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.

https://biblio.ugent.be/publication/5655667/file/5655749.pdf

The genome of Eucalyptus grandis

"Big" plant genera, those of 500 or more species, have not only occasioned interest among systematic botanists, but for geographical, ecological or horticultural reasons, have also become well-established popular concepts. Their size has rendered them difficult, if not impossible, to study in their entirety; there have been few full revisions since the nineteenth century. Despite their embodiment of significant taxonomic, biological and evolutionary questions, from the 1980s their importance has been more generally recognised, and recent technological and methodological developments have made it easier to come to grips with their study. This paper synthesizes growth impediments to our knowledge of these genera and possible approaches to studying them. Of the 57 genera currently thought to have 500 or more species, 22 of these were also considered in 1883 to be large (300 or more species). Others gained their prominence as a result of later exploration, some of it driven by enthusiasts. It is argued that comparisons of size, phenomena, and processes will only be possible by comprehensive study of the lineages comprising these genera and their immediate historical relatives; uncritical lists or relatively limited samples are not enough. Such studies will be of great scientific as well as cultural benefit.

History and Concepts of Big Plant Genera

Aim This paper reviews the biogeography of the Australian monsoon tropical
biome to highlight general patterns in the distribution of a range of organisms
and their environmental correlates and evolutionary history, as well as to identify
knowledge gaps.
Location Northern Australia, Australian Monsoon Tropics (AMT). The AMT
is defined by areas that receive more than 85% of rainfall between November
and April.
Methods Literature is summarized, including the origin of the monsoon
climate, present-day environment, biota and habitat types, and phylogenetic and
geographical relationships of selected organisms.
Results Some species are widespread throughout the AMT while others are
narrow-range endemics. Such contrasting distributions correspond to presentday
climates, hydrologies (particularly floodplains), geological features (such as
sandstone plateaux), fire regimes, and vegetation types (ranging from rain forest
to savanna). Biogeographical and phylogenetic studies of terrestrial plants
(e.g. eucalypts) and animals (vertebrates and invertebrates) suggest that distinct
bioregions within the AMT reflect the aggregated effects of landscape and
environmental history, although more research is required to determine and
refine the boundaries of biogeographical zones within the AMT. Phylogenetic
analyses of aquatic organisms (fishes and prawns) suggest histories of associations
with drainage systems, dispersal barriers, links to New Guinea, and the existence
of Lake Carpentaria, now submerged by the Gulf of Carpentaria. Complex
adaptations to the landscape and climate in the AMT are illustrated by a number
of species.
Main conclusions The Australian monsoon is a component of a single global
climate system, characterized by a dominant equator-spanning Hadley cell.
Evidence of hot, seasonally moist climates dates back to the Late Eocene, implying
that certain endemic elements of the AMT biota have a long history. Vicariant
differentiation is inferred to have separated the Kimberley and Arnhem Land
bioregions from Cape York Peninsula/northern Queensland. Such older patterns
are overlaid by younger events, including dispersal from Southeast Asia, and
range expansions and contractions. Future palaeoecological and phylogenetic
investigations will illuminate the evolution of the AMT biome. Understanding the
biogeography of the AMT is essential to provide a framework for ecological
studies and the sustainable development of the region.

Biogeography of the Australian monsoon tropics

Contents
 	Summary	911	
I.	Introduction	912	
II.	Eucalyptus biology and domestication	913	
III.	Eucalyptus breeding and clonal forestry	913	
IV.	Marker-assisted management of genetic variation in breeding populations	914	
V.	Genetic mapping and quantitative trait locus (QTL) analysis	915	
VI.	Gene discovery and genetical genomics	916	
VII.	Association mapping	918	
VIII.	Molecular breeding	920	
IX.	From gene sequences to breeding tools	922	
X.	Future developments and challenges	924	
 	Acknowledgements	926	
 	References	926	


Summary
Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.

Eucalyptus applied genomics: from gene sequences to breeding tools.

The status of genomics and genetics research in the Myrtaceae, a large family of dicotyledonous woody plants, is reviewed with Eucalyptus as the focal genus. The family contains over 5,650 species in 130 to 150 genera, predominantly of neo-tropical and Southern Hemisphere distribution. Several genera are well known for their economic importance worldwide. Myrtaceae are typically diploids with small to intermediate genome size. Microsatellites have been developed for several genera while higher throughput marker systems such as diversity arrays technology and single nucleotide polymorphism are available for Eucalyptus. Molecular data have been fundamental to current perspectives on the phylogeny, phylogeography and taxonomy of the Myrtaceae, while numerous studies of genetic diversity have been carried out particularly as it relates to endangered, rare, fragmented, overharvested or economically important species. Large expressed sequence tag collections for species of Eucalyptus have recently become public to support the annotation of the Eucalyptus grandis genome. Transcriptomics in Eucalyptus has advanced by microarrays and next-generation sequencing focusing on wood development. Linkage maps for Eucalyptus display high synteny across species and have been extensively used to map quantitative trait loci for a number of traits including growth, wood quality, disease and insect resistance. Candidate gene-based association genetics have successfully found marker–trait associations for wood and fiber traits. Genomic selection experiments have demonstrated clear potential to improve the efficiency of breeding programs while freeze-tolerant transgenic Eucalyptus trials have recently been initiated. The recently released E. grandis genome, sequenced to an average coverage of 8×, will open up exceptional opportunities to advance Myrtaceae genetics and genomics research.

/pdf/progress-in-myrtaceae-genetics-and-genomics-eucalyptus-as-e2xjdmeygz.pdf

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

A new formal classification of the genus Eucalyptus is presented. It divides the genus into seven polytypic subgenera: E. subg. Angophora, E. subg. Corymbia, E. subg. Blakella, E. subg. Eudesmia, E . subg. Symphyomyrtus, E. subg. Minutifructa and E. subg. Eucalyptus, and six monotypic subgenera: E. subg. Acerosa, E. subg. Cruciformes, E. subg. Alveolata, E. subg. Cuboidea, E. subg. Idiogenes and E. subg. Primitiva. The system is intentionally phylogenetic, proceeding from the generally assumed primitive ‘apples’ (E. subg. Angophora) and bloodwoods (E. subg. Corymbia) to the most advanced and modified group, the monocalypts (E. subg. Eucalyptus). The genus Corymbia Hill & Johnson is subsumed under Eucalyptus and is represented by E. subg. Corymbia (the bloodwoods) and E. subg. Blakella (the ghostgums). New infrageneric taxa are diagnosed and their names typified, while brief digests in English are given for established taxa. Three species of the former genus Angophora have names with epithets preoccupied by names of other Eucalyptus species and new names are presented for them. The study is introduced by a brief historical summary of previous work in Eucalyptus, an apologia for the inclusion of Angophora, the reason for requirement of a new classification and notes on the nomenclature used. A new infrageneric rank, ‘supraspecies’, is introduced and is intentionally divorced in application (as a rank) from the similar sounding ‘superspecies’. All species recognised by the author are named and assigned in this system.

M. I. H. Brooker

Papers

A new classification of the genus Eucalyptus L'Hér. (Myrtaceae)