Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

The biology of grafting and its applications in studying information exchange between plants

Grafting techniques have been used for centuries for trait improvement in agriculture and horticulture. In recent years, technical progress with the grafting of species previously thought to be recalcitrant to the formation of a graft union, and the discovery of new types of information exchange between grafted plants, have stirred renewed interest in the use of grafting as a research tool. In this Review, we describe our current understanding of the molecular and cellular processes involved in the establishment of successful grafts between plants of the same genotype (homografts) or different genotypes (heterografts). We also highlight recent progress with the elucidation of the mechanisms underlying the exchange of macromolecules (small RNAs, messenger RNAs and proteins) across graft junctions as well as the transfer of cell organelles and its role in horizontal gene and genome transfer. Finally, we discuss novel applications of grafting, including new opportunities for transgene-free genetic engineering, and the relevance of grafting in plant evolution.

Impacts of reproductive systems on grapevine genome and breeding

Diversified reproductive systems can be observed in the plant kingdom and applied in crop breeding; however, their impacts on crop genomic variation and breeding remain unclear. Grapevine (Vitis vinifera L.), a widely planted fruit tree, underwent a shift from dioecism to monoecism during domestication and involves crossing, self-pollination, and clonal propagation for its cultivation. In this study, we discover that the reproductive types, namely, crossing, selfing, and cloning, dramatically impact genomic landscapes and grapevine breeding based on comparative genomic and population genetics of wild grapevine and a complex pedigree of Pinot Noir. The impacts are widely divergent, which show interesting patterns of genomic purging and the Hill-Robertson interference. Selfing reduces genomic heterozygosity, while cloning increases it, resulting in a "double U-shaped" site frequency spectrum (SFS). Crossing and cloning conceal while selfing purges most deleterious and structural burdens. Moreover, the close leakage of large-effect deleterious and structural variations in repulsion phases maintains heterozygous genomic regions in 4.3% of the grapevine genome after successive selfing for nine generations. Our study provides new insights into the genetic basis of clonal propagation and genomic breeding of clonal crops by purging deleterious variants while integrating beneficial variants through various reproductive systems.

Response of Pedunculate Oak (Quercus robur L.) to Adverse Environmental Conditions in Genetic and Dendrochronological Studies

Pedunculate oak (Quercus robur L.) is widely distributed across Europe and serves critical ecological, economic, and recreational functions. Investigating its responses to stressors such as drought, extreme temperatures, pests, and pathogens provides valuable insights into its capacity to adapt to climate change. Genetic and dendrochronological studies offer complementary perspectives on this adaptability. Tree-ring analysis (dendrochronology) reveals how Q. robur has historically responded to environmental stressors, linking growth patterns to specific conditions such as drought or temperature extremes. By examining tree-ring width, density, and dynamics, researchers can identify periods of growth suppression or enhancement and predict forest responses to future climatic events. Genetic studies further complement this by uncovering adaptive genetic diversity and inheritance patterns. Identifying genetic markers associated with stress tolerance enables forest managers to prioritize the conservation of populations with higher adaptive potential. These insights can guide reforestation efforts and support the development of climate-resilient oak populations. By integrating genetic and dendrochronological data, researchers gain a holistic understanding of Q. robur's mechanisms of resilience. This knowledge is vital for adaptive forest management and sustainable planning in the face of environmental challenges, ultimately helping to ensure the long-term viability of oak populations and their ecosystems. The topics covered in this review are very broad. We tried to include the most relevant, important, and significant studies, but focused mainly on the relatively recent Eastern European studies because they include the most of the species' area. However, although more than 270 published works have been cited in this review, we have, of course, missed some published studies. We apologize in advance to authors of those relevant works that have not been cited.

Comparative transcriptome profiling reveals distinct regulatory responses of secondary defensive metabolism in Datura species (Solanaceae) under plant development and herbivory-mediated stress

Differential expression of genes is key to mediating developmental and stress-related plant responses. Here, we addressed the regulation of plant metabolic responses to biotic stress and the developmental variation of defense-related genes in four species of the genus Datura with variable patterns of metabolite accumulation and development. We combine transcriptome profiling with phylogenomic techniques to analyze gene expression and coexpression in plants subjected to damage by a specialist folivore insect. We found (1) common overall gene expression in species of similar chemical profiles, (2) species-specific responses of proteins involved in specialized metabolism, characterized by constant levels of gene expression coupled with transcriptional rearrangement, and (3) induction of transcriptional rearrangement of major terpene and tropane alkaloid genes upon herbivory. Our results indicate differential modulation of terpene and tropane metabolism linked to jasmonate signaling and specific transcription factors to regulate developmental variation and stress programs, and suggest plastic adaptive responses to cope with herbivory. The transcriptional profiles of specialized metabolism shown here reveal complex genetic control of plant metabolism and contribute to understanding the molecular basis of adaptations and the physiological variation of significant ecological traits.

Lifetime genealogical divergence within plants leads to epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae)

Epigenetic mosaicism is a possible source of within-plant phenotypic heterogeneity, yet its frequency and developmental origin remain unexplored. This study examines whether extant epigenetic heterogeneity within Lavandula latifolia (Lamiaceae) shrubs reflects recent epigenetic modifications experienced independently by different plant parts or, alternatively, it is the cumulative outcome of a steady lifetime process. Leaf samples from different architectural modules (branch tips) were collected from three L. latifolia plants and characterized epigenetically by global DNA cytosine methylation and methylation state of methylation-sensitive amplified fragment-length polymorphism (MS-AFLP) markers. Epigenetic characteristics of modules were then assembled with information on the branching history of plants. Methods borrowed from phylogenetic research were used to assess genealogical signal of extant epigenetic variation and reconstruct within-plant genealogical trajectory of epigenetic traits. Plants were epigenetically heterogeneous, as shown by differences among modules in global DNA methylation and variation in the methylation states of 6 to 8% of MS-AFLP markers. All epigenetic features exhibited significant genealogical signal within plants. Events of epigenetic divergence occurred throughout the lifespan of individuals and were subsequently propagated by branch divisions. Internal epigenetic diversification of L. latifolia individuals took place steadily during their development, a process which eventually led to persistent epigenetic mosaicism.

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

BACKGROUND

Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials.

RESULTS

Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.

CONCLUSION

Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.

Does variable epigenetic inheritance fuel plant evolution?

Epigenetic changes influence gene expression and contribute to the modulation of biological processes in response to the environment. Transgenerational epigenetic changes in gene expression have been described in many eukaryotes. However, plants appear to have a stronger propensity for inheriting novel epialleles. This mini-review discusses how plant traits, such as meristematic growth, totipotency, and incomplete epigenetic erasure in gametes promote epiallele inheritance. Additionally, we highlight how plant biology may be inherently tailored to reap the benefits of epigenetic metastability. Importantly, environmentally triggered small RNA expression and subsequent epigenetic changes may allow immobile plants to adapt themselves, and possibly their progeny, to thrive in local environments. The change of epigenetic states through the passage of generations has ramifications for evolution in the natural and agricultural world. In populations containing little genetic diversity, such as elite crop germplasm or habitually self-reproducing species, epigenetics may provide an important source of heritable phenotypic variation. Basic understanding of the processes that direct epigenetic shifts in the genome may allow for breeding or bioengineering for improved plant traits that do not require changes to DNA sequence.

Somatic Mutations and Genome Stability Maintenance in Clonal Coral Colonies

One challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17 to 22 branches from each of four Acropora hyacinthus colonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide in A. hyacinthus is on the same order of magnitude (10−7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Loss of heterozygosity variants outnumber gain of heterozygosity mutations ∼2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.

Somatic Mutation and Evolution in Plants

Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.

Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex

BACKGROUND

Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller's Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the Meselson effect and Muller's Ratchet. Dugesiidae planarians show outstanding regeneration capabilities, allowing them to naturally reproduce by fission, either strictly or combined with sex (facultative). Therefore, they are an ideal model to analyze the genetic footprint of fissiparous reproduction, both when it is alternated with sex and when it is the only mode of reproduction.

RESULTS

In the present study, we generate and analyze intraindividual cloned data of a nuclear and a mitochondrial gene of sexual, fissiparous and facultative wild populations of the species Dugesia subtentaculata. We find that most individuals, independently of their reproductive strategy, are mosaics. However, the intraindividual haplotype and nucleotide diversity of fissiparous and facultative individuals is significantly higher than in sexual individuals, with no signs of Muller's Ratchet. Finally, we also find that this high intraindividual genetic diversity of fissiparous and facultative individuals is composed by different combinations of ancestral and derived haplotypes of the species.

CONCLUSIONS

The intraindividual analyses of genetic diversity point out that fissiparous reproduction leaves a very special genetic footprint in individuals, characterized by mosaicism combined with the Meselson effect (named in the present study as the mosaic Meselson effect). Interestingly, the different intraindividual combinations of ancestral and derivate genetic diversity indicate that haplotypes generated during periods of fissiparous reproduction can be also transmitted to the progeny through sexual events, resulting in offspring showing a wide range of genetic diversity and putatively allowing purifying selection to act at both intraindividual and individual level. Further investigations, using Dugesia planarians as model organisms, would be of great value to delve into this new model of genetic evolution by the combination of fission and sex.

Inhibition of Satellite RNA Associated Cucumber Mosaic Virus Infection by Essential Oil of Micromeria croatica (Pers.) Schott

The present results dealing with the antiphytoviral activity of essential oil indicate that these plant metabolites can trigger a response to viral infection. The essential oil from Micromeria croatica and the main oil components β-caryophyllene and caryophyllene oxide were tested for antiphytoviral activity on plants infected with satellite RNA associated cucumber mosaic virus. Simultaneous inoculation of virus with essential oil or with the dominant components of oil, and the treatment of plants prior to virus inoculation, resulted in a reduction of virus infection in the local and systemic host plants. Treatment with essential oil changed the level of alternative oxidase gene expression in infected Arabidopsis plants indicating a connection between the essential oil treatment, aox gene expression and the development of viral infection.

Somatic Mutation Is a Function of Clone Size and Depth in Orbicella Reef-Building Corals

In modular organisms, the propagation of genetic variability within a clonal unit can alter the scale at which ecological and evolutionary processes operate. Genetic variation within an individual primarily arises through the accretion of somatic mutations over time, leading to genetic mosaicism. Here, we assess the prevalence of intraorganismal genetic variation and potential mechanisms influencing the degree of genetic mosaicism in the reef corals Orbicella franksi and Orbicella annularis. Colonies of both species, encompassing a range of coral sizes and depths, were sampled multiple times and genotyped at the same microsatellite loci to detect intraorganismal genetic variation. Genetic mosaicism was detected in 38% of corals evaluated, and mutation frequency was found to be positively related with clonal size and negatively associated with coral depth. We suggest that larger clones experience a greater number of somatic cell divisions and consequently have an elevated potential to accumulate mutations. Furthermore, corals at shallower depths may be exposed to abiotic conditions such as elevated thermal regimes, which promote increased mutation rates. The results highlight the pervasiveness of intraorganismal genetic variation in reef-building corals and emphasize potential mechanisms generating somatic mutations in modular organisms.

Plant somatic mutations in nature conferring insect and herbicide resistance

Because of the role of the meristem in plant growth and reproduction, somatic mutations in plants have long been suspected of conferring herbivore and pathogen resistance on individual plants and, in the case of trees, individual branches within single plants. A few instances of resistance to phytophagous insects owing to somatic mutations have been reported in the literature. More recently, a striking example has demonstrated how somatic mutations confer resistance to an herbicide on an invasive plant, Hydrilla verticillata. The array of new methods for manipulating genomes (e.g., gene-editing) plus existing examples of somatic mutation-associated resistance suggest that such mutations might be useful in silviculture, agriculture, and horticulture. Answering several general questions about somatic mutations in plants would facilitate such applications: Why are so few examples reported? Do other cases exist but go undetected for want of adequate attention or methods? Under what circumstances do somatic mutations enter gametophytes? © 2018 Society of Chemical Industry.

Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals

Plants have developed complex defense mechanisms to protect themselves against pathogens. A wide-host-range fungus, Austropuccinia psidii, which has caused severe damage to ecosystems and plantations worldwide, is a major threat to Australian ecosystems dominated by members of the family Myrtaceae. In particular, the east coast wetland foundation tree species Melaleuca quinquenervia, appears to be variably susceptible to this pathogen. Understanding the molecular basis of host resistance would enable better management of this rust disease. We identified resistant and susceptible individuals of M. quinquenervia and explored their differential gene expression in order to discover the molecular basis of resistance against A. psidii. Rust screening of germplasm showed a varying degree of response, with fully resistant to highly susceptible individuals. We used transcriptome profiling in samples collected before and at 5 days postinoculation (dpi). Differential gene expression analysis showed that numerous defense-related genes were induced in susceptible plants at 5 dpi. Mapping reads against the A. psidii genome showed that only susceptible plants contained fungal-derived transcripts. Resistant plants exhibited an overexpression of candidate A. psidii resistance-related genes such as receptor-like kinases, nucleotide-binding site leucine-rich repeat proteins, glutathione S-transferases, WRKY transcriptional regulators, and pathogenesis-related proteins. We identified large differences in the expression of defense-related genes among resistant individuals.

Within-plant variation in seed size and inflorescence fecundity is associated with epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae)

BACKGROUND AND AIMS

Sub-individual variation in traits of homologous structures has multiple ecological consequences for individuals and populations. Assessing the evolutionary significance of such effects requires an improved knowledge of the mechanisms underlying within-plant phenotypic heterogeneity. The hypothesis that continuous within-plant variation in some phenotypic traits can be associated with epigenetic mosaicism was examined.

METHODS

Fifteen individuals of the long-lived, evergreen Mediterranean shrub Lavandula latifolia were studied. Five widely spaced 'modules', each consisting of a single inflorescence plus all its subtending basal leaves, were collected from each shrub. Genomic DNA was extracted from leaf samples and genome-wide cytosine methylation determined by reversed phase high-performance liquid chromatography (HPLC) with spectrofluorimetric detection. The number and mean mass of seeds produced were determined for each inflorescence. An assessment was made of whether (1) leaves from different modules in the same plant differed significantly in global DNA cytosine methylation, and (2) mosaicism in cytosine methylation contributed to explain variation across modules in number and size of seeds.

KEY RESULTS

Leaves from different modules in the same plant differed in global DNA cytosine methylation. The magnitude of epigenetic mosaicism was substantial, as the variance in DNA methylation among modules of the same shrub was greater than the variance between individuals. Number and mean mass of seeds produced by individual inflorescences varied within plants and were quadratically related to cytosine methylation of subtending leaves, with an optimum at an intermediate methylation level (approx. 25 %).

CONCLUSIONS

The results support a causal link between global cytosine methylation of leaves in a module and the size and numbers of seeds produced by the associated inflorescence. It is proposed that variation in global DNA methylation within L. latifolia shrubs may result from the concerted action of plant sectoriality and differential exposure of different plant parts to some environmental factor(s) with a capacity to induce durable epigenetic changes.

Intraspecific Variation in Nutritional Composition Affects the Leaf Age Preferences of a Mammalian Herbivore

Ecologists have long been interested in how the nutritional composition of leaves changes as they age, and whether this affects herbivore feeding preferences. As a consequence, the literature abounds with reports that younger leaves contain higher concentrations of nitrogen and plant secondary metabolites (PSMs) than do older leaves. Most of these studies, however, base their conclusions on average values that often mean little to herbivores. We examined this issue in the well-studied marsupial-eucalypt system, using Eucalyptus melliodora and captive common brushtail possums (Trichosurus vulpecula) offered branches from individual trees containing both young and mature leaves. Like many plants, the concentrations of N and PSMs differed among individual E. melliodora. Although young leaves were, on average, "better defended" by the PSM sideroxylonal than were mature leaves, some trees produced leaves that were relatively undefended at both ages. In response, possums chose different proportions of young and mature leaves depending on the chemistry of the individual tree. Possums did not always prefer leaves with lower concentrations of sideroxylonal (mature leaves) or those with higher concentrations of available N (young leaves). Instead, the sideroxylonal concentration of young leaves dictated their choice: possums preferred young leaves with low sideroxylonal concentrations, but not with high concentrations. By skewing their feeding toward trees producing young leaves with low concentrations of PSMs, possums may influence plant fitness. Researchers will detect these potentially important interactions only if they are aware that measuring variation among plants discloses more information than do average relationships.

Low number of fixed somatic mutations in a long-lived oak tree

Because plants do not possess a defined germline, deleterious somatic mutations can be passed to gametes, and a large number of cell divisions separating zygote from gamete formation may lead to many mutations in long-lived plants. We sequenced the genome of two terminal branches of a 234-year-old oak tree and found several fixed somatic single-nucleotide variants whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems in trees are robustly protected from the accumulation of mutations.

Plant chimeras: The good, the bad, and the 'Bizzaria'

Chimeras - organisms that are composed of cells of more than one genotype - captured the human imagination long before they were formally described and used in the laboratory. These organisms owe their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (Citrus medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the 'Bizzaria'. Initially, the 'Bizzaria' was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the 'Bizzaria', along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.

Patterns of Stem Cell Divisions Contribute to Plant Longevity

The lifespan of plants ranges from a few weeks in annuals to thousands of years in trees. It is hard to explain such extreme longevity considering that DNA replication errors inevitably cause mutations. Without purging through meiotic recombination, the accumulation of somatic mutations will eventually result in mutational meltdown, a phenomenon known as Muller's ratchet. Nevertheless, the lifespan of trees is limited more often by incidental disease or structural damage than by genetic aging. The key determinants of tree architecture are the axillary meristems, which form in the axils of leaves and grow out to form branches. The number of branches is low in annual plants, but in perennial plants iterative branching can result in thousands of terminal branches. Here, we use stem cell ablation and quantitative cell-lineage analysis to show that axillary meristems are set aside early, analogous to the metazoan germline. While neighboring cells divide vigorously, axillary meristem precursors maintain a quiescent state, with only 7-9 cell divisions occurring between the apical and axillary meristem. During iterative branching, the number of branches increases exponentially, while the number of cell divisions increases linearly. Moreover, computational modeling shows that stem cell arrangement and positioning of axillary meristems distribute somatic mutations around the main shoot, preventing their fixation and maximizing genetic heterogeneity. These features slow down Muller's ratchet and thereby extend lifespan.

Transcriptome sequencing of two phenotypic mosaic Eucalyptus trees reveals large scale transcriptome re-modelling

Phenotypic mosaic trees offer an ideal system for studying differential gene expression. We have investigated two mosaic eucalypt trees from two closely related species (Eucalyptus melliodora and E. sideroxylon), which each support two types of leaves: one part of the canopy is resistant to insect herbivory and the remaining leaves are susceptible. Driving this ecological distinction are differences in plant secondary metabolites. We used these phenotypic mosaics to investigate genome wide patterns of foliar gene expression with the aim of identifying patterns of differential gene expression and the somatic mutation(s) that lead to this phenotypic mosaicism. We sequenced the mRNA pool from leaves of the resistant and susceptible ecotypes from both mosaic eucalypts using the Illumina HiSeq 2000 platform. We found large differences in pathway regulation and gene expression between the ecotypes of each mosaic. The expression of the genes in the MVA and MEP pathways is reflected by variation in leaf chemistry, however this is not the case for the terpene synthases. Apart from the terpene biosynthetic pathway, there are several other metabolic pathways that are differentially regulated between the two ecotypes, suggesting there is much more phenotypic diversity than has been described. Despite the close relationship between the two species, they show large differences in the global patterns of gene and pathway regulation.

Fungal Infection Increases the Rate of Somatic Mutation in Scots Pine (Pinus sylvestris L.)

Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8×10(-3) mutations per locus), as compared to the controls (2.0×10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (χ(2) = 12.9883, df = 1, P = 0.0003134).

Population divergence in the ontogenetic trajectories of foliar terpenes of a Eucalyptus species

BACKGROUND AND AIMS

The development of plant secondary metabolites during early life stages can have significant ecological and evolutionary implications for plant-herbivore interactions. Foliar terpenes influence a broad range of ecological interactions, including plant defence, and their expression may be influenced by ontogenetic and genetic factors. This study investigates the role of these factors in the expression of foliar terpene compounds in Eucalyptus globulus seedlings.

METHODS

Seedlings were sourced from ten families each from three genetically distinct populations, representing relatively high and low chemical resistance to mammalian herbivory. Cotyledon-stage seedlings and consecutive leaf pairs of true leaves were harvested separately across an 8-month period, and analysed for eight monoterpene compounds and six sesquiterpene compounds.

KEY RESULTS

Foliar terpenes showed a series of dynamic changes with ontogenetic trajectories differing between populations and families, as well as between and within the two major terpene classes. Sesquiterpenes changed rapidly through ontogeny and expressed opposing trajectories between compounds, but showed consistency in pattern between populations. Conversely, changed expression in monoterpene trajectories was population- and compound-specific.

CONCLUSIONS

The results suggest that adaptive opportunities exist for changing levels of terpene content through ontogeny, and evolution may exploit the ontogenetic patterns of change in these compounds to create a diverse ontogenetic chemical mosaic with which to defend the plant. It is hypothesized that the observed genetically based patterns in terpene ontogenetic trajectories reflect multiple changes in the regulation of genes throughout different terpene biosynthetic pathways.

Uncovering the defence responses of Eucalyptus to pests and pathogens in the genomics age

Long-lived tree species are subject to attack by various pests and pathogens during their lifetime. This problem is exacerbated by climate change, which may increase the host range for pathogens and extend the period of infestation by pests. Plant defences may involve preformed barriers or induced resistance mechanisms based on recognition of the invader, complex signalling cascades, hormone signalling, activation of transcription factors and production of pathogenesis-related (PR) proteins with direct antimicrobial or anti-insect activity. Trees have evolved some unique defence mechanisms compared with well-studied model plants, which are mostly herbaceous annuals. The genome sequence of Eucalyptus grandis W. Hill ex Maiden has recently become available and provides a resource to extend our understanding of defence in large woody perennials. This review synthesizes existing knowledge of defence mechanisms in model plants and tree species and features mechanisms that may be important for defence in Eucalyptus, such as anatomical variants and the role of chemicals and proteins. Based on the E. grandis genome sequence, we have identified putative PR proteins based on sequence identity to the previously described plant PR proteins. Putative orthologues for PR-1, PR-2, PR-4, PR-5, PR-6, PR-7, PR-8, PR-9, PR-10, PR-12, PR-14, PR-15 and PR-17 have been identified and compared with their orthologues in Populus trichocarpa Torr. & A. Gray ex Hook and Arabidopsis thaliana (L.) Heynh. The survey of PR genes in Eucalyptus provides a first step in identifying defence gene targets that may be employed for protection of the species in future. Genomic resources available for Eucalyptus are discussed and approaches for improving resistance in these hardwood trees, earmarked as a bioenergy source in future, are considered.

Spatial genetic structure reflects extensive clonality, low genotypic diversity and habitat fragmentation in Grevillea renwickiana (Proteaceae), a rare, sterile shrub from south-eastern Australia

BACKGROUND AND AIMS

The association of clonality, polyploidy and reduced fecundity has been identified as an extinction risk for clonal plants. Compromised sexual reproduction limits both their ability to adapt to new conditions and their capacity to disperse to more favourable environments. Grevillea renwickiana is a prostrate, putatively sterile shrub reliant on asexual reproduction. Dispersal is most likely limited by the rate of clonal expansion via rhizomes. The nine localized populations constituting this species provide an opportunity to examine the extent of clonality and spatial genotypic diversity to evaluate its evolutionary prospects.

METHODS

Ten microsatellite loci were used to compare genetic and genotypic diversity across all sites with more intensive sampling at four locations (n = 185). The spatial distribution of genotypes and chloroplast DNA haplotypes based on the trnQ-rps16 intergenic spacer region were compared. Chromosome counts provided a basis for examining genetic profiles inconsistent with diploidy.

KEY RESULTS

Microsatellite analysis identified 46 multilocus genotypes (MLGs) in eight multilocus clonal lineages (MLLs). MLLs are not shared among sites, with two exceptions. Spatial autocorrelation was significant to 1·6 km. Genotypic richness ranged from 0 to 0·33. Somatic mutation is likely to contribute to minor variation between MLGs within clonal lineages. The eight chloroplast haplotypes identified were correlated with eight MLLs defined by ordination and generally restricted to single populations. Triploidy is the most likely reason for tri-allelic patterns.

CONCLUSIONS

Grevillea renwickiana comprises few genetic individuals. Sterility has most likely been induced by triploidy. Extensive lateral suckering in long-lived sterile clones facilitates the accumulation of somatic mutations, which contribute to the measured genetic diversity. Genetic conservation value may not be a function of population size. Despite facing evolutionary stagnation, sterile clonal species can play a vital role in mitigating ecological instability as floras respond to rapid environmental change.

Tree immunity: growing old without antibodies

Perennial plants need to cope with changing environments and pathogens over their lifespan. Infections are compartmentalised by localised physiological responses, and multiple apical meristems enable repair and regrowth, but genes are another crucial component in the perception and response to pathogens. In this opinion article we suggest that the mechanism for dynamic pathogen-specific recognition in long-lived plants could be explained by extending our current understanding of plant defence genes. We propose that, in addition to physiological responses, tree defence uses a three-pronged genomic approach involving: (i) gene numbers, (ii) genomic architecture, and (iii) mutation loads accumulated over long lifespans.

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum)

Background

Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still incomplete and transcriptomic information is scarce. In addition, functional genomics investigations in this species are severely hampered by a lack of affordable tools for genome-wide gene expression studies.

Results

Here, we report the results of Thellungiella de novo transcriptome assembly and annotation based on 454 pyrosequencing and development and validation of a T. salsuginea microarray. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from samples covering different tissues and abiotic stress conditions. Both libraries yielded partially unique sequences, indicating their necessity to obtain comprehensive transcriptome coverage. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. These unigenes were compared to all available Thellungiella genome sequence information. In addition, the groups of Late Embryogenesis Abundant (LEA) proteins, Mitogen Activated Protein (MAP) kinases and protein phosphatases were annotated in detail. We also predicted the target genes for 384 putative miRNAs. From the sequence information, we constructed a 44 k Agilent oligonucleotide microarray. Comparison of same-species and cross-species hybridization results showed superior performance of the newly designed array for T. salsuginea samples. The developed microarrays were used to investigate transcriptional responses of T. salsuginea and Arabidopsis during cold acclimation using the MapMan software.

Conclusions

This study provides the first comprehensive transcriptome information for the extremophile Arabidopsis relative T. salsuginea. The data constitute a more than three-fold increase in the number of publicly available unigene sequences and will greatly facilitate genome annotation. In addition, we have designed and validated the first genome-wide microarray for T. salsuginea, which will be commercially available. Together with the publicly available MapMan software this will become an important tool for functional genomics of plant stress tolerance.