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Southern Cross Plant Science

Corymbia Genome Project

The Corymbia genome project was initiated in 2012 by Southern Cross Plant Science in collaboration with USC/DAF, UTas, and EMBRAPA.

The consortium welcomed a merger with an UQld initiative with JBEI, JGI and Hudson Alpha in March 2015.

Recent news

  • IUFRO Tree Biotechnology Conference Florence June 2015. Orzenil Bonfim da Silva Junior (EMBRAPA) will present an oral paper on the initial hybrid assembly of the SCU lead sequencing effort "Toward a Corymbia reference genome: comparative efficiencies of Illumina, PacBio and hybrid de novo assemblies of a complex heterozygous genome".
  • Corymbia genome project workshop - 13-15th October 2015 at SCU, Lismore, Australia. Interested persons should contact Dr Mervyn Shepherd.

Background

  • The aim is to generate a high quality genome sequence anchored to a dense genetic map of good coverage, to underpin pre-breeding trait analysis, germplasm management and conservation.
  • Genome sequence of over 400 fold coverage (both Illumina short read and Pacbio continuous long read) has been generated and initial assemblies completed for two reference genotypes. Effort is now focusing on improving and validating the genome for a release to members in 2015.
  • A linkage map is under construction and initial transcript data has been acquired.
  • We seek additional partners and funding in order to progress the generation of draft genome sequence anchored to high quality genetic maps, to assist in pre-breeding trait genetics and provide a basis for understanding key aspects of Corymbia biology, diversity and adaptation to the environment..
  • Spotted gums (Genus Corymbia Section Maculatae; Myrtaceae) and its hybrid with Corymbia torelliana (Section Cadageria), have contributed to the rapid expansion of hardwood plantations in subtropical Australia (Lee 2007; Nichols et al. 2010).
  • The reference genome for Eucalyptus grandis (which is probably twice the size of C. citriodora) was released in 2011 (http://www.phytozome.net/eucalyptus.php). The chloroplast genome for E. globulus was published in 2005 (Steane 2005).
  • Corymbia citriodora is an outcrossing diploid with 11 chromosomes and estimates of genome size from flow cytometry of 370 Mbp, a little over a half of the genome size of E. grandis (Grattapaglia and Bradshaw 1994).

Scientific Rationale

  • Small genome (370 Mb)
  • Generation of a Corymbia genome sequence will provide a key resource supporting research underpinning pre-breeding, for understanding genetic diversity, population structure, and geneflow.
  • C. citriodora is the most intensively studied Corymbia species, where molecular studies to date have provided a basis for understanding gene-flow and genetic population structure.
  • Probably at least 55 Mya of independent evolution from Eucalyptus (Rozefields 1996)
  • It is an excellent model for:
    • sub-tropical eucalypts
    • understanding the behaviour and consequences of tree hybrids and genetic incongruence due because of the potential of Corymbia hybrids for plantation forestry
    • genomic basis for heterosis in outcrossing tree species
    • study of the role of long-distance pollinators (birds, fruit bats) in population structuring of eucalypts
  • A complete genome anchored to high quality genetic maps will enable a deep understanding of the molecular basis of abiotic and biotic stress tolerances.
  • A platform resource for genomic selection in Corymbia

Industry and other Stakeholder Relevance

  • Spotted gum is the premier hardwood plantation taxon for solid wood from low-rainfall regions of the sub-tropics based on its productivity and biotic stress tolerance
  • Survives under adverse conditions/robust
  • Commercial consequences for hybrids
  • Value for low-rainfall forestry in Australia and elsewhere
  • Sought after timber for its durability, appearance and outdoor use
  • Pre-breeding - benefits include:
    • Accelerated breeding
    • Understanding genetic basis of traits - synthesis of precision genomic & phenomic technologies will provide a world-class germplasm development system.
    • Partitioning and resolving genotype x environment interactions
    • Resolving resistance genes for Myrtle Rust
  • Conservation and genepool management
    • Habitat conservation
    • Facilitate rehabilitation of conservation forests & allow these forests to act as natural carbon sink
  • Informing R&D on other Corymbia species, such as C. torelliana (an environmental weed)
    • Managing hybrids and geneflow between commercial and native stands
    • Identifying weedy genes and alleles

Timeliness

  • The E. grandis genome is now being used as a reference for a series of comparative genomics studies across the Myrtaceae.

  • Corymbia citriodora subsp variegata is nominated as the key representative taxon of the around 110 species in the Genus Corymbia and will benefit from global effort to understand genome evolution in this important southern hemisphere plant genus.

  • Other reasons
    • The expansion of plantations within sub-tropical Queensland and elsewhere (S. America; South Africa).
    • Concerns over genetic erosion and genetic pollution.
    • Climate change adaptability
    • A model system for the study of the tropical disease of eucalypts and other Myrtaceae taxa, Myrtle Rust

Progress to date

  • Genome sequence coverage > 400 fold (340 x Illumina short reads; 60 x Pacbio continuous long reads)
  • Reference genotype adopted from USC/DAFF
  • Independent genome assemblies for two reference genotypes
  • Genotyping of a reference mapping population is currently underway
  • Generation of a transcriptome (a total of 24.5 Gb from 5 tissues)

    Funding

    The following support is acknowledged:

    • Southern Cross University - Office of Research (2012-2014)
    • University of Tasmania - ARC Discovery Grant DP140102552
    • Department of Agriculture and Fisheries - Horticulture and Forestry Science
    • University of the Sunshine Coast - Forest Industries Research Centre
    • Brazilian Ministry of Science and Technology through FAP-DF and CNPq research grants
    • University of Queensland
    • Joint BioEnergy Institute
    • Joint Genome Initiative/Hudson Alpha

    Contact

    Dr Mervyn Shepherd: mervyn.shepherd@scu.edu.au

    Updated: 16 August 2016