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

Hudson, Corey J.; Kullan, Anand Raj Kumar; Freeman, Jules S.; Faria, Danielle Assis de; Grattapaglia, Dário; Kilian, Andrzej; Myburg, Alexander Andrew; Potts, Brad M.; Vaillancourt, René E.

doi:10.1007/s11295-011-0444-9

Cited by 51 publications

(83 citation statements)

References 58 publications

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“…variegata linkage maps (both directly and via comparison of these linkage maps with the E. grandis genome), suggests genome structure is largely conserved between these Corymbia species. These species represent separate sections within Corymbia [39], so in terms of taxonomic distance are comparable to the previous inter-sectional comparisons within Symphyomyrtus [32, 37, 38]. In contrast, much greater genomic differentiation was evident in our comparison between the closely related genera Eucalyptus and Corymbia .…”

Section: Discussionsupporting

confidence: 84%

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

et al. 2017

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BackgroundPrevious studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes.ResultsWe constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1–13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps.ConclusionsThese are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3782-7) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 84%

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

et al. 2017

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“…Despite having the same number of chromosomes (n 5 11) and highly co-linear genomes 18 , eucalypts vary considerably in genome size. E. grandis (640 Mb 19 ) and E. globulus (530 Mb 19 ) represent different sections (Latoangulatae and Maidenaria) within the subgenus Symphyomyrtus 20 , estimated to have diverged in the past 36 million years 21 .…”

Section: Research Articlementioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

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“…Because establishing the correct map position of tightly linked markers in high-density linkage maps can be difficult due to duplicated loci, genotyping errors, segregation distortion, and chiasma interference (Hackett and Broadfoot 2003;Ferreira et al 2006;Cheema and Dicks 2009;Collard et al 2009), minor ordering errors can arise. As such, a 2-cM threshold was applied for declaring noncollinearity (Hudson et al 2011). Thus, markers were only considered noncollinear when a shift in marker order and position exceeded 2 cM in both maps.…”

Section: Synteny Assessmentmentioning

confidence: 99%

Chromosomal Evolution and Patterns of Introgression inHelianthus

et al. 2014

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Knowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodones Dune sunflower (H. niveus ssp. tephrodes) genomes and compared them to a consensus map of cultivated sunflower (H. annuus) to identify chromosomal rearrangements between species. The genetic maps of H. argophyllus and H. niveus ssp. tephrodes included 17 linkage groups each and spanned 1337 and 1478 cM, respectively. Comparative analyses revealed greater divergence between H. annuus and H. niveus ssp. tephrodes (13 inverted segments, 18 translocated segments) than between H. annuus and H. argophyllus (10 inverted segments, 8 translocated segments), consistent with their known phylogenetic relationships. Marker order was conserved across much of the genome, with 83 and 64% of the H. argophyllus and H. niveus ssp. tephrodes genomes, respectively, being syntenic with H. annuus. Population genomic analyses between H. annuus and H. argophyllus, which are sympatric across a portion of the natural range of H. annuus, revealed significantly elevated genetic structure in rearranged portions of the genome, indicating that such rearrangements are associated with restricted gene flow between these two species.C HROMOSOMAL rearrangements are of considerable interest because they are often associated with barriers to gene flow between related species, either due to their direct effects on the fitness of heterozygotes or through the indirect effects of genic barriers embedded within them (White 1978;Barton and Bengtsson 1986;Rieseberg et al. 1995bRieseberg et al. , 1999Rieseberg 2001;Navarro and Barton 2003;Kirkpatrick and Barton 2006; reviewed in Faria and Navarro 2010;Gimenez et al. 2012). As such, detailed information on karyotypic differences between species provides insight into the nature of reproductive isolation and, more pragmatically, informs attempts to introgress beneficial alleles from wild species into crop gene pools (Chetelat and Meglic 2000;Foulongne et al. 2003;Dirlewanger et al. 2004). An improved understanding of synteny across species can also facilitate the identification and localization of functionally important genes in a taxon of interest through the extrapolation of gene order from model species (e.g., Choi et al. 2004;Dilbirligi et al. 2006).The genus Helianthus, which is composed of 49 species native to the Americas (Timme et al. 2007) and includes cultivated sunflower (Helianthus annuus L.; 2n = 2x = 34; hereafter referred to as ANN), has emerged as a model for genetic studies of adaptation, hybridization, and speciation (Rieseberg et al. 1995a,b;Lai et al. 2005;Reagon and Snow 2006;Massinga et al. 2009;Gutierrez et al. 2010;Vekemans 2010;Roumet et al. 2013). Insight into the nature and extent of reproductive barriers within Helianthus will ...

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

Cited by 51 publications

References 58 publications

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

The genome of Eucalyptus grandis

Chromosomal Evolution and Patterns of Introgression inHelianthus

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