A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin

Plant Molecular Biology

Volumn 81, Issue 1-2, 2013, Pages 139-147

  Kim, Changsoo ^a   Lee, Tae Ho ^a   Compton, Rosana O ^a   Robertson, Jon S ^a   Pierce, Gary J ^a   Paterson, Andrew H ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Comparative mapping; Saccharinae subtribe; Simple sequence repeat; Sorghum; Sugarcane cultivar R570

Indexed keywords

SACCHARUM; SORGHUM (GENUS);

EID: 84871448603     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-012-9987-x     Document Type: Article

References (41)

1. Berding N, Roach BT (1987) Germplasm Collection, Maintenence, and Use. In: Heinz DJ (ed) Sugarcane Improvement Through Breeding. Elsevier, Amsterdam, pp 143-210.
2. 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 CLJ, 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: 13206-13211.
3. Cheung F, Town CD (2007) A BAC end view of the Musa acuminata genome. BMC Plant Biol 7: 29.
4. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
5. Daniels J, Roach BT (1987) Taxonomy and Evolution. In: Heinz DJ (ed) Sugarcane Improvement Through Breeding. Elsevier, Amsterdam, pp 7-84.
6. D'Hont A, Grivet L, Feldmann P, Rao S, Berding N, Glaszmann J-C (1996) Characterization of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 250: 405-413.
7. D'Hont A, Ison D, Alix K, Roux C, Glaszmann J-C (1998) Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41: 221-225.
8. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
9. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
10. Figueira TR, Okura V, da Silva FR, da Silva MJ, Kundra D, Ammiraju JS, 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: 185.
11. Goff SA, Ricke D, Lan T, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange B, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W, Chen L, Cooper B, Park S, Wood T, Mao L, Quail P, Wing RA, 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 R, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
12. Gonzalez VM, Rodfiguez-Moreno L, Centeno E, Benjak A, Garcia-Mas J, Puigdomenech P, Aranda MA (2010) Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries. BMC Genom 11: 618.
13. Grivet L, Arruda P (2002) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5: 122-127.
14. Grivet L, Glaszmann J, D'Hont A (2006) Molecular evidence of sugarcane evolution and domestication. In: Motley TJ (ed) Darwin's harvest: New approaches to the origins, evolution and conservation of crops. Columbia University Press, New York, pp 49-66.
15. Guo Y, Saha S, Yu JZ, Jenkins JN, Kohel RJ, Scheffler BE, Stelly DM (2007) BAC-derived SSR markers chromosome locations in cotton. Euphytica 161: 361-370.
16. Ha S, Moore PH, Heinz DJ, Kato S, Ohmido N, Fukui K (1999) Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and imaging methods. Plant Mol Biol 39: 1165-1173.
17. Han Y, Korban SS (2008) An overview of the apple genome through BAC end sequence analysis. Plant Mol Biol 67: 581-588.
18. Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo M-C, Gu YQ (2008) The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genom 8: 135-147.
19. Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann J-C, Arruda P, D'Hont A (2007) Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J 50: 574-585.
20. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cyto Genome Res 110: 462-467.
21. Kim C, Tang H, Paterson AH (2009) Duplication and divergence of grass genomes: integrating the Cloridoids. Trop Plant Biol 2: 51-62.
22. Kim C, Robertson JS, Paterson AH (2011) Inference of subgenomic origin of BACs in an interspecific hybrid sugarcane cultivar by overlapping oligonucleotide hybridizations. Genome 54: 727-737.
23. Lai CW, Yu Q, Hou S, Skelton RL, Jones MR, Lewis KLT, Murray J, Eustice M, Guan P, Agbayani R, Moore PH, Ming R, Presting GG (2006) Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol Gen Genom 276: 1-12.
24. Le Cunff L, Garsmeur O, Raboin LM, Pauquet J, Telismart H, Selvi A, Grivet L, Philippe R, Begum D, Deu M, Costet L, Wing RA, Glaszmann JC, D'Hont A (2008) Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n ~ 12x ~ 115). Genetics 180: 649-660.
25. Menossi M, Silva-Filho MC, Vincentz M, Van-Sluys M-A, Souza GM (2008) Sugarcane functional genomics: gene discovery for agronomic trait development. Int J Plant Genom Article ID 458732.
26. Ming R, Liu S-C, Lin Y-R, 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: 1663-1682.
27. Ming R, Liu S-C, Moore PH, Irvine JE, Paterson AH (2001) QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane. Genome Res 11: 2075-2084.
28. Ming R, Del Monte TA, Hernandez E, Moore PH, Irvine JE, Paterson AH (2002a) Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes. Genome 45: 794-803.
29. Ming R, Wang YW, Draye X, Moore PH, Irvine JE, Paterson AH (2002b) Molecular dissection of complex traits in autopolyploids: mapping QTKs affecting sugar yield and related traits in sugarcane. Theor Appl Genet 105: 332-345.
30. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30: 194-200.
31. 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.
32. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Miltros 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, Rahman M, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
33. Piperidis G, Piperidis N, D'Hont A (2010) Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Mol Genet Genom 284: 65-73.
34. Rampant PF, Lesur I, Boussardon C, Bitton F, Martin-Magniette M-L, Bodenes C, Le Provost G, Berges H, Fluch S, Kremer A, Plomion C (2011) Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. BMC Genom 12: 292.
35. Schlueter JA, Goicoechea JL, Collura K, Gill N, Lin J-Y, Yu Y, Kudrna D, Zuccolo A, Vallejos CE, Munoz-Torres M, Blair MW, Tohme J, Tomkins J, McClean P, Wing RA, Jackson SA (2008) BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Trop Plant Biol 1: 40-48.
36. Sharma MK, Sharma R, Cao P, Jenkins J, Bartley LE, Qualls M, Grimwood J, Schmutz J, Rokhsar D, Ronald PC (2012) A genome-wide survey of switchgrass genome structure and organization. PLoS ONE 7: e33892.
37. Shultz JL, Kazi S, Bashir R, Afzal JA, Lightfoot DA (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114: 1081-1090.
38. Souza GM, Berges H, Bocs S, Casu R, D'Hont A, Ferreira JE, Henry R, Ming R, Potier B, van Sluys MA, Vincentz M, Paterson AH (2011) The sugarcane genome challenge: strategies for sequencing a highly complex genome tropical. Plant Biol 4: 145-156.
39. Sreenivasan TV, Ahloowalia BS, Heinz DJ (1987) Cytogenetics. In: Heinz DJ (ed) Sugarcane Improvement Through Breeding. Elsevier Press, Amsterdam, pp 211-253.
40. Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA (1999) A bacterial artificial chromosome library for sugarcane. Theor Appl Genet 99: 419-424.
41. Tomkins J, Fregene M, Main D, Kim H, Wing RA, Tohme J (2004) Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz). Plant Mol Biol 56: 555-561.