The genome of Eucalyptus grandis

Abstract

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

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

“…The roles of these genes in biomass formation are becoming increasingly revealed, being linked directly to either lignin (50,51) or hormone-mediated growth regulation (52). In addition, SCW polysaccharide biosynthesis genes known to be expressed in developing xylem (8) were mainly associated with variation in wood density and glucose release efficiency (Dataset S3). In the latter case, the majority were xylan modification genes, affecting patterns of acetylation, and glucuronic acid and methyl-glucuronic acid decoration of the xylan backbone (53, 54) (Dataset S3).…”

“…The DBH subnetwork contains a considerable number of ligninrelated genes. Most bona fide lignin biosynthesis genes that are highly expressed in developing xylem (8,38) (Dataset S3) were indeed associated with growth (DBH and bark thickness traits). In addition to these lignin-related genes, the DBH network contains several genes involved in hormone signaling (IAA9 and ARF7) and flavonoid biosynthesis (ANS, BAN, and A11).…”

“…Fast-growing trees such as poplars and eucalypts with short rotation times, small genome sizes (500-600 Mbp), large genetic diversity, and established breeding populations are widely cultivated as woody biomass crops and are well suited for biotechnological improvement (5)(6)(7)(8). A tree's amenability to bioprocessing for pulp, paper, cellulose, and other bioproducts is dependent on the aggregate of its wood properties, which are a function of cellular architecture and the chemistry and ultrastructure of the secondary cell walls (SCWs) of wood fiber cells that compose the bulk of woody biomass (9).…”

Brief history of Eucalyptus breeding in Brazil under perspective of biometric advances

“…MYBURG et al (2014) revolutionized the genotyping process by performing the complete mapping of E. grandis genome, being this information highly relevant to other species of the Eucalyptus genus and its hybrids. In this context, an Illumina 60K chip for large-scale genotyping of 12 Eucalyptus species were developed (SILVA-JUNIOR et al, 2015), being the landmark that consolidates the use of single nucleotides polymorphisms (SNP) in genomic studies of the genus.…”

Exploiting Natural Variation to Uncover an Alkene Biosynthetic Enzyme in Poplar

“…html#!info?alias=Org_Spurpurea), flax (Linum usitatissimum) (v1.0) (Wang et al, 2012b), and eucalyptus (Eucalyptus grandis) v2.0 (Myburg et al, 2014), and the Sol Genomics Network for tomato (Solanum lycopersicum) (ITAG release 2.40) (Tomato Genome Consortium, 2012). This led to the identification of 37 putative KCS-encoding genes in poplar, a larger number than previously reported, likely due to the inclusion of sequences that lack one of the two protein domains (Guo et al, 2016).…”