1932

Abstract

Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants. Our review of the published data suggests that, although many gene families are conserved among herbaceous and tree species, some gene families, such as those involved in resistance to biotic and abiotic stresses and in the synthesis and transport of sugars, are often expanded in tree genomes. As the genomes of more tree species are sequenced, comparative genomics will further elucidate the complexity of tree genomes and how this relates to traits unique to trees.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-arplant-042916-041049
2017-04-28
2024-06-16
Loading full text...

Full text loading...

/deliver/fulltext/arplant/68/1/annurev-arplant-042916-041049.html?itemId=/content/journals/10.1146/annurev-arplant-042916-041049&mimeType=html&fmt=ahah

Literature Cited

  1. Airoldi CA, Davies B. 1.  2012. Gene duplication and the evolution of plant MADS-box transcription factors. J. Genet. Genom. 39:157–65 [Google Scholar]
  2. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H. 2.  et al. 2011. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat. Biotechnol. 29:521–27 [Google Scholar]
  3. Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W. 3.  et al. 2013. Genome sequence of the date palm Phoenix dactylifera L. Nat. Commun. 4:2274 [Google Scholar]
  4. 4. Angiosperm Phylogeny Group 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 1811–20 [Google Scholar]
  5. 5. Arabidopsis Genome Initat 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408796–815 [Google Scholar]
  6. Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G. 6.  et al. 2011. The genome of Theobroma cacao. Nat. Genet. 43:101–8 [Google Scholar]
  7. Avia K, Kärkkäinen K, Lagercrantz U, Savolainen O. 7.  2014. Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris). New Phytol. 204:159–70 [Google Scholar]
  8. Barghini E, Natali L, Cossu RM, Giordani T, Pindo M. 8.  et al. 2014. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. Genome Biol. Evol. 6:776–91 [Google Scholar]
  9. Bennett MD, Leitch IJ. 9.  2011. Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann. Bot. 107:467–590 [Google Scholar]
  10. Bennetzen JL.10.  2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29–36 [Google Scholar]
  11. Bennetzen JL, Kellogg EA. 11.  1997. Do plants have a one-way ticket to genomic obesity?. Plant Cell 9:1509–14 [Google Scholar]
  12. Bennetzen JL, Ma J, Devos KM. 12.  2005. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95:127–32 [Google Scholar]
  13. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R. 13.  et al. 2013. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29:1492–97 [Google Scholar]
  14. Böhlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S. 14.  et al. 2006. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312:1040–43 [Google Scholar]
  15. Cao PB, Azar S, SanClemente H, Mounet F, Dunand C. 15.  et al. 2015. Genome-wide analysis of the AP2/ERF family in Eucalyptus grandis: an intriguing over-representation of stress-responsive DREB1/CBF genes. PLOS ONE 10:e0121041 [Google Scholar]
  16. Castel SE, Martienssen RA. 16.  2013. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet. 14:100–12 [Google Scholar]
  17. Chagné D.17.  2015. Whole genome sequencing of fruit tree species. See Ref. 92 1–37
  18. Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C. 18.  et al. 2014. The draft genome sequence of European pear (Pyrus communis L. “Bartlett”). PLOS ONE 9:e92644 [Google Scholar]
  19. Chardon F, Damerval C. 19.  2005. Phylogenomic analysis of the PEBP gene family in cereals. J. Mol. Evol. 61:579–90 [Google Scholar]
  20. Chen C-H, Kuo TC-Y, Yang M-H, Chien T-Y. 20.  Chu M-J. et al. 2014. Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha. BMC Genom 15:578 [Google Scholar]
  21. Chen J, Tian Q, Pang T, Jiang L, Wu R. 21.  et al. 2014. Deep-sequencing transcriptome analysis of low temperature perception in a desert tree. Populus euphratica. BMC Genom. 15:326 [Google Scholar]
  22. Chen SC, Cannon CH, Kua CS, Liu JJ, Galbraith DW. 22.  2014. Genome size variation in the Fagaceae and its implications for trees. Tree Genet. Genomes 10:977–88 [Google Scholar]
  23. Christie N, Tobias PA, Naidoo S, Külheim C. 23.  2016. The Eucalyptus grandis NBS-LRR gene family: physical clustering and expression hotspots. Front. Plant Sci. 6:1238 [Google Scholar]
  24. Cossu RM, Giordani T, Cavallini A, Natali L. 24.  2014. High-throughput analysis of transcriptome variation during water deficit in a poplar hybrid: a general overview. Tree Genet. Genomes 10:53–66 [Google Scholar]
  25. D'Hont A, Denoeud F, Aury J, Baurens F, Carreel F. 25.  et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–19 [Google Scholar]
  26. Dai X, Hu Q, Cai Q, Feng K, Ye N. 26.  et al. 2014. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res 24:1274–77 [Google Scholar]
  27. Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. 27.  2013. A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genom 14:683 [Google Scholar]
  28. De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S. 28.  et al. 2014. Insights into conifer giga-genomes. Plant Physiol 166:1–9 [Google Scholar]
  29. De La Torre AR, Lin YC, Van De Peer Y, Ingvarsson PK. 29.  2015. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families. Genome Biol. Evol. 7:1002–15 [Google Scholar]
  30. Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R. 30.  et al. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345:1181–84 [Google Scholar]
  31. Devos KM, Brown JKM, Bennetzen JL. 31.  2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12:1075–79 [Google Scholar]
  32. DeYoung BJ, Innes RW. 32.  2006. Plant NBS-LRR proteins in pathogen sensing and host defense. Nat. Immunol. 7:1243–49 [Google Scholar]
  33. Ensminger I, Yao-Yun Chang C, Bräutigam K. 33.  2015. Tree responses to environmental cues. See Ref. 92 229–63 [Google Scholar]
  34. Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P. 34.  et al. 2014. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat. Genet. 46:1089–96Describes the first large-scale whole-genome resequencing study, which provided insights into the genomics of local adaptation in poplar. [Google Scholar]
  35. Flavell RB, Bennett MD, Smith JB, Smith DB. 35.  1974. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12:257–69 [Google Scholar]
  36. Friedman J, Rubin MJ. 36.  2015. All in good time: understanding annual and perennial strategies in plants. Am. J. Bot. 102:497–99 [Google Scholar]
  37. Geraldes A, Farzaneh N, Grassa CJ, McKown AD, Guy RD. 37.  et al. 2014. Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure. Evolution 68:3260–80 [Google Scholar]
  38. Giovannoni JJ.38.  2004. Genetic regulation of fruit development and ripening. Plant Cell 16:S170–80 [Google Scholar]
  39. Giovannoni JJ.39.  2007. Fruit ripening mutants yield insights into ripening control. Curr. Opin. Plant Biol. 10:283–89 [Google Scholar]
  40. Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA. 40.  et al. 2016. Assessing the gene content of the megagenome: sugar pine (Pinus lambertiana). G3 6:3787–802 [Google Scholar]
  41. Gramzow L, Theißen G. 41.  2010. A hitchhiker's guide to the MADS world of plants. Genome Biol 11:214 [Google Scholar]
  42. Gramzow L, Theißen G. 42.  2013. Phylogenomics of MADS-box genes in plants—two opposing life styles in one gene family. Biology 2:1150–64 [Google Scholar]
  43. Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR, Foley W. 43.  et al. 2012. Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus. Tree Genet. Genomes 8:463–508 [Google Scholar]
  44. Groover AT.44.  2005. What genes make a tree a tree?. Trends Plant Sci 10:210–14 [Google Scholar]
  45. Gyllenstrand N, Clapham D, Källman T, Lagercrantz U, Ka T. 45.  2007. A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers. Plant Physiol 144:248–57 [Google Scholar]
  46. Harfouche A, Meilan R, Altman A. 46.  2014. Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement. Tree Physiol 34:1181–98 [Google Scholar]
  47. He N, Zhang C, Qi X, Zhao S, Tao Y. 47.  et al. 2013. Draft genome sequence of the mulberry tree Morus notabilis. Nat. Commun. 4:2445 [Google Scholar]
  48. Hedman H, Källman T, Lagercrantz U. 48.  2009. Early evolution of the MFT-like gene family in plants. Plant Mol. Biol. 70:359–69 [Google Scholar]
  49. Hirakawa H, Nakamura Y, Kaneko T, Isobe S, Sakai H. 49.  et al. 2011. Survey of the genetic information carried in the genome of Eucalyptus camaldulensis. Plant Biotechnol 28:471–80 [Google Scholar]
  50. Holliday JA, Zhou L, Bawa R, Zhang M, Oubida RW. 50.  2016. Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa. New Phytol. 209:1240–51 [Google Scholar]
  51. Hsu C-Y, Adams JP, Kim H, No K, Ma C. 51.  et al. 2011. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. PNAS 108:10756–61 [Google Scholar]
  52. Hsu C-Y, Liu Y, Luthe DS, Yuceer C. 52.  2006. Poplar FT2 shortens the juvenile phase and promotes seasonal flowering. Plant Cell 18:1846–61 [Google Scholar]
  53. Huang S, Ding J, Deng D, Tang W, Sun H. 53.  et al. 2013. Draft genome of the kiwifruit Actinidia chinensis. Nat. Commun. 4:2640 [Google Scholar]
  54. Hudson CJ, Kullan ARK, Freeman JS, Faria DA, Grattapaglia D. 54.  et al. 2012. High synteny and colinearity among eucalyptus genomes revealed by high-density comparative genetic mapping. Tree Genet. Genomes 8:339–52 [Google Scholar]
  55. Ireland HS, Yao JL, Tomes S, Sutherland PW, Nieuwenhuizen N. 55.  et al. 2013. Apple SEPALLATA1/2-like genes control fruit flesh development and ripening. Plant J 73:1044–56 [Google Scholar]
  56. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C. 56.  et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–67Describes the sequenced genome with the most conserved arrangement from the paleohexaploid from which all eudicots originated. [Google Scholar]
  57. Karlgren A, Gyllenstrand N, Clapham D, Lagercrantz U. 57.  2013. FLOWERING LOCUS T/TERMINAL FLOWER1-like genes affect growth rhythm and bud set in Norway spruce. Plant Physiol. 163:792–803 [Google Scholar]
  58. Karlgren A, Gyllenstrand N, Källman T, Sundström JF, Moore D. 58.  et al. 2011. Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol 156:1967–77 [Google Scholar]
  59. Karlova R, Chapman N, David K, Angenent GC, Seymour GB, De Maagd RA. 59.  2014. Transcriptional control of fleshy fruit development and ripening. J. Exp. Bot. 65:4527–41 [Google Scholar]
  60. Kersting AR, Mizrachi E, Bornberg-Bauer E, Myburg AA. 60.  2015. Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus. New Phytol. 206:1328–36 [Google Scholar]
  61. Klee HJ.61.  2010. Improving the flavor of fresh fruits: genomics, biochemistry, and biotechnology. New Phytol 187:44–56 [Google Scholar]
  62. Klintenäs M, Pin PA, Benlloch R, Ingvarsson PK, Nilsson O. 62.  2012. Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage. New Phytol. 196:1260–73 [Google Scholar]
  63. Knapp S, Litt A. 63.  2013. Fruit—an angiosperm innovation. The Molecular Biology and Biochemistry of Fruit Ripening GB Seymour, M Poole, JJ Giovannoni, GA Tucker 21–42 Ames, IA: Wiley-Blackwell [Google Scholar]
  64. Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D. 64.  et al. 2008. Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol. Biol. 66:619–36 [Google Scholar]
  65. Krishnan NM, Pattnaik S, Jain P, Gaur P, Choudhary R. 65.  et al. 2012. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genom. 13:464 [Google Scholar]
  66. Lau N, Makita Y, Kawashima M, Taylor TD, Kondo S. 66.  et al. 2016. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Sci. Rep. 6:28594 [Google Scholar]
  67. Leitch AR, Leitch IJ. 67.  2008. Genomic plasticity and the diversity of polyploid plants. Science 320:481–83 [Google Scholar]
  68. Leitch AR, Leitch IJ. 68.  2012. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol 194:629–46 [Google Scholar]
  69. Lesur I, Le Provost G, Bento P, Da Silva C, Leplé J-C. 69.  et al. 2015. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genom 16:112 [Google Scholar]
  70. Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW. 70.  et al. 2015. Early genome duplications in conifers and other seed plants. Sci. Adv. 1:e1501084 [Google Scholar]
  71. Liu M-J, Zhao J, Cai Q-L, Liu G-C, Wang J-R. 71.  et al. 2014. The complex jujube genome provides insights into fruit tree biology. Nat. Commun. 5:5315 [Google Scholar]
  72. Liu Y-Y, Yang K-Z, Wei X-X, Wang X-Q. 72.  2016. Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. New Phytol 212:730–44 [Google Scholar]
  73. Loescher WH.73.  1987. Physiology and metabolism of sugar alcohols in higher plants. Physiol. Plant. 70:553–57 [Google Scholar]
  74. Ma T, Wang J, Zhou G, Yue Z, Hu Q. 74.  et al. 2013. Genomic insights into salt adaptation in a desert poplar. Nat. Commun. 4:2797 [Google Scholar]
  75. Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J. 75.  et al. 2016. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols. Plant J 87:507–32 [Google Scholar]
  76. Matzke MA, Mosher RA. 76.  2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15:394–408 [Google Scholar]
  77. McAtee PA, Richardson AC, Nieuwenhuizen NJ, Gunaseelan K, Hoong L. 77.  et al. 2015. The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of mads-box transcription factors. BMC Plant Biol 15:304 [Google Scholar]
  78. McCourt RM, Chapman RL, Buchheim M, Mishler BD. 78.  1996. Green plants. Tree of Life Web Project http://www.tolweb.org/Green_plants [Google Scholar]
  79. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A. 79.  et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–96 [Google Scholar]
  80. Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z. 80.  et al. 2009. Evolution of genome size and complexity in Pinus. PLOS ONE 4:e4332 [Google Scholar]
  81. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD. 81.  et al. 2014. The genome of Eucalyptus grandis. Nature 510:356Describes a comprehensive study of gene families involved in lignocellulosic biomass production and secondary metabolism and oils in Eucalyptus [Google Scholar]
  82. Navarro M, Marque G, Ayax C, Keller G, Borges JP. 82.  et al. 2009. Complementary regulation of four Eucalyptus CBF genes under various cold conditions. J. Exp. Bot. 60:1–12 [Google Scholar]
  83. Neale DB, Kremer A. 83.  2011. Forest tree genomics: growing resources and applications. Nat. Rev. Genet. 12:111–22 [Google Scholar]
  84. Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D. 84.  et al. 2014. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15:R59Describes the first Pinus species sequenced and provides insights into the genomic organization of gymnosperms and how they differ from flowering plants. [Google Scholar]
  85. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C. 85.  et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–84Provides the first comparative genomics study of transposable elements in gymnosperm species. [Google Scholar]
  86. Palazzo AF, Gregory TR. 86.  2014. The case for junk DNA. PLOS Genet 10:e1004351 [Google Scholar]
  87. Parent GJ, Raherison E, Sena J, Mackay JJ. 87.  2015. Forest tree genomics: review of progress. See Ref. 92 39–92 [Google Scholar]
  88. Park WA, Allen CD, Macalady AK, Griffin D, Woodhouse CA. 88.  et al. 2013. Temperature as a potent driver of regional forest drought stress and tree mortality. Nat. Clim. Change 3:292–97 [Google Scholar]
  89. Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J. 89.  2012. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol 10:84 [Google Scholar]
  90. Pellicer J, Fay MF, Leitch IJ. 90.  2010. The largest eukaryotic genome of them all?. Bot. J. Linn. Soc. 164:10–15 [Google Scholar]
  91. Perazzolli M, Malacarne G, Baldo A, Righetti L, Bailey A. 91.  et al. 2014. Characterization of resistance gene analogues (RGAs) in apple (Malus×domestica Borkh.) and their evolutionary history of the Rosaceae family. PLOS ONE 9:e83844 [Google Scholar]
  92. Plomion C, Adam-Blondonpp A-F. 92.  2015. Land Plants - Trees Adv. Bot. Res 74 London: Academic [Google Scholar]
  93. Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V. 93.  et al. 2016. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol. Ecol. Resour. 16:254–65 [Google Scholar]
  94. Plomion C, Bastien C, Bogeat-Triboulot M-B, Bouffier L, Déjardin A. 94.  et al. 2016. Forest tree genomics: 10 achievements from the past 10 years and future prospects. Ann. For. Sci. 73:77–103 [Google Scholar]
  95. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE. 95.  et al. 2007. Phylogeny and classification of Rosaceae. Plant Syst. Evol. 266:5–43 [Google Scholar]
  96. Quinn JJ, Chang HY. 96.  2015. Unique features of long non-coding rna biogenesis and function. Nat. Rev. Genet. 17:47–62 [Google Scholar]
  97. Rahman AYA, Usharraj AO, Misra BB, Thottathil GP, Jayasejaran K. 97.  et al. 2013. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genom 14:75 [Google Scholar]
  98. Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A. 98.  et al. 2011. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18:65–76 [Google Scholar]
  99. Scott AD, Stenz NWM, Ingvarsson PK, Baum DA. 99.  2016. Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers. New Phytol 211:186–93 [Google Scholar]
  100. Seymour GB, Ostergaard L, Chapman NH, Knapp S, Martin C. 100.  2013. Fruit development and ripening. Annu. Rev. Plant Biol. 64:219–41 [Google Scholar]
  101. Shuai P, Liang D, Tang S, Zhang Z, Ye CY. 101.  et al. 2014. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J. Exp. Bot. 65:4975–83 [Google Scholar]
  102. Singh R, Ong-Abdullah M, Low E-TL, Manaf MAA, Rosli R. 102.  et al. 2013. Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature 500:335–39 [Google Scholar]
  103. Soltis DE, Soltis PS, Bennett MD, Leitch IJ. 103.  2003. Evolution of genome size in the angiosperms. Am. J. Bot. 90:1596–603 [Google Scholar]
  104. Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M. 104.  et al. 2016. Sequence of the sugar pine megagenome. Genetics 204:1613–26 [Google Scholar]
  105. Tang C, Yang M, Fang Y, Luo Y, Gao S. 105.  et al. 2016. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat. Plants 2:1–10 [Google Scholar]
  106. Tang S, Dong Y, Liang D, Zhang Z, Ye CY. 106.  et al. 2015. Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing. Plant Mol. Biol. Rep. 33:424–38 [Google Scholar]
  107. Tang S, Liang H, Yan D, Zhao Y, Han X. 107.  et al. 2013. Populus euphratica: the transcriptomic response to drought stress. Plant Mol. Biol. 83:539–57 [Google Scholar]
  108. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I. 108.  et al. 2006. The genome of black cottonwood, Populustrichocarpa (Torr. & Gray). Science 313:1596–604Describes the first tree genome sequenced and the first comparative genomics study of a tree species (poplar) and a nontree species (Arabidopsis). [Google Scholar]
  109. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A. 109.  et al. 2010. The genome of the domesticated apple (Malus×domestica Borkh.). Nat. Genet. 42:833–39Provides evidence that the expansion of MADS-box genes in the apple genome may be related to the development of the pome. [Google Scholar]
  110. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A. 110.  et al. 2007. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLOS ONE 2:e1326 [Google Scholar]
  111. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S. 111.  et al. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat. Genet. 45:487–94Describes a high-quality assembly of a double haploid that has been used as a reference for studies in several other Prunus species. [Google Scholar]
  112. Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D. 112.  et al. 2002. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296:343–46 [Google Scholar]
  113. Wang N, Thomson M, Bodles WJA, Crawford RMM, Hunt HV. 113.  et al. 2013. Genome sequence of dwarf birch (Betula nana) and cross-species rad markers. Mol. Ecol. 22:3098–111 [Google Scholar]
  114. Wang Y, Hu Z, Yang Y, Chen X, Chen G. 114.  2010. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in grapevine. Russ. J. Plant Physiol. 57:273–82 [Google Scholar]
  115. Warren RL, Keeling CI, Saint Yuen MM, Raymond A, Taylor GA. 115.  et al. 2015. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant J 83:189–212 [Google Scholar]
  116. Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA. 116.  et al. 2014. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891–909 [Google Scholar]
  117. Wisniewski M, Nassuth A, Teulières C, Marque C, Rowland J. 117.  et al. 2014. Genomics of cold hardiness in woody plants. CRC Crit. Rev. Plant Sci. 33:92–124 [Google Scholar]
  118. Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U. 118.  et al. 2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat. Biotechnol. 32:656–62 [Google Scholar]
  119. Wu J, Wang Z, Shi Z, Zhang S, Ming R. 119.  et al. 2013. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408 [Google Scholar]
  120. Xu Q, Chen L-L, Ruan X, Chen D, Zhu A. 120.  et al. 2013. The draft genome of sweet orange (Citrus sinensis). Nat. Genet. 45:59–66 [Google Scholar]
  121. Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N. 121.  et al. 2004. Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Hortic 663:51–56 [Google Scholar]
  122. Yang S, Feng Z, Zhang X, Jiang K, Jin X. 122.  et al. 2006. Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol. Biol. 62:181–93 [Google Scholar]
  123. Yang S, Zhang X, Yue JX, Tian D, Chen JQ. 123.  2008. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol. Genet. Genom. 280:187–98 [Google Scholar]
  124. Yoon S-K, Park E-J, Choi Y-I, Bae E-K, Kim J-H. 124.  et al. 2014. Response to drought and salt stress in leaves of poplar (Populus alba×Populus glandulosa): expression profiling by oligonucleotide microarray analysis. Plant Physiol. Biochem. 84158–68
  125. Zhang J, Jiang D, Liu B, Luo W, Lu J. 125.  et al. 2014. Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress. Plant Cell Rep 33:1565–79 [Google Scholar]
  126. Zhang Q, Chen W, Sun L, Zhao F, Huang B. 126.  et al. 2012. The genome of Prunus mume. Nat. Commun. 3:1318 [Google Scholar]
  127. Zhao T, Liang D, Wang P, Liu J, Ma F. 127.  2012. Genome-wide analysis and expression profiling of the dreb transcription factor gene family in Malus under abiotic stress. Mol. Genet. Genom. 287:423–36 [Google Scholar]
  128. Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M. 128.  et al. 2014. Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics 196:875–90 [Google Scholar]
/content/journals/10.1146/annurev-arplant-042916-041049
Loading
/content/journals/10.1146/annurev-arplant-042916-041049
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error