Plant scientists celebrate new woody plant genome

Our friends often remind us that scientists are strange beasts. As such, it is fitting that we should rejoice at the release of a major new genome by further scholarship and analysis – using the genome to unravel new elements of plant physiology and evolution. In this Feature Issue we celebrate the completion of the genome of Eucalyptus grandis (Myburg et al., 2014), the first representative of the plant order Myrtales, an early diverging rosid lineage, and a species-rich genus that evolved in isolation on the Australian continent. Compared to plant genomes sequenced to date, it represents an independent evolutionary experiment on what it means to be a large woody perennial plant evolving in diverse, and often stressful, habitats. Eucalyptus contains some of the fastest growing hardwood trees and the tallest flowering plant (Eucalyptus regnans) on Earth, and also has many species adapted to extremely dry, hot, and nutrient deficient soils. It also produces a diverse array of plant-specific metabolites (including the well-known eucalyptus oils). Members of the genus are among the most productive manufacturers of lignocellulosic biomass on the planet, which makes the genome a rich source of genetic information to inform the development of new kinds of bioproducts, including chemicals, wood, pulp, and bioenergy (Fig. 1). We have gathered together 13 scientific papers that look more deeply into the genome, and use it to guide further studies important for plant biology and biotechnology. One major theme of the papers is that the many novelties of the eucalypt genome, both structural and functional, appear to bear the fingerprints of natural selection that – aswe probe themmore deeply –will provide lessons in adaptive evolution for years to come. The same lessons will inform breeding, biotechnology, and genetic engineering. The extraordinary diversity of topics covered in this small volume illustrates the wide applicability of the genome resource. For example, several papers provided tools or analyses that advance the state of the genome resource or provide new tools for molecular genetic analyses or breeding. Bartholom e et al. (2015b, this issue pp. 1283–1296) used genetic recombination data from a hybrid cross and study of 6000 single nucleotide polymorphism (SNP) markers to create a dense genetic map to more precisely organize and collapse genome segments, guiding amore accurate version 2.0 of the genome assembly in the process. Silva-Junior et al. (2015, this issue pp. 1527–1540) created a chip with 60 000 SNPmarkers based on analysis of 240 representative genomes from 12 species. They show that the chip is effective for analyzing genome diversity in a wide variety of eucalypt species, and in a related study (O. B. Silva-Junior & D. Grattagalia, unpublished), they used it to characterize patterns of recombination, polymorphism, and linkage disequilibrium in depth. Their work showed that this new genotyping resource will be very useful for genetic analysis and genome-assisted breeding. Several papers weremotivated by ecological problems. Plett et al. (2015, this issue pp. 1423–1436) used genomic resources and genetic diversity to understand how eucalypts and an important rootmutualist, the ectomycorrhizal fungus Pisolithus,may respond to climate change. The authors reported high variation in root transcriptomes and susceptibility to infection as a result of exposure to differentCO2 concentrations.Different isolates ofPisolithus also colonized E. grandis in a complex, differential manner. Building on their high-density genetic maps, Bartholom e et al. (2015a, this issue pp. 1437–1449) studied genetic variation in carbon isotope composition that may help inform about adaptation to drought andbreeding for stress tolerance.They report 15quantitative trait loci (QTLs) for isotope composition (dC), widely used as a surrogate for water use efficiency, and find that most are stable across test environments and unrelated to QTLs for growth rate. This suggests that molecular breeding could be used to improve water use efficiency without impacting productivity; getting this tradeoff right is a long-standing problem in Eucalyptus plantation forestry. Several papers probed macroevolution, comparing E. grandis genes or genomic patterns to those of other eucalypt species ormore distant taxa. This includes a study byHudson et al. (2015, this issue pp. 1378–1390) that investigated genomic patterns of diversity in six eucalypt species based on 2840 DNA markers. Analysis of range-wide collections of the six species revealed that individual loci varied widely in their diversity and extent of population differentiation, though genomic regions often had similar characteristics in different species. The authors reported the identification of a number of species-differentiating markers that are widely distributed in the genome – indicating the likely occurrence of multiple selective sweeps, or lineage-specific mutations. Kersting et al. (2015, this issue pp. 1328–1336) studied the evolutionary changes of protein domains encoded in the Eucalyptus genome across key angiosperm evolutionary nodes. By reference to gene ontology and transcriptome databases, they suggested that natural selection played a major role in domain gains, losses, and specialization – and that these were overrepresented in Eucalyptus’s many tandemly duplicated genes (versus those fromwhole genome duplication). Many cases of enrichment were associated with reproduction and stress related genes, and were particularly prominent in genes related to pollen development.