The genome of Eucalyptus grandis

Nature

Volumn 510, Issue 7505, 2014, Pages 356-362

  Myburg, Alexander A ^a   Grattapaglia, Dario ^b,c   Tuskan, Gerald A ^d,e   Hellsten, Uffe ^d   Hayes, Richard D ^d   Grimwood, Jane ^f   Jenkins, Jerry ^f   Lindquist, Erika ^d   Tice, Hope ^d   Bauer, Diane ^d   Goodstein, David M ^d   Dubchak, Inna ^d   Poliakov, Alexandre ^d   Mizrachi, Eshchar ^a   Kullan, Anand R K ^a   Hussey, Steven G ^a   Pinard, Desre ^a   Van Der Merwe, Karen ^a   Singh, Pooja ^a   Van Jaarsveld, Ida ^a   Silva Junior, Orzenil B ^b   Togawa, Roberto C ^b   Pappas, Marilia R ^b   Faria, Danielle A ^b   Sansaloni, Carolina P ^b   Petroli, Cesar D ^e   Yang, Xiaohan ^e   Ranjan, Priya ^e   Tschaplinski, Timothy J ^e   Ye, Chu Yu ^e   Li, Ting ^e   Sterck, Lieven ^g   Vanneste, Kevin ^g   Murat, Florent ^h   Soler, Marçal ⁱ   Clemente, Hélène San ⁱ   Saidi, Naijib ⁱ   Cassan Wang, Hua ⁱ   Dunand, Christophe ⁱ   Hefer, Charles A ^a,j   Bornberg Bauer, Erich ^k   Kersting, Anna R ^k,l   Vining, Kelly ^m   Amarasinghe, Vindhya ^m   Ranik, Martin ^m   Naithani, Sushma ^m   Elser, Justin ^m   Boyd, Alexander E ^m   Liston, Aaron ^m   Spatafora, Joseph W ^m   Dharmwardhana, Palitha ^m   Raja, Rajani ^m   Sullivan, Christopher ^m   Romanel, Elisson ^n,o   Alves Ferreira, Marcio ⁿ   Külheim, Carsten ^p   Foley, William ^p   Carocha, Victor ^i,q,r   Paiva, Jorge ^q,r   Kudrna, David ^s   Brommonschenkel, Sergio H ^t   Pasquali, Giancarlo ^u   Byrne, Margaret ^v   Rigault, Philippe ^w   Tibbits, Josquin ^x   Spokevicius, Antanas ^y   Jones, Rebecca C ^z   Steane, Dorothy A ^z,aa   Vaillancourt, René E ^z   Potts, Brad M ^z   Joubert, Fourie ^a   Barry, Kerrie ^d   Pappas, Georgios J ^ab   Strauss, Steven H ^m   Jaiswal, Pankaj ^m   Grima Pettenati, Jacqueline ⁱ   Salse, Jérôme ^h   Van De Peer, Yves ^a,g   Rokhsar, Daniel S ^d   Schmutz, Jeremy ^d,f   more..

^a UNIVERSITY OF PRETORIA   (South Africa)

^b EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^c UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^g GHENT UNIVERSITY   (Belgium)

^h Diversity and Ecophysiology of Cereals   (France)

ⁱ Centre National de la Recherche Scientifique   (France)

^j UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^k UNIVERSITY OF MÜNSTER   (Germany)

^l HEINRICH HEINE UNIVERSITY   (Germany)

^m OREGON STATE UNIVERSITY   (United States)

ⁿ FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^o UNIVERSITY OF SÃO PAULO   (Brazil)

^p AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^q INSTITUTO DE INVESTIGAÇÃO CIENTÍFICA TROPICAL   (Portugal)

^r INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^s UNIVERSITY OF ARIZONA   (United States)

^t FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^u FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^v Crop Variety Testing Group   (Australia)

^w Gydle Inc   (Canada)

^x DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^y UNIVERSITY OF MELBOURNE   (Australia)

^z UNIVERSITY OF TASMANIA   (Australia)

^aa UNIVERSITY OF THE SUNSHINE COAST   (Australia)

^ab UNIVERSITY OF BRASILIA   (Brazil)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EUCALYPTUS OIL;

BIOTECHNOLOGY; EVERGREEN TREE; GENE EXPRESSION; GENOME; INBREEDING DEPRESSION; METABOLISM; METABOLITE; RENEWABLE RESOURCE; SPECIES DIVERSITY;

ARTICLE; BIOMASS PRODUCTION; EUCALYPTUS; EUCALYPTUS GRANDIS; GENE DUPLICATION; GENE SEQUENCE; GENETIC LOAD; HETEROZYGOSITY; INBREEDING DEPRESSION; METABOLITE; MYRTALES; NONHUMAN; PHYLOGENY; PLANT BREEDING; PLANT GENOME; PRIORITY JOURNAL;

EUCALYPTUS; EUCALYPTUS GLOBULUS; EUCALYPTUS GRANDIS; MYRTALES;

EUCALYPTUS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, PLANT; INBREEDING; PHYLOGENY;

EID: 84903203459     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13308     Document Type: Article

References (70)

1. Byrne, M. Phylogeny, diversity and evolution of eucalypts. in Plant Genome: Biodiversity and Evolution, Part E: Phanerogams-Angiosperm Vol. 1 (eds Sharma, A. K. & Sharma, A. ) 303-346 (Science Publishers, 2008).
2. Iglesias, I. & Wiltermann, D. in Eucalyptologics Information Resources on Eucalypt Cultivation Worldwide http://www. git-forestry. com (GIT Forestry Consulting, retrieved, 29 March 2009).
3. Bauhus, J., van der Meer, P. J. & Kanninen, M. Ecosystem Goods and Services from Plantation Forests 254 (Earthscan, 2010).
4. Costa e Silva, J., Hardner, C., Tilyard, P. & Potts, B. M. The effects of age and environment on the expression of inbreeding depression in Eucalyptus globulus. Heredity 107, 50-60 (2011).
5. Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604 (2006).
6. Kullan, A. R. K. et al. High-density genetic linkage maps with over 2, 400 sequenceanchored DArT markers for genetic dissection in an F2 pseudo-backcross of Eucalyptus grandis 3 E. urophylla. Tree Genet. Genomes 8, 163-175 (2012).
7. Petroli, C. D. et al. Genomic characterization of DArT markers based on highdensity linkage analysis and physical mapping to the Eucalyptus genome. PLoS ONE 7, e44684 (2012).
8. Wang, H. et al. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc. Natl Acad. Sci. USA 106, 3853-3858 (2009).
9. D'Hont, A. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488, 213-217 (2012).
10. Shulaev, V. et al. The genome of woodland strawberry (Fragaria vesca). Nature Genet. 43, 109-116 (2011).
11. Martin, W., Deusch, O., Stawski, N., Grunheit, N. & Goremykin, V. Chloroplast genome phylogenetics: why we need independent approaches to plantmolecular evolution. Trends Plant Sci. 10, 203-209 (2005).
12. Jeffroy, O., Brinkmann, H., Delsuc, F. & Philippe, H. Phylogenomics: the beginning of incongruence? Trends Genet. 22, 225-231 (2006).
13. Fawcett, J. A., Maere, S. & Van de Peer, Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl Acad. Sci. USA 106, 5737-5742 (2009).
14. Bell, C. D., Soltis, D. E. & Soltis, P. S. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97, 1296-1303 (2010).
15. Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467 (2007).
16. Hanada, K., Zou, C., Lehti-Shiu, M. D., Shinozaki, K. & Shiu, S. H. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148, 993-1003 (2008).
17. Freeling, M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453 (2009).
18. Hudson, C. J. et al. High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping. Tree Genet. Genomes 8, 339-352 (2012).
19. Grattapaglia, D. & Bradshaw, H. D. Nuclear DNA content of commercially important Eucalyptus species and hybrids. Can. J. For. Res. 24, 1074-1078 (1994).
20. Brooker, M. I. H. A new classification of the genus Eucalyptus L'Her. (Myrtaceae). Aust. Syst. Bot. 13, 79-148 (2000).
21. Crisp, M. D., Burrows, G. E., Cook, L. G., Thornhill, A. H. & Bowman, D. M. Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary. Natuer Commun. 2, 193 (2011).
22. Agren, J. A. & Wright, S. I. Co-evolution between transposable elements and their hosts: a major factor in genome size evolution? Chromosome Res. 19, 777-786 (2011).
23. Külheim, C., Hui Yeoh, S., Maintz, J., Foley, W. & Moran, G. Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways. BMC Genomics 10, 452 (2009).
24. Novaes, E. et al. High-throughput gene andSNPdiscovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9, 312 (2008).
25. Resende, M. D. et al. Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol. 194, 116-128 (2012).
26. Grattapaglia, D. et al. Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus. Tree Genet. Genomes 8, 463-508 (2012).
27. Groover, A. T. What genesmake a tree a tree? Trends Plant Sci. 10, 210-214(2005).
28. Boerjan, W., Ralph, J. & Baucher, M. Lignin biosynthesis. Annu. Rev. Plant Biol. 54, 519-546 (2003).
29. Mizrachi, E., Mansfield, S. D. & Myburg, A. A. Cellulose factories: advancing bioenergy production from forest trees. New Phytol. 194, 54-62 (2012).
30. Scheller, H. V. & Ulvskov, P. Hemicelluloses. Annu. Rev. Plant Biol. 61, 263-289 (2010).
31. Eschler, B. M., Pass, D. M., Willis, R. & Foley, W. J. Distribution of foliar formylated phloroglucinol derivatives amongst Eucalyptus species. Biochem. Syst. Ecol. 28, 813-824 (2000).
32. Goodger, J. Q. & Woodrow, I. E. a, b-Unsaturated monoterpene acid glucose esters: structural diversity, bioactivities and functional roles. Phytochemistry 72, 2259-2266 (2011).
33. Petit, R. J. &Hampe, A. Someevolutionary consequences of being a tree. Annu. Rev. Ecol. Evol. Syst. 37, 187-214 (2006).
34. Lee, J. & Lee, I. Regulation and function of SOC1, a flowering pathway integrator. J. Exp. Bot. 61, 2247-2254 (2010).
35. House, S. M. Reproductive biology of eucalypts. in Eucalypt Ecology: Individuals to Ecosystems (ed. Woinarski, J. ) 30-56 (Cambridge Univ. Press, 1997).
36. Jaffe, D. B. et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91-96 (2003).
37. Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654-5666 (2003).
38. Remm, M., Storm, C. E. &Sonnhammer, E. L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052 (2001).
39. Ostlund, G. et al. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38, D196-D203 (2010).
40. Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211-D215 (2009).
41. Bendtsen, J. D., Nielsen, H., von Heijne, G. & Brunak, S. Improved prediction of signal peptides: SignalP 3. 0. J. Mol. Biol. 340, 783-795 (2004).
42. Small, I., Peeters, N., Legeai, F. & Lurin, C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4, 1581-1590 (2004).
43. Sonnhammer, E. L., von Heijne, G. & Krogh, A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175-182 (1998).
44. Stamatakis, A. RAxML-VI-HPC: maximumlikelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
45. Salse, J., Abrouk, M., Murat, F., Quraishi, U. M. & Feuillet, C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief. Bioinform. 10, 619-630 (2009).
46. Salse, J. et al. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc. Natl Acad. Sci. USA 106, 14908-14913 (2009).
47. Frazer, K. A., Pachter, L., Poliakov, A., Rubin, E. M. & Dubchak, I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32, W273-W279 (2004).
48. Dubchak, I., Poliakov, A., Kislyuk, A. & Brudno, M. Multiple whole-genome alignments without a reference organism. Genome Res. 19, 682-689 (2009).
49. Salse, J. In silico archeogenomics unveils modern plant genome organisation, regulation and evolution. Curr. Opin. Plant Biol. 15, 122-130 (2012).
50. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511-515 (2010).
51. Kent, W. J. BLAT-theBLAST-like alignment tool. GenomeRes. 12, 656-664(2002).
52. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
53. Youens-Clark, K. et al. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 39, D1085-D1094 (2011).
54. Jaiswal, P. Gramene database: a hub for comparative plant genomics. Methods Mol. Biol. 678, 247-275 (2011).
55. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
56. Robbertse, B., Yoder, R. J., Boyd, A., Reeves, J. & Spatafora, J. W. Hal: an automated pipeline for phylogenetic analyses of genomic data. PLoS Curr. 3, RRN1213 (2011).
57. Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29-W37 (2011).
58. Buljan, M., Frankish, A. &Bateman, A. Quantifying themechanisms of domain gain in animal proteins. Genome Biol. Evol. 11, R74 (2010).
59. Ekman, D., Bjorklund, A. K., Frey-Skott, J. & Elofsson, A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J. Mol. Biol. 348, 231-243 (2005).
60. Forslund, K., Henricson, A., Hollich, V. & Sonnhammer, E. L. Domain treebased analysis of protein architecture evolution. Mol. Biol. Evol. 25, 254-264 (2008).
61. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
62. Langmead, B., Trapnell, C., Pop, M. &Salzberg, S. L. Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
63. Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1. 0: inference of RNA alignments. Bioinformatics 25, 1335-1337 (2009).
64. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. &Eddy, S. R. Rfam: anRNA family database. Nucleic Acids Res. 31, 439-441 (2003).
65. Gardner, P. P. et al. Rfam: Wikipedia, clansand the ''decimal'' release. Nucleic Acids Res. 39, D141-D145 (2011).
66. Brudno, M. et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731 (2003).
67. Peterson, D. G., Kevin, S. & Stephen, M. Isolation of milligramquantities of nuclear DNA from tomato (Lycopersicon esculentum), a plant containing high levels of polyphenolic compounds. Plant Mol. Biol. Rep. 15, 148-153 (1997).
68. Tibbits, J. F. G., McManus, L. J., Spokevicius, A. V. &Bossinger, G. A rapidmethod for tissue collection and high-throughput isolation of genomic DNA from mature trees. Plant Mol. Biol. Rep. 24, 81-91 (2006).
69. Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066 (2002).
70. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol. Biol. Evol. 24, 1596-1599 (2007).