar
  91. Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C (2009) Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci USA 106:14908–14913PubMedPubMedCentralCrossRefGoogle Scholar
  92. Schnable JC, Lyons E (2011) Comparative genomics with maize and other grasses: from genes to genomes. Maydica 56:77–93Google Scholar
  93. Schnable JC, Springer NM, Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci USA 108(10):4069–4074PubMedPubMedCentralCrossRefGoogle Scholar
  94. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar
  95. Shultz JL, Ray JD, Lightfoot DA (2007) A sequence based synteny map between soybean and Arabidopsis thaliana. BMC Genom 8:8CrossRefGoogle Scholar
  96. Simillion C, Janssens K, Sterck L, Van de Peer Y (2008) i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24(1):127–128Google Scholar
  97. Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, Ooi LC, Ooi SE, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA, Sambanthamurthi R (2013) Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature 500:335–339PubMedPubMedCentralCrossRefGoogle Scholar
  98. Sinha AU, Meller J (2007) Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinform 8:82CrossRefGoogle Scholar
  99. Sobral BWS, Braga DPV, LaHood ES, Keim P (1994) Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae griseb. subtribe of the Andropogoneae Dumort. tribe. Theor Appl Genet 87(7):843–853PubMedCrossRefGoogle Scholar
  100. Soderlund C, Nelson W, Shoemaker A, Paterson A (2006) SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res 16(9):1159–1168PubMedPubMedCentralCrossRefGoogle Scholar
  101. Soderlund C, Nelson W, Shoemaker A, Paterson A (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 39(10):e68PubMedPubMedCentralCrossRefGoogle Scholar
  102. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96:336–348PubMedCrossRefGoogle Scholar
  103. Srinivas G, Satish K, Murali Mohan S, Nagaraja Reddy R, Madhusudhana R, Balakrishna D, Venkatesh Bhat B, Howarth CJ, Seetharama N (2008) Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice. Theor Appl Genet 117:283–296PubMedCrossRefGoogle Scholar
  104. Srinivasachary Dida MM, Gale MD, Devos KM (2007) Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet 115:489–499PubMedCrossRefGoogle Scholar
  105. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J (2004) Close split of sorghum and maize genome progenitors. Genome Res 14(10):1916–1923PubMedPubMedCentralCrossRefGoogle Scholar
  106. Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH (2008a) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res 18:1944–1954PubMedPubMedCentralCrossRefGoogle Scholar
  107. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008b) Synteny and collinearity in plant genomes. Science 320:486–488PubMedCrossRefGoogle Scholar
  108. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 12:102PubMedPubMedCentralCrossRefGoogle Scholar
  109. Tang H, Cuevas HE, Das S, Sezen UU, Zhou C, Guo H, Goff VH, Ge Z, Clemente TE, Paterson AH (2013) Seed shattering in a wild sorghum is conferred by a locus unrelated to domestication. Proc Natl Acad Sci USA 110(39):15824–15829PubMedPubMedCentralCrossRefGoogle Scholar
  110. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  111. The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716Google Scholar
  112. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  113. The International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. 345(6194):1251788Google Scholar
  114. The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 3:20Google Scholar
  115. Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R (2006) Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 173:2227–2235PubMedPubMedCentralCrossRefGoogle Scholar
  116. Ureta-Vidal A, Ettwiller L, Birney E (2003) Comparative genomics: genomewide analysis in metazoan eukaryotes. Nat Rev Genet 4:251–262PubMedCrossRefGoogle Scholar
  117. Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res 12:1792–1801PubMedPubMedCentralCrossRefGoogle Scholar
  118. Van de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10:725–732PubMedCrossRefGoogle Scholar
  119. Ventelon M, Deu M, Garsmeur O, Doligez A, Ghesquière A, Lorieux M, Rami JF, Glaszmann JC, Grivet L (2001) A direct comparison between the genetic maps of sorghum and rice. Theor Appl Genet 102:379–386CrossRefGoogle Scholar
  120. Vergara C, Caraballo L, Mercado D, Jimenez S, Rojas W, Rafaels N, Hand T, Campbell M, Tsai YJ, Gao L, Duque C, Lopez S, Bedoya G, Ruiz-Linares A, Barnes KC (2009) African ancestry is associated with risk of asthma and high total serum IgE in a population from the Caribbean Coast of Colombia. Hum Genet 125:565–579PubMedCrossRefGoogle Scholar
  121. Vergara IA, Chen H (2010) Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genom 11:516CrossRefGoogle Scholar
  122. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedPubMedCentralCrossRefGoogle Scholar
  123. Wang H, Su Y, Mackey AJ, Kraemer ET, Kissinger JC (2006) SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics 22:2308–2309PubMedCrossRefGoogle Scholar
  124. Wang XY, Shi XL, Hao BL, Ge S, Luo JC (2005) Duplication and DNA segmental loss in the rice genome: Implications for diploidization. New Phytol 165:937–946PubMedCrossRefGoogle Scholar
  125. Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genom 11:261CrossRefGoogle Scholar
  126. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039CrossRefGoogle Scholar
  127. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40(7):e49PubMedPubMedCentralCrossRefGoogle Scholar
  128. Wei F, Coe E, Nelson W, Bharti AK, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3(7):e123PubMedPubMedCentralCrossRefGoogle Scholar
  129. Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W, Rock SM, Graves TA, Fulton RS, Coe E, Schnable PS, Schwartz DC, Ware D, Clifton SW, Wilson RK, Wing RA (2009) The physical and genetic framework of the maize B73 genome. PLoS Genet 5(11):e1000715PubMedPubMedCentralCrossRefGoogle Scholar
  130. Wei L, Liu Y, Dubchak I, Shon J, Park J (2002) Comparative genomics approaches to study organism similarities and differences. J Biomed Inform 35(2):142–150PubMedCrossRefGoogle Scholar
  131. Whitkus R, Doebley J, Lee M (1992) Comparative genome mapping of sorghum and maize. Genetics 132:1119–1130PubMedPubMedCentralGoogle Scholar
  132. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38PubMedPubMedCentralCrossRefGoogle Scholar
  133. Zeng X, Pei J, Vergara IA, Nesbitt MJ, Wang K, Chen N (2008) OrthoCluster: A new tool for mining syntenic blocks and applications in comparative genomics. In: Proceedings of the 11th international conferences on extending database technology (EDBT’08), Nantes, France, 25–30 March 2008Google Scholar
  134. Zhang W, Lee HR, Koo DH, Jiang J (2008) Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 20:25–34PubMedPubMedCentralCrossRefGoogle Scholar
  135. Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, Huang P, Chen Q, Li Y, Wang J, Zhao Z, Wang J (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30:549–554PubMedCrossRefGoogle Scholar
  136. Zhu H, Kim DJ, Baek JM, Choi HK, Ellis LC, Kuester H, McCombie WR, Peng HM, Cook DR (2003) Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiol 131:1018–1026PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.ICAR - Indian Institute of Millets ResearchRajendranagar, HyderabadIndia

Personalised recommendations