Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Wang, Jianping ^a   Roe, Bruce ^b   Macmil, Simone ^b   Yu, Qingyi ^c   Murray, Jan E ^a   Tang, Haibao ^d   Chen, Cuixia ^a   Najar, Fares ^b   Wiley, Graham ^b   Bowers, John ^d   Van Sluys, Marie Anne ^e   Rokhsar, Daniel S ^f   Hudson, Matthew E ^a   Moose, Stephen P ^a   Paterson, Andrew H ^d   Ming, Ray ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

^d UNIVERSITY OF GEORGIA   (United States)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOPOLYPLOIDY; BACTERIAL ARTIFICIAL CHROMOSOME; CONTROLLED STUDY; DIPLOIDY; GENE EXPRESSION; GENE FREQUENCY; GENE LOCUS; GENE REARRANGEMENT; GENE SEQUENCE; HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SORGHUM; SUGARCANE; CYTOLOGY; DNA SEQUENCE; FEASIBILITY STUDY; GENETICS; NUCLEOTIDE REPEAT; PLANT CHROMOSOME; PLANT GENE; POLYPLOIDY; REPRODUCIBILITY; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); SACCHARUM; SACCHARUM OFFICINARUM; SACCHARUM SPONTANEUM;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DIPLOIDY; FEASIBILITY STUDIES; GENES, PLANT; GENOME, PLANT; POLYPLOIDY; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; SACCHARUM; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SORGHUM;

EID: 77951143508     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-261     Document Type: Article

References (47)

1. Lam E, Shine J, da Silva J, Lawton M, Bonos S, Calvino M, Carrer H, Silva-Filho MC, Glynn N, Helsel Z, Ma J, Richard E, Souza G, Ming R. Improving Sugarcane for Biofuel: Engineering for an even better feedstock. Global Change Biology Bioenergy 2009, 1:251-255.
2. Aragon C, Carvalho LC, Gonzalez J, Escalona M, Amancio S. Sugarcane (Saccharum sp. Hybrid) propagated in headspace renovating systems shows autotrophic characteristics and develop improved anti-oxidative response. Tropical Plant Biology 2009, 2:38-50.
3. De Maria Felix J, Papini-Terzi FS, Rocha FR, Vencio RZN, Vicentini R, Nishiyama MY, Cesar Ulian E, Souza GM, Menossi M. Expression profiling of signal transduction components in a sugarcane population segregating for sugar content. Tropical Plant Biology 2009, 2:98-109.
4. Rae AL, Jackson MA, Nguyen CH, Bonnett GD. Functional specialization of vacuoles in sugarcane leaf and stem. Tropical Plant Biology 2009, 2:13-22.
5. Heichel GH. Comparative efficiency of energy use in crop production. Bull Conn Ag Expt Sta 1974, 739:1-26.
6. Tew TL. Genetic engeneering for greater energy efficiency in sugarcane. Conf Renewable Energy Technol. Dec 5, 1980; Honolulu
7. D'Hont A, Paulet F, Glaszmann JC. Oligoclonal interspecific origin of 'North Indian' and 'Chinese' sugarcanes. Chromosome Res 2002, 10(3):253-262. 10.1023/A:1015204424287, 12067214.
8. Daniels J, Roach BT. Taxonomy and evolution. Sugarcane Improvement Through Breeding 1987, 7-84. Amsterdam: Elsevier Press, Heinz DJ.
9. D'Hont A, Grivet L, Feldmann P, Rao PS, Berding N, Glaszmann JC. Identification and characterization of sugarcane intergeneric hybrids, Saccharum officinarum x Erianthus arundinaceus, with molecular markers and DNA in situ hybridization. Theor Appl Genet 1995, 91:320-326.
10. D'Hont A, Grivet L, Feldmann P, Rao S, Berding N, Glaszmann JC. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 1996, 250(4):405-413. 10.1007/BF02174028, 8602157.
11. D'Hont A, Ison D, Alix K, Roux C, Glaszmann JC. Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 1998, 41:221-225.
12. Ha S, Moore PH, Heinz D, Kato S, Ohmido N, Fukui K. Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and imaging methods. Plant Mol Biol 1999, 39(6):1165-1173. 10.1023/A:1006133804170, 10380803.
13. Irvine JE. Saccharum species as horticultural classes. Theor Appl Genet 1999, 98:186-194.
14. Bremer G. Problems in breeding and cytology of sugarcane. Euphytica 1961, 10:59-78.
15. Grivet L, D'Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC. RFLP Mapping in Cultivated Sugarcane (Saccharum spp.): Genome Organization in a Highly Polyploid and Aneuploid Interspecific Hybrid. Genetics 1996, 142:987-1000. 1207035, 8849904.
16. Hoarau JY, Grivet L, Offmann B, Raboin LM, Diorflar JP, Payet J, Hellmann M, D'Hont A, Glaszmann JC. Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). II. Detection of QTLs for yield components. Theor Appl Genet 2002, 105(6-7):1027-1037. 10.1007/s00122-002-1047-5, 12582930.
17. Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing R. A bacterial artificial chromosome library for sugarcane. Theor Appl Genet 1999, 99:419-424.
18. D'Hont A. Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res 2005, 109(1-3):27-33. 10.1159/000082378, 15753555.
19. 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. Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 1998, 150(4):1663-1682. 1460436, 9832541.
20. Ming R, Moore PH, Wu KK, D'Hont A, Glaszmann JC, Tew TL, Mirkov TE, da Silva J, Jifon J, Rai M, Schnell RJ, Brumbley SM, Lakshmanan P, Comstock JC, Paterson AH. Sugarcane improvement through breeding and biotechnology. Plant Breeding Review 2005, 27:15-118.
21. Aitken KS, Jackson PA, McIntyre CL. A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet 2005, 110(5):789-801. 10.1007/s00122-004-1813-7, 15700149.
22. Garcia AA, Kido EA, Meza AN, Souza HM, Pinto LR, Pastina MM, Leite CS, Silva JA, Ulian EC, Figueira A, Souza AP. Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 2006, 112(2):298-314. 10.1007/s00122-005-0129-6, 16307229.
23. 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. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457(7229):551-556. 10.1038/nature07723, 19189423.
24. Clayton WD. Andropogoneae. Grass Systematics and Evolution 1987, 307-309. Smithsonian Institution Press, Washington, DC, Soderstrom TR, Hilu KW, Campbell CS, Barkworth ME.
25. Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann JC, Arruda P, D'Hont A. Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J 2007, 50(4):574-585. 10.1111/j.1365-313X.2007.03082.x, 17425713.
26. 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, 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. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA 2005, 102(37):13206-13211. 10.1073/pnas.0502365102, 1201573, 16141333.
27. da Silva JA, Honeycutt RJ, Burnquist W, Al-Janabi SM, Sorrells ME, Tanksley SD, Sobral WS. Saccharum spontaneum L. 'SES208' genetic linkage map containing RFLP and PCR-based markers. Mol Breeding 1995, 1:165-179.
28. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, Nobrega MP, Carrer H, Franca SC, Bacci Junior M, Goldman MH, Gomes SL, Nunes LR, Camargo LE, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon ML, Ferro JA, Silveira HC, Marini DC, Lemos EG, Monteiro-Vitorello CB, Tambor JH, Carraro DM, Roberto PG, Martins VG, Goldman GH, de Oliveira RC, Truffi D, Colombo CA, Rossi M, de Araujo PG, Sculaccio SA, Angella A, Lima MM, de Rosa Junior VE, Siviero F, Coscrato VE, Machado MA, Grivet L, Di Mauro SM, Nobrega FG, Menck CF, Braga MD, Telles GP, Cara FA, Pedrosa G, Meidanis J, Arruda P. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 2003, 13(12):2725-2735. 10.1101/gr.1532103, 403815, 14613979.
29. International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436(7052):793-800. 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project.
30. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596-1604. 10.1126/science.1128691, 16973872.
31. Glaz B. Integrated crop management for sustainable crop production: Recent advances. International Sugar Journal 2003, 105:175-186.
32. Cassman KG. Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. Proc Natl Acad Sci USA 1999, 96(11):5952-5959. 10.1073/pnas.96.11.5952, 34211, 10339523.
33. Heffner EL, Sorrells ME, Jannink JL. Genomic selection for crop improvement. Crop Sci 2009, 49:1-12.
34. Bodenteich A, Chissoe S, Wang YF, Roe BA. Shotgun Cloning as the Strategy of Choice to Generate Templates for High-throughput Dideoxynucleotide Sequencing. Automated DNA Sequencing and Analysis Techniques 1993, 42-50. London: Academic Press, Venter JC.
35. Roe B, Crabtree J, Khan A. DNA Isolation and Sequencing: Essential Techniques Series. 1996, New York: J. Wiley and Sons, Rickwood D.
36. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
37. Roe BA. Shotgun library construction for DNA sequencing. Methods Mol Biol 2004, 255:171-187.
38. Cai WW, Chen R, Gibbs RA, Bradley A. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res 2001, 11(10):1619-1623. 10.1101/gr.198101, 11591638.
39. Csuros M, Li B, Milosavljevic A. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform 2003, 14:186-195.
40. Csuros M, Milosavljevic A. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol 2004, 11(5):1001-1021.
41. Green P. Phrap. 1999, , http://phrap.org
42. Abbott JC, Aanensen DM, Bentley SD. WebACT: an online genome comparison suite. Methods Mol Biol 2007, 395:57-74.
43. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
44. Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 2006, 34:609-612.
45. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3(5):418-26.
46. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
47. Gaut BS, Morton BR, McCaig BC, Clegg MT. Substitution rate comparisons between grasses and palms: Synonymous ratedifferences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 1996, 93:10274-10279. 10.1073/pnas.93.19.10274, 38374, 8816790.