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Myrtle rust poses a significant biosecurity threat to Australia with potential for long‐term damaging impacts on native flora and plant industries. This study describes the disease cycle of Austropuccinia psidii, the myrtle rust pathogen, in Eucalyptus globulus and Eucalyptus obliqua, two commercially and ecologically important species from different subgenera of Eucalyptus. Ontogeny and morphology of infection structures of A. psidii on plants of both Eucalyptus species with different rust response phenotypes, i.e. completely resistant, hypersensitive and highly susceptible, were investigated. Plants were inoculated with single‐uredinium‐derived urediniospores and examined by scanning electron microscopy. No differences between rust response phenotypes were observed in germination of urediniospores, formation of appressoria or length of germ tubes. The growth of germ tubes had no affinity towards stomata of either species. Histological observations indicated direct penetration by infection pegs through the leaf cuticle and no penetration beyond the epidermis on rust‐resistant E. obliqua. Eucalyptus obliqua plants that were identified as susceptible to A. psidii at 3‐ and 6‐months‐old showed no disease when reinoculated with A. psidii at 12‐months‐old; this indicated possible early acquisition of adult plant resistance to A. psidii in this species. In the susceptible phenotype of E. globulus rust inoculation led to rapid colonization of leaf parenchyma cells with the disease cycle completed within 10 days. These findings provide valuable insights into host–pathogen interactions in the Eucalyptus–A. psidii pathosystem, which might be useful for the development of effective rust control strategies across Eucalyptus subgenera. [ABSTRACT FROM AUTHOR]

Canola ( Brassica napus L.) is a valuable oilseed crop worldwide. However, trait improvement by breeding has been limited by its low genetic diversity and polyploid genetics. Whilst offering many potential benefits, the application of transgenic technology is challenged by the stringent and expensive regulatory processes associated with the commercialisation of genetically modified organisms, coupled with a prevailing low public acceptance of such modifications. DNA-free genome editing using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 ribonucleoproteins (RNPs) offers a promising way to achieve trait improvements without the limitations of transgenic methods. Here, we present a method for DNA-free genome editing via the direct delivery of RNPs to canola mesophyll protoplasts. This method allows high-throughput in vivo testing of the efficacy of gRNA design as part of the transformation process to facilitate the selection of optimal designs prior to the generation of edited events. Of the 525 shoots regenerated via tissue culture from RNP-transfected protoplasts and screened for the presence of mutations in the targeted gene, 62% had one or more mutated target alleles, and 50% had biallelic mutations at both targeted loci. This high editing efficiency compares favourably with similar CRISPR-Cas9 approaches used in other crop plants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Sahab, Runa, Ponnampalam, Kay, Jaya, Viduka, Panter, Tibbits and Hayden.)

Competing Interests: Declaration of interests None are declared by the authors.

Purpose: Sexual and relationship violence has devasting effects on the health and well-being of college students. This study assessed the prevalence of dating abuse victimization and harassment among sexual and gender minority (SGM) college students within the first 3 months of college enrollment and identified potential demographic differences in exposure. Methods: Data are from the 2020 to 2021 Sexual Assault Prevention for Undergraduates digital sexual assault prevention program ( N  = 250,359). Descriptive statistics were used to determine 3-month prevalence of dating abuse victimization and harassment among gender identity and sexual orientation subgroups and to examine within-group differences based on race and ethnicity. Results: Dating abuse victimization during college was reported by 6.5% of transgender women, 5.0% of transgender men, 5.0% of genderqueer/nonconforming students, 2.0% of "women," and 1.0% of "men." Harassment during college was reported by 13.7% of genderqueer/nonconforming students, 11.2% of transgender women, 8.9% of transgender men, 8.7% of "women," and 1.6% of "men." Students who identified with more than one sexual orientation identity reported the highest rates of dating abuse (3.9%) and harassment (14.9%) during college. SGM students with particular racial/ethnic identities (i.e., Indigenous, multiracial) reported disproportionately higher rates, particularly American Indian/Alaska Native/Native Hawaiian/Pacific Islander students who identified as transgender men (42.9%), transgender women (41.7%), genderqueer/nonconforming students (26.1%), queer/pansexual/questioning students (20%), and students with multiple sexual orientation identities (36.4%). Conclusion: Targeted intervention strategies and resources are needed on college campuses to support the needs and experiences of SGM students, including students who identify as Indigenous, multiracial, and other persons of color.

Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.

Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community., Competing Interests: HR, JG, AR, DMo, DMu, and TW were employed by InterGrain. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Keeble-Gagnère, Pasam, Forrest, Wong, Robinson, Godoy, Rattey, Moody, Mullan, Walmsley, Daetwyler, Tibbits and Hayden.)

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat., (© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread., (© The Author(s) 2020. Published by Oxford University Press on behalf of Genetics Society of America.)

We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr, respectively. Single-trait genome-wide association studies (GWAS) revealed several environment-specific and multi-environment quantitative trait loci (QTL). Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B within a 4.4-cM region. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exist within the 3B cluster including the durable rust resistance gene Yr30. An Sr/Lr QTL on chromosome 3D was found mainly in the synthetic-derived germplasm from Annuello background which is known to carry the Agropyron elongatum 3D translocation involving the Sr24/Lr24 resistance locus. Interestingly, estimating the SNP effects using a BayesR method showed that the correlation among the highest 1% of QTL effects across environments (excluding GWAS QTL) had significant correlations, with average r values of 0.26, 0.16 and 0.55 for Lr, Sr and Yr, respectively. These results indicate the importance of small effect QTL in achieving durable rust resistance which can be captured using genomic selection.

The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Key Message: Exploring large genomic data sets based on the latest reference genome assembly identifies the rice ortholog APO1 as a key candidate gene for number of rachis nodes per spike in wheat. Increasing grain yield in wheat is a key breeding objective worldwide. Several component traits contribute to grain yield with spike attributes being among the most important. In this study, we performed a genome-wide association analysis for 12 grain yield and component traits measured in field trials with contrasting agrochemical input levels in a panel of 220 hexaploid winter wheats. A highly significant, environmentally consistent QTL was detected for number of rachis nodes per rachis (NRN) on chromosome 7AL. The five most significant SNPs formed a strong linkage disequilibrium (LD) block and tagged a 2.23 Mb region. Using pairwise LD for exome SNPs located across this interval in a large worldwide hexaploid wheat collection, we reduced the genomic region for NRN to a 258 Kb interval containing four of the original SNP and six high-confidence genes. The ortholog of one (TraesCS7A01G481600) of these genes in rice was ABBERANT PANICLE ORGANIZATION1 (APO1), which is known to have significant effects on panicle attributes. The APO1 ortholog was the best candidate for NRN and was associated with a 115 bp promoter deletion and two amino acid (C47F and D384 N) changes. Using a large worldwide collection of tetraploid and hexaploid wheat, we found 12 haplotypes for the NRN QTL and evidence for positive enrichment of two haplotypes in modern germplasm. Comparison of five QTL haplotypes in Australian yield trials revealed their relative, context-dependent contribution to grain yield. Our study provides diagnostic SNPs and value propositions to support deployment of the NRN trait in wheat breeding.

Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target-capture method was used to detect genome-wide polymorphisms in a panel of 174 flowering time-related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas., (© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

In barley and other cereal crops, phenological diversity drives adaptation to different cultivation areas. Improvement of barley yield and quality traits requires adaptation to specific production areas with introgression of favorable alleles dependent upon precise identification of the underlying genes. Combining targeted sequence capture systems with next-generation sequencing provides an efficient approach to explore target genetic regions at high resolution, and allows rapid discovery of thousands of genetic polymorphisms. Here, we apply a versatile target-capture method to detect genome-wide polymorphisms in 174 flowering time-related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Sequences were generated across a phenologically diverse panel of 895 barley varieties, resulting a high mean depth coverage of ~25x allowing reliable discovery and calling of insertion-deletion (InDel) and single nucleotide polymorphisms (SNPs). Sequences of InDel and SNPs from the targeted enrichment were utilized to develop 67 Kompetitive Allele Specific PCR (KASP) markers for validation. This work provides researchers and breeders a comprehensive molecular toolkit for the selection of phenology-related traits in barley.

Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome., Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region., Conclusions: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

Key Message: Imputing genotypes from the 90K SNP chip to exome sequence in wheat was moderately accurate. We investigated the factors that affect imputation and propose several strategies to improve accuracy. Imputing genetic marker genotypes from low to high density has been proposed as a cost-effective strategy to increase the power of downstream analyses (e.g. genome-wide association studies and genomic prediction) for a given budget. However, imputation is often imperfect and its accuracy depends on several factors. Here, we investigate the effects of reference population selection algorithms, marker density and imputation algorithms (Beagle4 and FImpute) on the accuracy of imputation from low SNP density (9K array) to the Infinium 90K single-nucleotide polymorphism (SNP) array for a collection of 837 hexaploid wheat Watkins landrace accessions. Based on these results, we then used the best performing reference selection and imputation algorithms to investigate imputation from 90K to exome sequence for a collection of 246 globally diverse wheat accessions. Accession-to-nearest-entry and genomic relationship-based methods were the best performing selection algorithms, and FImpute resulted in higher accuracy and was more efficient than Beagle4. The accuracy of imputing exome capture SNPs was comparable to imputing from 9 to 90K at approximately 0.71. This relatively low imputation accuracy is in part due to inconsistency between 90K and exome sequence formats. We also found the accuracy of imputation could be substantially improved to 0.82 when choosing an equivalent number of exome SNP, instead of 90K SNPs on the existing array, as the lower density set. We present a number of recommendations to increase the accuracy of exome imputation.

Background: Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E. globulus and E. cladocalyx), this study combines physiological characterizations with 'second-generation' sequencing to identify key genes involved in eucalypt responses to medium-term water limitation., Results: One hundred twenty Million high-quality HiSeq reads were created from 14 tissue samples in plants that had been successfully subjected to a water deficit treatment or a well-watered control. Alignment to the E. grandis genome saw 23,623 genes of which 468 exhibited differential expression (FDR < 0.01) in one or both ecotypes in response to the treatment. Further analysis identified 80 genes that demonstrated a significant species-specific response of which 74 were linked to the 'dry' species E. cladocalyx where 23 of these genes were uncharacterised. The majority (approximately 80%) of these differentially expressed genes, were expressed in stem tissue. Key genes that differentiated species responses were linked to photoprotection/redox balance, phytohormone/signalling, primary photosynthesis/cellular metabolism and secondary metabolism based on plant metabolic pathway network analysis., Conclusion: These results highlight a more definitive response to water deficit by a 'dry' climate eucalypt, particularly in stem tissue, identifying key pathways and associated genes that are responsible for the differences between 'wet' and 'dry' climate eucalypts. This knowledge provides the opportunity to further investigate and understand the mechanisms and genetic variation linked to this important environmental response that will assist with genomic efforts in managing native populations as well as in tree improvement programs under future climate scenarios.

Key Message: BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases. Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920-1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker-trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.

Secondary stem growth in trees and associated wood formation are significant both from biological and commercial perspectives. However, relatively little is known about the molecular control that governs their development. This is in part due to physical, resource and time limitations often associated with the study of secondary growth processes. A number of in vitro techniques have been used involving either plant part or whole plant system in both woody and non-woody plant species. However, questions about their applicability for the study of secondary stem growth processes, the recalcitrance of certain species and labor intensity are often prohibitive for medium to high throughput applications. Also, when looking at secondary stem development and wood formation the specific traits under investigation might only become measurable late in a tree's lifecycle after several years of growth. In addressing these challenges alternative in vivo protocols have been developed, named Induced Somatic Sector Analysis, which involve the creation of transgenic somatic tissue sectors directly in the plant's secondary stem. The aim of this protocol is to provide an efficient, easy and relatively fast means to create transgenic secondary plant tissue for gene and promoter functional characterization that can be utilized in a range of tree species. Results presented here show that transgenic secondary stem sectors can be created in all live tissues and cell types in secondary stems of a variety of tree species and that wood morphological traits as well as promoter expression patterns in secondary stems can be readily assessed facilitating medium to high throughput functional characterization.

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.

We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia). We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genomes. Maximum parsimony and Bayesian analyses, based on >7000 variable nucleotide positions, produced one fully resolved phylogenetic tree (35 supported nodes, 27 with 100% bootstrap support). Eucalyptus and its sister lineage Angophora+Corymbia show a deep divergence. Within Eucalyptus, three lineages are resolved: the 'eudesmid', 'symphyomyrt' and 'monocalypt' groups. Corymbia is paraphyletic with respect to Angophora. Gene content and order do not vary among eucalypt chloroplasts; length mutations, especially frame shifts, are uncommon in protein-coding genes. Some non-synonymous mutations are highly incongruent with the overall phylogenetic signal, notably in rbcL, and may be adaptive. Application of custom informatics pipelines (GYDLE Inc.) enabled direct chloroplast genome assembly, resolving each genome to finished-quality with no need for PCR gap-filling or contig order resolution. Analysis of whole chloroplast genomes resolved major eucalypt clades and revealed variable regions of the genome that will be useful in lower-level genetic studies (including phylogeography and geneflow)., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Large-scale functional analysis of genes and transgenes suspected to be involved in wood development in trees is hindered by long generation times, low transformation and regeneration efficiencies and difficulties with phenotypic assessment of traits, especially those that appear late in a tree's development. To avoid such obstacles many researchers have turned to model plants such as Arabidopsis thaliana (L.) Heynh., Zinnia elegans Jacq. and Nicotiana ssp., or have focused their attention on in vitro wood formation systems or in vivo approaches targeting primary meristems for transformation. Complementing such efforts, we report the use of Agrobacterium to introduce transgenes directly into cambial cells of glasshouse-grown trees in order to create transgenic somatic tissue sectors. These sectors are suitable for phenotypic evaluation and analysis of target gene function. In our experiments the wood formation zone containing the cambium of Eucalyptus, Populus and Pinus species of varying age was inoculated with Agrobacterium containing a CaMV 35S::GUS construct. Following an initial wound response, frequent and stable transformation was observed in the form of distinct GUS-staining patterns (sectors) in newly formed secondary tissues. Sector size and extent depended on the cell type transformed, the species and the length of time treated plants were allowed to grow (more than two years in some cases). Induced somatic sector analysis (ISSA) can now be efficiently used to study cell fate and gene function during secondary growth in stems of forest tree species.