Survey of the genetic information carried in the genome of Eucalyptus camaldulensis

Plant Biotechnology

Volumn 28, Issue 5, 2011, Pages 471-480

  Hirakawa, Hideki ^a   Nakamura, Yasukazu ^a,b   Kaneko, Takakazu ^a,c   Isobe, Sachiko ^a   Sakai, Hiroe ^a   Kato, Tomohiko ^d   Hibino, Takashi ^a   Sasamoto, Shigemi ^a   Watanabe, Akiko ^a   Yamada, Manabu ^a   Nakayama, Shinobu ^a   Fujishiro, Tsunakazu ^a   Kishida, Yoshie ^a   Kohara, Mitsuyo ^a   Tabata, Satoshi ^a   Sato, Shusei ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c KYOTO SANGYO UNIVERSITY   (Japan)

^d OJI PAPER CO LTD   (Japan)

Author keywords

cDNA sequencing; Eucalyptus camaldulensis; Genetic diversity; Genome sequencing; Microsatellite markers

Indexed keywords

EUCALYPTUS; EUCALYPTUS CAMALDULENSIS;

EID: 84857171896     PISSN: 13424580     EISSN: 13476114     Source Type: Journal    
DOI: 10.5511/plantbiotechnology.11.1027b     Document Type: Article

References (50)

1. Altschul SF, Madden TL, Schäffer AA (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Asamizu E, Nakamura Y, Sato S, Fukuzawa H, Tabata S (1999) A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 nonredundant expressed sequence tags. DNA Res 6: 369-373.
3. Ashburner M, Ball CA, Blake JA, et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
4. Bairoch A, Apweiler R (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res 24: 21-25.
5. Bao Z, Eddy SR (2002) Automated de novo Identification of Repeat Sequence Families in Sequenced Genomes. Genome Res 12: 1269-1276.
6. Bocca SN, Magioli C, Mangeon A, Junqueira RM, Cardeal V, Margis R, Sachetto-Martins G (2005) Survey of glycine-rich proteins (GRPs) in the Eucalyptus expressed sequence tag database (ForEST). Genet Mol Biol 28: 608-624.
7. Brendel V, Kleffe J (1998) Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Res 26: 4748-4757.
8. Brondani RP, Williams ER, Brondani C, Grattapaglia D (2006) A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6: 20.
9. Brondani RPV, Brondani C, Grattapaglia D (2002) Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol Genet Genomics 267: 338-347.
10. Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theor Appl Genet 97: 816-827.
11. Brooker MIH (2000) A new classification of the genus Eucalyptus L'Her. (Myrtaceae). Aust Syst Bot 13: 79-148.
12. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
13. Butcher PA, Otero A, Mcdocald MW, Moran GF (2002) Nuclear RFLP variation in Eucalyptus camaldulensis Dehnh. from northern Australia. Heredity 88: 402-412.
14. Byrne M, Marquezgarcia MI, Uren T, Smith DS, Moran GF (1996) Conservation and Genetic Diversity of Microsatellite loci in the Genus Eucalyptus. Aust J Bot 44: 331-341.
15. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 15: 288-289.
16. Chaix G, Gerber S, Razafimaharo V, Vigneron P, Verhaegen D, Hamon S (2003) Gene flow estimation with microsatellites in a Malagasy seed orchard of Eucalyptus grandis. Theor Appl Genet 107: 705-712.
17. Chen F, Ro D, Petri J, Gershenzon J, Bohlmann J, Pichersky E, Tholl D (2004) Characterization of a Root-Specific Arabidopsis Terpene Synthase Responsible for the Formation of the Volatile Monoterpene 1,8-Cineole1. Plant Physiol 135: 1956-1966.
18. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159.
19. Ewing B, Hillier L, Wendl M, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
20. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
21. Garcia-Hernandez M, Berardini TZ, Chen G, Crist D, Doyle A, Huala E, Knee E, Lambrecht M, Miller N, Mueller LA, et al. (2002) TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2: 239-253.
22. Giamakis A, Kretsi O, Chinou I, Spyropoulos CG (2001) Eucalyptus camaldulensis: volatiles from immature flowers and high production of 1,8-cineole and beta-pinene by in vitro cultures. Phytochemistry 58: 351-355.
23. Glaubitz JC, Emebiri LC, Moran GF (2001) Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences. Genome 44: 1041-1045.
24. Glaubitz JC, Murrell JC, Moran GF (2003) Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana. Theor Appl Genet 107: 422-431.
25. Grattapaglia D and Bradshaw HD (1994) Nuclear DNA content of commercially important Eucalyptus species and hybrids. Can J For Res 24: 1074-1078.
26. Grattapaglia D, Silva-Junior OB, Kirst M, de Lima BM, Faria DA, Pappas GJ Jr (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol 11: 65.
27. Grattapaglia D, Ribeiro VJ, Rezende GD (2004) Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus. Theor Appl Genet 109: 192-199.
28. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouzé P, Brunak S (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 24: 3439-3452.
29. Higgins HG (1984) Pulp and Paper. In: Hillis WE and Brown AG (eds) Eucalyptus for wood production. Academic Press Inc, London, pp 290-316.
30. Huang X, Zhang J (1996) Methods for comparing a DNA sequence with a protein sequence. Comput Appli in the Biosci 12: 497-506.
31. Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK (2006) Application of a superword array in genome assembly. Nucleic Acids Res 34: 201-205.
32. Hunter S, Apweiler R, Attwood TK, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-215.
33. Kampranis SC, Ioannidis D, Purvis A, Mahrez W, Ninga E, Katerelos NA, Anssour S, Dunwell JM, Degenhardt J, Makris AM, et al. (2007) Rational conversion of substrate and product specificity in a Salvia monoterpene synthase: structural insights into the evolution of terpene synthase function. Plant Cell 19: 1994-2005.
34. Kirst M, Cordeiro CM, Rezende GD, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96: 161-166.
35. Koren S, Miller JR, Walenz BP, Sutton G (2010) An algorithm for automated closure during assembly. BMC Bioinform 11: 457.
36. Lukashin A, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26: 1107-1115.
37. Mullins KV, Llewellyn DJ, Hartney VJ, Strauss S, Dennis ES (1997) Regeneration and transformation of Eucalyptus camaldulensis. Plant Cell Rep 16: 787-791.
38. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34.
39. Ottewell KM, Donnellan SC, Moran GF, Paton DC (2005) Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other eucalyptus species. J Hered 96: 445-451.
40. Ranik M, Myburg AA (2006) Six new cellulose synthase genes from Eucalyptus are associated with primary and secondary cell wall biosynthesis. Tree Physiol 26: 545-556.
41. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, et al. (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15: 227-239.
42. Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34(Web Server issue): W435-439.
43. Steane DA, Nicolle D, McKinnon GE, Vaillancourt RE, Potts BM (2002) Higher-level relationships among the eucalypts are resolved by ITS-sequence data. Aust Syst Bot 15: 49-62.
44. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
45. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4: 41-54.
46. Thamarus K, Groom K, Bradley A, Raymond CA, Schimleck LR, Williams ER, Moran GF (2004) Identification of quantitative trait loci for wood and fibre properties in two full-sib properties of Eucalyptus globulus. Theor Appl Genet 109: 856-864.
47. Tholl D, Chen F, Petri J, Gershenzon J, Pichersky E (2005) Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J 42: 757-771.
48. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 122: 4673-4680.
49. Turnbull JW, Pryor LD (1984) Choice of specific and seed sources. In: Hillis WE and Brown AG (eds) Eucalyptus for wood production. Academic Press Inc, London, pp 6-65.
50. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The Genome of Black Cottonwood, Populus trichocarpa (Torr & Gray). Science 15: 1596-1604