Skip to main content
SpringerLink
Log in

High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Understanding genome differentiation is important to compare and transfer genomic information between taxa, such as from model to non-model organisms. Comparative genetic mapping can be used to assess genome differentiation by identifying similarities and differences in chromosome organization. Following release of the assembled Eucalyptus grandis genome sequence (January 2011; http://www.phytozome.net/), a better understanding of genome differentiation between E. grandis and other commercially important species belonging to the subgenus Symphyomyrtus is required. In this study, comparative genetic mapping analyses were conducted between E. grandis, Eucalyptus urophylla, and Eucalyptus globulus using high-density linkage maps constructed from Diversity Array Technology and microsatellite molecular markers. There were 236–393 common markers between maps, providing the highest resolution yet achieved for comparative mapping in Eucalyptus. In two intra-section comparisons (section Maidenaria–E. globulus and section Latoangulatae–E. grandis vs. E. urophylla), ∼1% of common markers were non-syntenic and within chromosomes 4.7–6.8% of markers were non-colinear. Consistent with increasing taxonomic distance, lower synteny (6.6% non-syntenic markers) was observed in an inter-section comparison between E. globulus and E. grandis × E. urophylla consensus linkage maps. Two small chromosomal translocations or duplications were identified in this comparison representing possible genomic differences between E. globulus and section Latoangulatae species. Despite these differences, the overall high level of synteny and colinearity observed between section Maidenaria–Latoangulatae suggests that the genomes of these species are highly conserved indicating that sequence information from the E. grandis genome will be highly transferable to related Symphyomyrtus species.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Bachir O, Abdellah B (2006) Chromosome numbers of the 59 species of Eucalyptus L'Herit (Myrtaceae). Caryologia 59:207–212

    Google Scholar 

  • Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. The Plant Cell 12:1021–1029

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL (2007) Patterns in grass genome evolution. Current Opinion in Plant Biology 10:176–181

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL, Ma J, Devos K (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132

    Article  PubMed  CAS  Google Scholar 

  • Brondani RPV, Brondani C, Grattapaglia D (2002) Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Molecular Genetics and Genomics 267:338–347

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Brondani RPV, 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 Biology 6:20

    Article  PubMed  Google Scholar 

  • Brooker MIH (2000) A new classification of the genus Eucalyptus L'Her. (Myrtaceae). Aust Syst Bot 13:79–148

    Article  Google Scholar 

  • Byrne M, Marquez-garcia M, Uren T, Smith D, Moran G (1996) Conservation and genetic diversity of microsatellite loci in the genus Eucalyptus. Aust J Bot 44:331–341

    Article  CAS  Google Scholar 

  • Byrne M (2008) Phylogeny, diversity and evolution of eucalypts. In: Sharma AK, Sahrma A (eds) Plant genome—biodiversity and evolution. Science Publishers, Enfield (NH), pp 303–346

    Google Scholar 

  • Carver E, Stubbs L (1997) Zooming in on the human-mouse comparative map: genome conservation re-examined on a high-resolution scale. Genome Res 7:1123–1137

    PubMed  CAS  Google Scholar 

  • Celton J-M, Chagne D, Tustin S, Terakami S, Nishitani C, Yamamoto T, Gardiner S (2009) Update on comparative genome mapping between Malus and Pyrus. BMC Research Notes 2:182–188

    Article  PubMed  Google Scholar 

  • Cheema J, Dicks J (2009) Computional approaches and software tools for genetic linkage map estimation in plants. Briefings in Bioinformatics 10:595–608

    Article  PubMed  CAS  Google Scholar 

  • Collard B, Mace E, McPhail M, Wenzl P, Cakir M, Fox G, Poulsen D, Jordan D (2009) How accurate are the marker orders in crop linkage maps generated from large marker datasets? Crop and Pasture Science 60:362–372

    Article  CAS  Google Scholar 

  • Crisp M, Cook L, Steane D (2004) Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present day communities? Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 359:1551–1571

    Article  PubMed  Google Scholar 

  • Doughty R (2000) The Eucalyptus: a natural and commercial history of the gum tree. John Hopkins University Press, Baltimore, MD

    Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Eldridge KG, Davidson J, Harwood C, van Wyk G (1993) Eucalypt breeding and domestication. Oxford, Clarendon Press

    Google Scholar 

  • Faria D, Mamani E, Pappas G, Grattapaglia D (2011) Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests. Tree Genetics & Genomes 7:63–77

    Article  Google Scholar 

  • Ferreira A, Flores da Silva M, da Costa e Silva L, Cruz CD (2006) Estimating the effects of population size and type on the accuracy of genetic maps. Genetics and Molecular Biology 29:187–192

    Article  CAS  Google Scholar 

  • Feschotte C, Jiang N, Wessler S (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341

    Article  PubMed  CAS  Google Scholar 

  • Freeman JS, Potts BM, Shepherd M, Vaillancourt RE (2006) Parental and consensus linkage maps of Eucalyptus globulus using AFLP and microsatellite markers. Silvae Genetica 55:202–217

    Google Scholar 

  • Glaubitz JC, Emebiri LC, Moran GF (2001) Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of single-based differences. Genome 44:1041–1045

    PubMed  CAS  Google Scholar 

  • Grattapaglia D, Bradshaw HD (1994) Nuclear DNA content of commercially important Eucalyptus species and hybrids. Can J For Res 24:1074–1078

    Article  Google Scholar 

  • Grattapaglia D, Kirst M (2008) Tansley review: Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol 179:911–929

    Article  PubMed  CAS  Google Scholar 

  • Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR, Foley W, Kulheim C, Potts BM, Myburg AA (2011) Progress in Myrtaceae genomics: Eucalyptus as the pivotal genus (in press)

  • Gustafson J, Ma X-F, Korzun V, Snape J (2009) A consensus map of rye integrating mapping data from five mapping populations. TAG Theor Appl Genet 118:793–800

    Article  Google Scholar 

  • Hackett CA, Broadfoot LB (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33–38

    Article  PubMed  CAS  Google Scholar 

  • Hamanishi ET, Campbell MM (2011) Genome-wide responses to drought in forest trees. Forestry 84:273–283

    Article  Google Scholar 

  • Hougaard BK, Madsen LH et al (2008) Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics 179:2299–2312

    Article  PubMed  Google Scholar 

  • Iglesias-Trabado G, Wilstermann D (2008) Eucalyptus universalis; global cultivated eucalypt forests map 2008 (Version 1.0.1). GIT Forestry Consulting—EUCALYPTOLOGICS. http://git-forestry.com/download_git_eucalyptus_map.htm. Accessed 1/5/2011.

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research 29(4):e25

    Article  PubMed  CAS  Google Scholar 

  • Kaló P, Seres A, Taylor S, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis T, Kiss G (2004) Comparative mapping between Medicago sativa and Pisum sativum. Molecular Genetics and Genomics 272:235–246

    Article  PubMed  Google Scholar 

  • Keats BJB, Sherman SL et al (1991) Guidelines for human linkage maps: an international system for human linkage maps (ISLM, 1990). Genomics 9:557–560

    Article  PubMed  CAS  Google Scholar 

  • Komulainen P, Brown GR, Mikkonen M, Karhu A, García-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. TAG Theor Appl Genet 107:667–678

    Article  CAS  Google Scholar 

  • Kremer A, Casasoli M (2007) Fagaceae trees. In: Kole C (ed) Genome mapping and molecular breeding in plants. Springer, Berlin, pp 161–188

    Google Scholar 

  • Krishnan A, Guiderdoni E et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170

    Article  PubMed  CAS  Google Scholar 

  • Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447–461

    Article  PubMed  CAS  Google Scholar 

  • Kullan ARK, van Dyk MM, Jones N, Kanzler A, Bayley A, Myburg AA (2011) High-density genetic linkage maps with over 2400 sequence-anchored DArT markers for genetic dissection in an F2 pseudo-backcross of Eucalyptus grandis × E. urophylla. Tree Genetics & Genomes (in press)

  • Ladiges PY, Udovicic F, Nelson G (2003) Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae. J Biogeogr 30:989–998

    Article  Google Scholar 

  • Lai J, Ma J et al (2004) Gene loss and movement in the Maize genome. Genome Res 14:1924–1931

    Article  PubMed  CAS  Google Scholar 

  • Laurie D, Devos K (2002) Trends in comparative genetics and their potential impacts on wheat and barley research. Plant Mol Biol 48:729–740

    Article  PubMed  CAS  Google Scholar 

  • Lysak M, Koch M, Beaulieu J, Meister A, Leitch I (2009) The dynamic ups and downs of genome size evolution in Brassicaceae. Mol Biol Evol 26:85–98

    Article  PubMed  CAS  Google Scholar 

  • Marques C, Brondani R, Grattapaglia D, Sederoff R (2002) Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species. Theor Appl Genet 105:474–478

    Article  PubMed  CAS  Google Scholar 

  • Morgante M, De Paoli E, Radovic S (2007) Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology 10:149–155

    Article  PubMed  CAS  Google Scholar 

  • Myburg AA, Griffin AR, Sederoff RR, Whetten RW (2003) Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach. Theor Appl Genet 107:1028–1042

    Article  PubMed  CAS  Google Scholar 

  • Myburg AA, Potts BM, Marques CM, Kirst M, Gion J, Grattapaglia D, Grima-Pettenatti J (2007) Eucalypts. In: Kole C (ed) Genome mapping and molecular breeding in plants. Springer, Berlin, pp 115–160

    Google Scholar 

  • Neale DB, Krutovsky KV (2005) Comparative genetic mapping in trees: the group of conifers. In: Lorz H, Wenzel G (eds) Biotechnology in agriculture and forestry, Vol. 55. Molecular marker systems in plant breeding and crop improvement. Springer-Verlag, Berlin, pp 267–277

    Chapter  Google Scholar 

  • Paolucci I, Gaudet M, Jorge V, Beritognolo I, Terzoli S, Kuzminsky E, Muleo R, Scarascia Mugnozza G, Sabatti M (2010) Genetic linkage maps of Populus alba L. and comparative mapping analysis of sex determination across Populus species. Tree Genetics & Genomes 6:863–875

    Article  Google Scholar 

  • Paterson AH, Bowers JE et al (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1540

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH, Bowers JE, Feltus FA, Tang H, Lin L, Wang X (2009) Comparative genomics of grasses promises a bountiful harvest. Plant Physiol 149:125–131

    Article  PubMed  CAS  Google Scholar 

  • Payn KG, Dvorak WS, Myburg AA (2007) Chloroplast DNA phylogeography reveals the island colonisation route of Eucalyptus urophylla (Myrtaceae). Aust J Bot 55:673–683

    Article  CAS  Google Scholar 

  • Pelgas B, Beauseigle S, Acheré V, Jeandroz S, Bousquet J, Isabel N (2006) Comparative genome mapping among Picea glauca, P. mariana × P. rubens and P. abies, and correspondence with other Pinaceae. TAG Theor Appl Genet 113:1371–1393

    Article  CAS  Google Scholar 

  • Peng JH, Zadeh H et al (2004) Chromosome bin map of expressed sequence tags in homoeologous Group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 168:609–623

    Article  PubMed  CAS  Google Scholar 

  • Pepe B, Surata K, Suhartono F, Sipayung M, Purwanto A, Dvorak WS (2004) Conservation status of natural populations of Eucalyptus urophylla in Indonesia and international efforts to protect dwindling gene pools. Forest Genetic Resources 31:62–64

    Google Scholar 

  • Praça MM, Carvalho CR, Novaes CRDB (2009) Nuclear DNA content of three Eucalyptus species estimated by flow and image cytometry. Aust J Bot 57:524–531

    Article  Google Scholar 

  • Sansaloni C, Petroli C, Carling J, Hudson C, Steane D, Myburg A, Grattapaglia D, Vaillancourt R, Kilian A (2010) A high-density diversity arrays technology (DArT) microarray for genome-wide genotyping in Eucalyptus. Plant Methods 6:16

    Article  PubMed  Google Scholar 

  • Semagn K, Bjornstad A, Ndjiondjop MN (2006) Principles, requirements and prospects of genetic mapping in plants. Afr J Biotechnol 5:2569–2587

    CAS  Google Scholar 

  • Slate J (2008) Robustness of linkage maps in natural populations: a simulation study. Proceedings of the Royal Society B 275:695–702

    Article  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant Journal 3:739–744

    Article  CAS  Google Scholar 

  • Steane DA, Vaillancourt RE, Russell J, Powell W, Marshall D, Potts BM (2001) Development and characterisation of microsatellite loci in Eucalyptus globulus (Myrtaceae). Silvae Genetica 50:89–91

    Google Scholar 

  • Steane DA, Myburg AA, Sansaloni CP, Petroli CD, Grattapaglia D, Kilian A, Vaillancourt RE (2011) DArT arrays for genetic mapping and diversity analysis of Eucalyptus. Molecular Phylogenetics and Evolution 59:206–224

    Article  PubMed  Google Scholar 

  • Studer B, Kolliker R et al (2010) EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.). BMC Plant Biology 10:177

    Article  PubMed  Google Scholar 

  • Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320:486–488

    Article  PubMed  CAS  Google Scholar 

  • Tuskan GA, DiFazio S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen J (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V, Wageningen, Netherlands

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. Heredity 93:77–78

    Article  CAS  Google Scholar 

  • Williams JE, Brooker MIH (1997) Eucalypts: an introduction. In: Williams J, Woinarski J (eds) Eucalypt ecology: individuals to ecosytems. Cambridge University Press, Cambridge U.K, pp 1–15

    Google Scholar 

  • Wu F, Eannetta N, Xu Y, Durrett R, Mazourek M, Jahn M, Tanksley S (2009) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. TAG Theor Appl Genet 118:1279–1293

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Norske Skog, Forestry Tasmania, Gunns Ltd, Australian Bluegum Plantations Pty Ltd, Western Australian Plantation Resources (WAPRES), David Pilbeam of the Southern Tree Breeding Association (STBA) and STBA for access to, and maintenance of E. globulus mapping family trials. Valérie Hecht is thanked for her assistance with BLAST work. Funding for this project was provided by the Australian Research Council (DP0770506 & DP110101621) as well as the Cooperative Research Centre for Forestry (Australia). We also thank Sappi Forest Research (South Africa) who generated and maintained the E. grandis × E. urophylla backcross mapping plant materials and the following organisations who provided financial support that contributed to the E. grandis× E. urophylla linkage mapping work; Sappi, Mondi, the Technology and Human Resources for Industry Program (THRIP), the National Research Foundation (NRF) and the Department of Science and Technology (DST) of South Africa.

Author information

Authors and Affiliations

  1. School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia

    Corey J. Hudson, Jules S. Freeman, Brad M. Potts & René E. Vaillancourt

  2. Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

    Anand R. K. Kullan & Alexander A. Myburg

  3. EMBRAPA Genetic Resources and Biotechnology—Parque Estação Biológica, PqEB—Av. W5 Norte (final), Brasília, DF, Brazil, 70770-917

    Danielle A. Faria & Dario Grattapaglia

  4. Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160, DF, Brasilia, Brazil

    Dario Grattapaglia

  5. Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla, ACT 2600, Australia

    Andrzej Kilian

Authors
  1. Corey J. Hudson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anand R. K. Kullan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jules S. Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Danielle A. Faria
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dario Grattapaglia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrzej Kilian
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alexander A. Myburg
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Brad M. Potts
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. René E. Vaillancourt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Corey J. Hudson.

Additional information

Communicated by S. González-Martínez

Electronic supplementary materials

Below is the link to the electronic supplementary material.

ESM 1

(PDF 221 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hudson, C.J., Kullan, A.R.K., Freeman, J.S. et al. High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping. Tree Genetics & Genomes 8, 339–352 (2012). https://doi.org/10.1007/s11295-011-0444-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-011-0444-9

Keywords

Search

Navigation