Skip to main content

Introduction: Comparative Genomics of Angiosperm Trees: A New Era of Tree Biology

  • Chapter
  • First Online:
Plant Genetics and Genomics: Crops and Models

Abstract

Forest tree genomics has made enormous strides in recent years, by describing the expression and function of genes influencing tree growth and development, and even sequencing the entire genomes of select “model” tree species. We believe that the next chapter of forest tree genomics will focus on cross-species comparative approaches, which will have the ability to provide fundamental new insights into the unique biology and evolutionary history of tree species. Angiosperm trees in particular are fascinating in light of evolution. Angiosperm trees represent the extensive genome evolution, including whole genome duplications, exhibited by different angiosperm lineages. Angiosperm trees also present amazing morphological, physiological and biochemical diversity, providing the opportunity to use comparative genomic approaches to understand the evolutionary origin and diversification of traits associated with trees. This book provides background on biological, genomic, and evolutionary aspects of angiosperm trees, in support of researchers exploring the use of comparative and evolutionary genomic approaches. This introduction briefly reviews the diversity of angiosperm trees and sets out the conceptual framework for comparative and evolutionary study of angiosperm tree biology using genomic tools, and highlights individual chapters within this book.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  • Bolin B, Keeling CD. Large-scale atmospheric mixing as deduced from the seasonal and meridional variations of carbon dioxide. J Geophys Res. 1963;68(13):3899–920.

    Article  ADS  CAS  Google Scholar 

  • Bradshaw Jr HD, Stettler RF. Molecular genetics of growth and development in Populus. II Segregation distortion due to genetic load. Theor Appl Genet. 1994;89(5):551–8.

    Article  CAS  PubMed  Google Scholar 

  • Bräutigam K, Vining KJ, Lafon-Placette C, Fossdal CG, Mirouze M, Marcos JG, Fluch S, Fraga MF, Guevara M, Abarca D, Johnsen Ø. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol. 2013;3(2):399–415.

    Article  PubMed  PubMed Central  Google Scholar 

  • Davin N, Edger PP, Hefer CA, Mizrachi E, Schuetz M, Smets E, Myburg AA, Douglas CJ, Schranz ME, Lens F. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. Plant J. 2016;86(5):376–90.

    Article  CAS  PubMed  Google Scholar 

  • Denis M, Bouvet JM. Genomic selection in tree breeding: testing accuracy of prediction models including dominance effect. BMC Proc. 2011;5(Suppl 7, IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and Delivery):O13.

    Article  PubMed Central  Google Scholar 

  • Erwin TL. Tropical forests: their richness in Coleoptera and other arthropod species. Coleopt Bull. 1982;36(1):74–5.

    Google Scholar 

  • FAO. Global forest resources assessment 2000 – main report (FRA 2000). Forestry Paper No. 140, Food and Agriculture Organization of the United Nations, Rome. 2001.

    Google Scholar 

  • FAO. State of the world’s forests – 2014. Rome: Food and Agriculture Organization of the United Nations; 2014.

    Google Scholar 

  • Geraldes A, Farzaneh N, Grassa CJ, McKown AD, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB. Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure. Evolution. 2014;68:3260–80.

    Article  PubMed  Google Scholar 

  • Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QC. Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol. 2015;24(13):3243–56.

    Article  CAS  PubMed  Google Scholar 

  • Hefer CA, Mizrachi E, Myburg AA, Douglas CJ, Mansfield SD. Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis. New Phytol. 2015;206(4):1391–405.

    Article  CAS  PubMed  Google Scholar 

  • Henry IM, Zinkgraf MS, Groover AT, Comai L. A system for dosage-based functional genomics in poplar. Plant Cell. 2015;27(9):2370–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson LA, Douglas CJ. Populus trichocarpa MONOPTEROS/AUXIN RESPONSE FACTOR5 (ARF5) genes: comparative structure, sub-functionalization, and Populus-Arabidopsis microsynteny. Botany. 2007;85(11):1058–70.

    CAS  Google Scholar 

  • Mark J, Newton AC, Oldfield S, Rivers M. The international timber trade: a working list of commercial timber tree species. Richmond: Botanic Gardens Conservation International; 2014.

    Google Scholar 

  • McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QC, El-Kassaby YA, Mansfield SD, Douglas CJ. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytol. 2014;203(2):535–53.

    Article  CAS  PubMed  Google Scholar 

  • Mock KE, Callahan CM, Islam-Faridi MN, Shaw JD, Rai HS, Sanderson SC, Rowe CA, Ryel RJ, Madritch MD, Gardner RS, Wolf PG. Widespread triploidy in western North American aspen (Populus tremuloides). PLoS One. 2012;7(10):e48406.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Moyers BT, Rieseberg LH. Divergence in gene expression is uncoupled from divergence in coding sequence in a secondarily woody sunflower. Int J Plant Sci. 2013;174:1079–89.

    Article  CAS  Google Scholar 

  • Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QCB, El-Kassaby YA, Douglas CD, Mansfield SD. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. New Phytol. 2013;200:710–26.

    Article  CAS  PubMed  Google Scholar 

  • RBG Kew. The state of the world’s plants report – 2016. Kew: Royal Botanic Gardens; 2016.

    Google Scholar 

  • Rottmann WH, Meilan R, Sheppard LA, Brunner AM, Skinner JS, Ma C, Cheng S, Jouanin L, Pilate G, Strauss SH. Diverse effects of overexpression of LEAFY and PTLF, a poplar (Populus) homolog of LEAFY/FLORICAULA, in transgenic poplar and Arabidopsis. Plant J. 2000;22(3):235–45.

    Article  CAS  PubMed  Google Scholar 

  • Segura V, Cilas C, Costes E. Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures. New Phytol. 2008;178:302–14.

    Article  PubMed  Google Scholar 

  • Xu B, Ohtani M, Yamaguchi M, Toyooka K, Wakazaki M, Sato M, Kubo M, Nakano Y, Sano R, Hiwatashi Y, Murata T. Contribution of NAC transcription factors to plant adaptation to land. Science. 2014;343:1505–8.

    Article  ADS  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The editors wish to acknowledge the helpful assistance of Eric Stannard and other Springer staff in bringing this book to fruition. Work in the laboratory of QC is funded by Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants Program (grant no. RGPIN-2014-05820). Work in the laboratory of AG is funded by USDA AFRI (grant no. 2015-67013-22891) and DOE Office of Science, Office of Biological and Environmental Research (BER grant no. DE-SC0007183).

Postscript

While this book was in preparation, but after the manuscript of his chapter was submitted, we received the news of the tragic death of Carl Douglas in a climbing accident in the mountains of British Columbia. We have lost a great colleague and trusted friend. Carl was a true leader in the field of the genomics of angiosperm trees and will be greatly missed. We dedicate this volume as a small tribute to his memory.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Quentin C.B. Cronk .

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing AG

About this chapter

Cite this chapter

C.B. Cronk, Q., T. Groover, A. (2016). Introduction: Comparative Genomics of Angiosperm Trees: A New Era of Tree Biology. In: Plant Genetics and Genomics: Crops and Models. Springer, New York, NY. https://doi.org/10.1007/7397_2016_33

Download citation

  • DOI: https://doi.org/10.1007/7397_2016_33

  • Published:

  • Publisher Name: Springer, New York, NY

Publish with us

Policies and ethics