pp 1-15

Part of the Plant Genetics and Genomics: Crops and Models book series

Emerging Genomics of Angiosperm Trees

  • Elizabeth Sollars
  • Richard Buggs
Chapter

Abstract

Genome sequence assemblies of many angiosperm trees used in forestry are now emerging, in addition to the well-characterised genomes of black poplar and eucalyptus reviewed in previous chapters of this book. Whilst the number of published genomes of angiosperm forest trees lags behind that of angiosperm trees grown commercially for fruit or nuts, many new projects are underway. This is aided by the ever-decreasing cost of DNA sequencing technologies and has diverse motivations including tree improvement, ecological and evolutionary studies. In this chapter, we briefly review a number of recent whole genome projects including Chinese chestnut, European ash, dwarf birch, pedunculate oak, purple willow and shrub willow. We also describe new projects not yet in the public domain or with non-genomic data, and list various online resources where data and information can be accessed. We discuss potential future steps in improving genome assemblies, and the uses of such information in fields such as genomic selection to assist tree breeding.

Keywords

Genome sequencing Angiosperm Tree Breeding Transcriptomics 

References

  1. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol. 2011;29(6):521–7.CrossRefPubMedGoogle Scholar
  2. Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8(1):61–5.CrossRefPubMedGoogle Scholar
  3. Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu X, et al. Genome sequence of the date palm Phoenix Dactylifera L. Nat Commun. 2013;4:2274.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  4. Anagnostakis SL. Chestnut blight: the classical problem of an introduced pathogen. Mycologia. 1987;79(1):23–37. Mycological Society of America: 23–37.CrossRefGoogle Scholar
  5. Argout X, Salse J, Aury J, Guiltinan MJ, Droc G, Gouzy J, Allegre M, et al. The genome of Theobroma cacao. Nat Genet. 2011;43(2):101–8.CrossRefPubMedGoogle Scholar
  6. Bao E, Jiang T, Girke T. AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. Bioinformatics. 2014;30(12):i319–28.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, et al. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC Plant Biol. 2012;12:153.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Boyd IL, Freer-Smith PH, Gilligan CA, Godfray HCJ. The consequence of tree pests and diseases for ecosystem services. Science. 2013;342(6160):1235773.CrossRefPubMedGoogle Scholar
  9. Brasier CM. The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathol. 2008;57(5):792–808. Blackwell Publishing Ltd: 792–808.CrossRefGoogle Scholar
  10. Carlson JE. The chestnut genome project. In: Plant and animal genome XXII conference. Plant and Animal Genome. 2014. https://pag.confex.com/pag/xxii/webprogram/Paper9777.html.
  11. Carlson CH, Gouker FE, Serapiglia MJ, Tang H, Krishnakumar V, Town CD, Tuskan GA, et al. Annotation of the Salix purpurea L. genome and gene families important for biomass production. In: Plant and animal genome XXII conference. Plant and Animal Genome. 2014. https://pag.confex.com/pag/xxii/webprogram/Paper12085.html.
  12. Carlson CH, Gouker FE, DiFazio S, Zhou R, Smart L. High-resolution mapping of biomass-related traits in shrub willow (Salix purpurea L.). In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper21612.html.
  13. Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, et al. The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLoS One. 2014;9(4):e92644.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  14. Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome essemblies. Bioinformatics. 2013;29(4):435–43.CrossRefPubMedGoogle Scholar
  15. Cruz F, Julca I, Gómez-Garrido J, Loska D, Marcet-Houben M, Cano E, Galán B, et al. Genome sequence of the olive tree, Olea europaea. GigaScience. 2016;5:29.Google Scholar
  16. Dai X, Hu Q, Cai Q, Feng K, Ye N, Tuskan GA, Milne R, et al. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res. 2014;24(10):1274–7.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Denis M, Bouvet J-M. Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding. Tree Genet Genomes. 2012;9(1):37–51. Springer-Verlag: 37–51.CrossRefGoogle Scholar
  18. Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014;345(6201):1181–4.ADSCrossRefPubMedGoogle Scholar
  19. Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW. Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput Biol. 2014;10(12):e1003998.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  20. Durand J, Bodénès C, Chancerel E, Frigerio J-M, Vendramin G, Sebastiani F, Buonamici A, et al. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics. 2010;11:570.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, et al. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics. 2014;15:86.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C. Analysis of BAC end sequences in oak, providing insights into the composition of the genome of this keystone species. BMC Genomics. 2011;12:292.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Fan D, Liu T, Li C, Jiao B, Li S, Hou Y, Luo K. Efficient CRISPR/Cas9-mediated targeted mutagenesis in Populus in the first generation. Sci Rep. 2015;5:12217.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  24. Fang G-C, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, et al. A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genet Genomes. 2013;9(2):525–37. Springer: 525–37.CrossRefGoogle Scholar
  25. Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P. Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome. BioRxiv. 2015. www.biorxiv.org, http://biorxiv.org/content/early/2015/01/06/013490.short.
  26. Gouker FE, Zhou R, Evans L, DiFazio S, Bubner B, Zander M, Smart L. Genotypic-phenotypic variation and marker-based heritability estimates of a shrub willow (Salix purpurea) association population. In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper19730.html.
  27. Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, et al. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using associative transcriptomics. Sci Rep. 2016;6:19335.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  28. Hebard FV, Islam-Faridi N, Staton ME, Georgi L. Biotechnology of trees: chestnut. In: Tree biotechnology. Boca Raton: CRC Press; 2014. p. 1.Google Scholar
  29. Heffner EL, Sorrells ME, Jannink J-L. Genomic selection for crop improvement. Crop Sci. 2009;49(1):1–12. Crop Science Society of America: 1–12.CrossRefGoogle Scholar
  30. Helm D. Natural capital: valuing the planet. New Haven: Yale University Press; 2015.Google Scholar
  31. Howe K, Wood JMD. Using optical mapping data for the improvement of vertebrate genome assemblies. Gigascience. 2015;4:10.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kafkas S. Whole genome sequencing and high density genetic maps in pistachio reveal a large non-recombining region of sex chromosomes. In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper21642.html.
  33. Kelly LJ, Leitch AR, Fay MF, Renny-Byfield S, Pellicer J, Macas J, Leitch IJ. Why size really matters when sequencing plant genomes. Plant Ecolog Divers. 2012;5(4):415–25.CrossRefGoogle Scholar
  34. Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG. More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet. 2009;25(9):404–13.CrossRefPubMedGoogle Scholar
  35. Kim J, Larkin DM, Asan CQ, Zhang Y, Ge R-L, Auvil L, et al. Reference-assisted chromosome assembly. Proc Natl Acad Sci U S A. 2013;110(5):1785–90.ADSMathSciNetCrossRefPubMedPubMedCentralGoogle Scholar
  36. Kubisiak TL, Nelson CD, Staton ME, Zhebentyayeva T, Smith C, Olukolu BA, Fang G-C, et al. A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica). Tree Genet Genomes. 2013;9(2):557–71.CrossRefGoogle Scholar
  37. LaBonte N, Woeste KE. Exploring patterns of sequence variation in regions associated with chestnut blight resistance using whole-genome resequencing of Chinese chestnut (Castanea mollissima). In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper20702.html.
  38. Lesur I, Durand J, Sebastiani F, Gyllenstrand N, Bodénès C, Lascoux M, Kremer A, Vendramin GG, Plomion C. A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries. Tree Genet Genomes. 2011;7(6):1277–85.CrossRefGoogle Scholar
  39. Martínez-García PJ, Crepeau M, Puiu D, Gonzalez-Ibeas D, Stevens K, Whalen J, Butterfield T, et al. The genome sequence of walnut (Juglans regia L.) Cv ‘Chandler’. In: Plant and animal genome XXIII conference. Plant and Animal Genome. 2015. https://pag.confex.com/pag/xxiii/webprogram/Paper14583.html.
  40. Mathew LS, Spannagl M, Al-Malki A, George B, Torres MF, Al-Dous EK, Al-Azwani EK, et al. A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genomics. 2014;15:285.CrossRefPubMedPubMedCentralGoogle Scholar
  41. McKinney LV, Nielsen LR, Hansen JK, Kjær ED. Presence of natural genetic resistance in Fraxinus excelsior (Oleraceae) to Chalara fraxinea (Ascomycota): an emerging infectious disease. Heredity. 2011;106(5):788–97.CrossRefPubMedGoogle Scholar
  42. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452(7190):991–6.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  43. Naudts K, Chen Y, McGrath MJ, Ryder J, Valade A, Otto J, Luyssaert S. Europe’s forest management did not mitigate climate warming. Science. 2016;351(6273):597–600.ADSCrossRefPubMedGoogle Scholar
  44. Neale DB, Kremer A. Forest tree genomics: growing resources and applications. Nat Rev Genet. 2011;12(2):111–22.CrossRefPubMedGoogle Scholar
  45. Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol. 2013;14(6):120.PubMedPubMedCentralGoogle Scholar
  46. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23(9):1061–7.CrossRefPubMedGoogle Scholar
  47. Pautasso M, Aas G, Queloz V, Holdenrieder O. European ash (Fraxinus excelsior) dieback – a conservation biology challenge. Biol Conserv. 2013;158:37–49.CrossRefGoogle Scholar
  48. Plomion C, Aury J-M, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, et al. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour. 2016;16(1):254–65.CrossRefPubMedGoogle Scholar
  49. Rahman AYA, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, Feng Y, Hou S, et al. Draft genome sequence of the rubber tree Hevea Brasiliensis. BMC Genomics. 2013;14:75.CrossRefPubMedPubMedCentralGoogle Scholar
  50. Rajaraman S, Salojärvi JT. Silver birch – a model for tree genetics? In: Plant and animal genome XXIII. 2015. https://pag.confex.com/pag/xxiii/webprogram/Paper15896.html.
  51. Resende MDV, Resende Jr MFR, Sansaloni CP, Petroli CD, Missiaggia AA, Aguiar AM, Abad JM, 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. 2012;194(1):116–28.CrossRefPubMedGoogle Scholar
  52. Rowley ER, Fox SA, Bryant DW, Sullivan C, Givan SA, Mehlenbacher SA, Mockler TC. Assembly and characterization of the European Hazelnut (Corylus avellana L.) ‘Jefferson’ transcriptome. Crop Sci. 2012;52:2679–86.CrossRefGoogle Scholar
  53. Rowley ER, Genomic resource development for European hazelnut (Corylus avellana L.) PhD Thesis, Oregon State University. 2016. http://hdl.handle.net/1957/59368.
  54. Salmon J, Ward SP, Hanley SJ, Leyser O, Karp A. Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing responseg. Plant Biotechnol J. 2014;12(4):480–91.CrossRefPubMedPubMedCentralGoogle Scholar
  55. Shen Z, Sun J, Yao J, Wang S, Ding M, Zhang H, Qian Z, et al. High rates of virus-induced gene silencing by tobacco rattle virus in Populus. Tree Physiol. 2015;35(9):1016–29.CrossRefPubMedGoogle Scholar
  56. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2.CrossRefPubMedGoogle Scholar
  57. Singh R, Ong-Abdullah M, Low ETL, Manaf MAA, Rosli R, Nookiah R, Ooi LC, et al. Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature. 2013;500(7462):335–9.Google Scholar
  58. Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, et al. Genome sequence and genetic diversity of European ash trees. Nature. In press, doi:10.1038/nature20786.
  59. Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, et al. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. PLoS One. 2015;10(12):e0145031.CrossRefPubMedPubMedCentralGoogle Scholar
  60. Suarez-Gonzalez A, Hefer CA, Christe C, Corea O, Lexer C, Cronk QCB, Douglas CJ. Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood). Mol Ecol. 2016. doi:10.1111/mec.13539.PubMedGoogle Scholar
  61. VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature. 2015;527(7579):508–11.ADSCrossRefPubMedGoogle Scholar
  62. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, et al. The genome of the domesticated apple (Malus x Domestica Borkh.). Nat Genet. 2010;42(10):833–9.CrossRefPubMedGoogle Scholar
  63. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45(5):487–94.CrossRefPubMedGoogle Scholar
  64. Vezzi F, Narzisi G, Mishra B. Feature-by-feature – evaluating de novo sequence assembly. PLoS One. 2012;7(2):e31002.ADSCrossRefPubMedPubMedCentralGoogle Scholar
  65. Wang N, Thomson M, Bodles WJA, Crawford RMM, Hunt HV, Featherstone AW, Pellicer J, Buggs RJA. Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol. 2013;22(11):3098–111.CrossRefPubMedGoogle Scholar
  66. Wegrzyn JL, Lee JM, Tearse BR, Neale DB. TreeGenes: a forest tree genome database. Int J Plant Genomics. 2008;2008:412875.CrossRefPubMedPubMedCentralGoogle Scholar
  67. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23(2):396–408.CrossRefPubMedPubMedCentralGoogle Scholar
  68. Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. 2014;32(7):656–62.CrossRefPubMedPubMedCentralGoogle Scholar
  69. Xu Q, Chen L-L, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, et al. The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013;45(1):59–66.CrossRefPubMedGoogle Scholar
  70. Zhang J, Li Y, Jia H-X, Li J-B, Huang J, Lu M-Z, Hu J-J. The heat shock factor gene family in Salix suchowensis: a genome-wide survey and expression profiling during development and abiotic stresses. Front Plant Sci. 2015;6:748.PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Elizabeth Sollars
    • 1
    • 2
  • Richard Buggs
    • 1
    • 2
  1. 1.School of Biological and Chemical Sciences, Queen Mary University of LondonLondonUK
  2. 2.Royal Botanic Gardens KewRichmondUK

Personalised recommendations