Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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The strategy and current status of Brassica rapa genome project

배추 유전체 염기서열 해독 전략과 현황

  • Mun, Jeong-Hwan (Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration) ;
  • Kwon, Soo-Jin (Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration) ;
  • Park, Beom-Seok (Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration)
  • 문정환 (농촌진흥청 국립농업과학원 농업생명자원부 유전자분석개발과) ;
  • 권수진 (농촌진흥청 국립농업과학원 농업생명자원부 유전자분석개발과) ;
  • 박범석 (농촌진흥청 국립농업과학원 농업생명자원부 유전자분석개발과)
  • Received : 2010.04.08
  • Accepted : 2010.05.13
  • Published : 2010.06.30
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Abstract

Brassica rapa is considered an ideal candidate to act as a reference species for Brassica genomic studies. Among the three basic Brassica species, B. rapa (AA genome) has the smallest genome (529 Mbp), compared to B. nigra (BB genome, 632 Mbp) and B. oleracea (CC genome, 696 Mbp). There is also a large collection of available cultivars of B. rapa, as well as a broad array of B. rapa genomic resources available. Under international consensus, various genomic studies on B. rapa have been conducted, including the construction of a physical map based on 22.5X genome coverage, end sequencing of 146,000 BACs, sequencing of >150,000 expressed sequence tags, and successful phase 2 shotgun sequencing of 589 euchromatic region-tiling BACs based on comparative positioning with the Arabidopsis genome. These sequenced BACs mapped onto the B. rapa genome provide beginning points for genome sequencing of each chromosome. Applying this strategy, all of the 10 chromosomes of B. rapa have been assigned to the sequencing centers in seven countries, Korea, UK, China, India, Canada, Australia, and Japan. The two longest chromosomes, A3 and A9, have been sequenced except for several gaps, by NAAS in Korea. Meanwhile a China group, including IVF and BGI, performed whole genome sequencing with Illumina system. These Sanger and NGS sequence data will be integrated to assemble a draft sequence of B. rapa. The imminent B. rapa genome sequence offers novel insights into the organization and evolution of the Brassica genome. In parallel, the transfer of knowledge from B. rapa to other Brassica crops would be expected.

Keywords

References

  1. Ananiev EV, Phillips RL, Rines HW (1998) Chromosomespecific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 95:13073-13078 https://doi.org/10.1073/pnas.95.22.13073
  2. Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15:487-495 https://doi.org/10.1101/gr.3176505
  3. Beilstein MA, Al-Shehbaz IA, Kellogg EA (2006) Brassicaceae phylogeny and trichome evolution. Am J Bot 93: 607-619 https://doi.org/10.3732/ajb.93.4.607
  4. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438 https://doi.org/10.1038/nature01521
  5. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103:14959-14964 https://doi.org/10.1073/pnas.0603228103
  6. Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545 https://doi.org/10.1105/tpc.010485
  7. Choi HK, Mun J-H, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289-15294 https://doi.org/10.1073/pnas.0402251101
  8. Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS, Lim YP (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 115:777-792 https://doi.org/10.1007/s00122-007-0608-z
  9. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, Mc-Combie WR, Martienssen RA, Marra M, Preuss D (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468-2474 https://doi.org/10.1126/science.286.5449.2468
  10. Ding Y, Johnson MD, Chen WQ, Wong D, Chen YJ, Benson SC, Lam JY, Kim YM, Shizuya H (2001) Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74:142-154 https://doi.org/10.1006/geno.2001.6547
  11. Economic Research Service USDA. (2008) Vegetables and melons outlook: http://www.ers.usda.gov/Publications/VGS/Tables/World.pdf
  12. Gregory SG, Howell GR, Bentley DR (1997) Genome mapping by fluorescent fingerprinting. Genome Res 7:1162-1168 https://doi.org/10.1101/gr.7.12.1162
  13. Harrison GE, Heslop-Harrison JS (1995) Centromeric repetitive DNA sequences in the genus Brassica. Theor Appl Genet 90:157-165
  14. International Human Genome Sequencing Consortium (2001) A physical map of the human genome. Nature 409: 934-941 https://doi.org/10.1038/35057157
  15. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229-235 https://doi.org/10.1093/aob/mci016
  16. Kim JS, Chung TY, King GJ, Jin M, Yang TJ, Jin YM, Kim HI, Park BS (2006) A sequence-tagged linkage map of Brassica rapa. Genetics 174:29-39 https://doi.org/10.1534/genetics.106.060152
  17. Koo DH, Plaha P, Lim YP, Hur Y, Bang JW (2004) A high-resolution karyotype of Brassica rapa ssp. pekinensis revealed by pachytene analysis and multicolor fluorescence in situ hybridization. Theor Appl Genet 109:1346-1352 https://doi.org/10.1007/s00122-004-1771-0
  18. Kulikova O, Geurts R, Lamine M, Kim DJ, Cook DR, Leunissen J, de Jong H, Roe BA, Bisseling T(2004) Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula. Chromosoma 113:276-283 https://doi.org/10.1007/s00412-004-0315-3
  19. Kwon SJ, Kim DH, Lim MH, Long Y, Meng JL, Lim KB, Kim JA, Kim JS, Jin M, Kim HI, Ahn SN, Wessler SR, Yang TJ, Park BS (2007) Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genom 278:361-370 https://doi.org/10.1007/s00438-007-0249-6
  20. Lee SC, Lim MH, Kim JA, Lee SI, Kim JS, Jin M, Kwon SJ, Mun JH, Kim YK, Kim HU, Hur Y,Park BS (2008) Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray. Mol Cells 26:595-606
  21. Lim KB, de Jong H, Yang TJ, Park JY, Kwon SJ, Kim JS, Lim MH, Kim JA, Jin M, Jin YM, Kim SH, Lim YP, Bang JW, Kim HI, Park BS (2005) Characterization of rDNAs and tandem repeats in the heterochromatin of Brassica rapa. Mol Cells 19:436-444
  22. Lim KB, Yang TJ, Hwang YJ, Kim JS, Park JY, Kwon SJ, Kim J, Choi BS, Lim MH, Jin M, Kim HI, de Jong H, Bancroft I, Lim YP, Park BS (2007) Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species. Plant J 49:173-183 https://doi.org/10.1111/j.1365-313X.2006.02952.x
  23. Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC (2004) Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol J Linn Soc Lond 82:665-674 https://doi.org/10.1111/j.1095-8312.2004.00352.x
  24. Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378-389 https://doi.org/10.1016/S0888-7543(03)00128-9
  25. Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516-525 https://doi.org/10.1101/gr.3531105
  26. Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund C, McCombie WR, McDonald K, McPherson J, Mudd N, Parnell L, Schein J, Seim R, Shelby P, Waterston R, Wilson R (1999) A map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet 22:265-270 https://doi.org/10.1038/10327
  27. Mun J-H, Kim DJ, Choi HK, Gish J, Debelle F, Mudge J, Denny R, Endre G, Saurat O, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps. Genetics 172:2541-2555 https://doi.org/10.1534/genetics.105.054791
  28. Mun J-H, Kwon SJ, Yang TJ, Kim HS, Choi BS, Baek S, Kim JS, Jin M, Kim JA, Lim MH, Lee SI, Kim HI, Kim H, Lim YP, Park BS (2008) The first generation of a BACbased physical map of Brassica rapa. BMC Genom 9:280 https://doi.org/10.1186/1471-2164-9-280
  29. Mun J-H, Kwon SJ, Yang TJ, Seol YJ, Jin M, Kim JA, Lim MH, Kim JS, Baek S, Choi BS, Yu HJ, Kim DS, Kim N, Lim KB, Lee SI, Hahn JH, Lim YP, Bancroft I, Park BS (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111 https://doi.org/10.1186/gb-2009-10-10-r111
  30. Nelson WM, Bharti AK, Butler E, Wei F, Fuks G, Kim H, Wing RA, Messing J, Soderlund C (2005) Whole-genome validation of high-information-content fingerprinting. Plant Physiol 139:27-38 https://doi.org/10.1104/pp.105.061978
  31. O'Neill CM, Bancroft I (2000) Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoelogous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J 23:233-243 https://doi.org/10.1046/j.1365-313x.2000.00781.x
  32. Park JY, Koo DH, Hong CP, Lee SJ, Jeon JW, Lee SH, Yun PY, Park BS, Kim HR, Bang JW, Plaha P, Bancroft I, Lim YP (2005) Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Genet Genom 274:579-588 https://doi.org/10.1007/s00438-005-0041-4
  33. Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA (2003) Structure and evolution of cereal genomes. Curr Opin Genet Dev 13:644-650 https://doi.org/10.1016/j.gde.2003.10.002
  34. Quiniou SMA, Waldbieser GC, Duke MV (2007) A first generation BAC-based physical map of the channel catfish. BMC Genom 8:40 https://doi.org/10.1186/1471-2164-8-40
  35. Rana D, van den Boogaart T, O'Neill CM, Hynes L, Bent E, Macpherson L, Park JY, Lim YP, Bancroft I. (2004) Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J 40:725-33 https://doi.org/10.1111/j.1365-313X.2004.02244.x
  36. Schmidt R, Acarkan A, Boivin K (2001) Comparative structural genomics in the Brassicaceae family. Plant Physiol Biochem 39:253-262 https://doi.org/10.1016/S0981-9428(01)01239-6
  37. Soderlund C, Humphray S, Dunham I, French L (2000) Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 11:934-941
  38. The Arabidopsis Genome Initiative (2004) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815 https://doi.org/10.1038/35048692
  39. Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348-1359 https://doi.org/10.1105/tpc.106.041665
  40. U N (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7:389-452
  41. Xu Z, Sun S, Covaleda L, Ding K, Zhang A, Wu C, Scheuring C, Zhang HB (2004) Genome physical mapping with largeinsert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality. Genomics 84:941-951 https://doi.org/10.1016/j.ygeno.2004.08.014
  42. Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, Park BS (2006) Sequencelevel analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18:1339-1347 https://doi.org/10.1105/tpc.105.040535
  43. Yang TJ, Kim JS, Lim KB, Kwon SJ, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Kim SH, Lim YP, Park BS (2005) The Korea Brassica Genome Projects: a glimpse of the Brassica genome based on comparative genome analysis with Arabidopsis. Compar Funct Genom 6:138-146 https://doi.org/10.1002/cfg.465
  44. Yang TJ, Kwon SJ, Choi BS, Kim JS, Jin M, Lim KB, Park JY, Kim JA, Lim MH, Kim HI, Lee HJ, Lim YP, Paterson AH, Park BS (2007) Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theor Appl Genet 114:627-636 https://doi.org/10.1007/s00122-006-0463-3
  45. Zhang X, Wessler SR (2004) Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci USA 101:5589-5594 https://doi.org/10.1073/pnas.0401243101
  46. Zhang Y, Huang Y, Zhang L, Li Y, Lu T, Lu Y, Feng Q, Zhao Q, Cheng Z, Xue Y, Wing RA, Han B (2004) Structural features of the rice chromosome 4 centromere. Nucl Acid Res 32:2023-2030 https://doi.org/10.1093/nar/gkh521

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