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

BACKGROUND Long-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a single canopy. These "mosaic" trees support foliage with distinct chemotypes which are differentially favoured by insect and vertebrate herbivores, resulting in susceptible and resistant branches within a single canopy. These mosaic trees provide a unique opportunity to explore the biosynthesis and genetic regulation of chemical defences in the foliage. The biosynthesis of the principal defence compounds, terpenoid-dominated essential oils, is well understood. However, the regulation of the genes involved and thus the control of phenotypic variation within a single tree canopy remains a mystery. RESULTS We sequenced the transcriptomes of the leaves of the two different chemotypes of a chemically mosaic Eucalyptus melliodora tree using 454 pyrosequencing technology. We used gene set enrichment analysis to identify differentially expressed transcripts and found the proportion of differentially expressed genes in the resistant and susceptible foliage similar to the transcript difference between functionally distinct tissues of the same organism, for example roots and leaves. We also investigated sequence differences in the form of single nucleotide polymorphisms and found 10 nucleotides that were different between the two branches. These are likely true SNPs and several occur in regulatory genes. CONCLUSION We found three lines of evidence that suggest changes to a 'master switch' can result in large scale phenotypic changes: 1. We found differential expression of terpene biosynthetic genes between the two chemotypes that could contribute to chemical variation within this plant. 2. We identified many genes that are differentially expressed between the two chemotypes, including some unique genes in each branch. These genes are involved in a variety of processes within the plant and many could contribute to the regulation of secondary metabolism, thus contributing to the chemical variation. 3. We identified 10 SNPs, some of which occur in regulatory genes that could influence secondary metabolism and thus contribute to chemical variation. Whilst this research is inherently limited by sample size, the patterns we describe could be indicative of other plant genetic mosaics.This work was supported by a Discovery grant from the Australian Research Council to WJF (DP0877063)

Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea

Unlike agricultural crops, most forest species have not had millennia of improvement through phenotypic selection, but can contribute energy and material resources and possibly help alleviate climate change. Yield gains similar to those achieved in agricultural crops over millennia could be made in forestry species with the use of genomic methods in a much shorter time frame. Here we compare various methods of genomic prediction for eight traits related to foliar terpene yield in Eucalyptus polybractea, a tree grown predominantly for the production of Eucalyptus oil. The genomic markers used in this study are derived from shallow whole genome sequencing of a population of 480 trees. We compare the traditional pedigree-based additive best linear unbiased predictors (ABLUP), genomic BLUP (GBLUP), BayesB genomic prediction model, and a form of GBLUP based on weighting markers according to their influence on traits (BLUP|GA). Predictive ability is assessed under varying marker densities of 10,000, 100,000 and 500,000 SNPs. Our results show that BayesB and BLUP|GA perform best across the eight traits. Predictive ability was higher for individual terpene traits, such as foliar α-pinene and 1,8-cineole concentration (0.59 and 0.73, respectively), than aggregate traits such as total foliar oil concentration (0.38). This is likely a function of the trait architecture and markers used. BLUP|GA was the best model for the two biomass related traits, height and 1 year change in height (0.25 and 0.19, respectively). Predictive ability increased with marker density for most traits, but with diminishing returns. The results of this study are a solid foundation for yield improvement of essential oil producing eucalypts. New markets such as biopolymers and terpene-derived biofuels could benefit from rapid yield increases in undomesticated oil-producing species.Funding for this project was provided by the Australian Research Council Linkage Program (LP110100184) toWJF, the Rural Industries Research and Development Corporation (RIRDC), Australia. Support was also provided by the Center for BioEnergy Innovation (CBI), a U.S DOE Bioenergy Research Center supported by the DOE office of science

High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus

Terpenoid based essential oils are economically important commodities, yet beyond their biosynthetic pathways, little is known about the genetic architecture of terpene oil yield from plants. Transport, storage, evaporative loss, transcriptional regulation and precursor competition may be important contributors to this complex trait. Here, we associate 2.39 M single nucleotide polymorphisms derived from shallow whole genome sequencing of 468 Eucalyptus polybractea individuals with 12 traits related to the overall terpene yield, eight direct measures of terpene concentration and four biomass‐related traits. Our results show that in addition to terpene biosynthesis, development of secretory cavities where terpenes are both synthesised and stored, and transport of terpenes were important components of terpene yield. For sesquiterpene concentrations, the availability of precursors in the cytosol was important. Candidate terpene synthase genes for the production of 1,8‐cineole and α‐pinene, and β‐pinene, (which made up more than 80% of the total terpenes) were functionally characterised as a 1,8‐cineole synthase and a β / α‐pinene synthase. Our results provide novel insights of the genomic architecture of terpene yield and we provide candidate genes for breeding or engineering of crops for biofuels or the production of industrially valuable terpenes

Genomic analyses suggest strong population connectivity over large spatial scales of the commercially important baitworm, Australonuphis teres (Onuphidae)

Barriers to dispersal can disrupt gene flow between populations, resulting in genetically distinct populations. Although many marine animals have potential for long-distance dispersal via a planktonic stage, gene flow among populations separated by large geographic distances is not always evident. Polychaetes are ecologically important and have been used as biological surrogates for marine biodiversity. Some polychaete species are used as bait for recreational fisheries, with this demand supporting commercial fisheries for polychaetes to service the retail bait market. However, despite their ecological and economic importance, very little is known about the life history or population dynamics of polychaetes, and few studies have used genetic or genomic approaches to understand polychaete population connectivity. Here, we investigate the population structure of one commonly collected beachworm species used for bait on the eastern coast of Australia, namely, Australonuphis teres, by using genome-wide single-nucleotide polymorphism data. We sampled A. teres from hierarchical nested spatial scales along 900 km of the coast in New South Wales. We identified six genetic groups, but there was no clear geographic pattern of distribution. Our results suggest that there is considerable gene flow among the sampled populations. These high-resolution genomic data support the findings of previous studies, and we infer that oceanographic processes promote genetic exchange among polychaete populations in south-eastern Australia.This work was funded by the New South Wales Recreational Fishing Saltwater Trust, Project DPIS011 (to RCC). C. I. Fraser was supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand (UOO1803)

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

Four terpene synthases contribute to the generation of chemotypes in tea tree (Melaleuca alternifolia)

BACKGROUND: Terpene rich leaves are a characteristic of Myrtaceae. There is significant qualitative variation in the terpene profile of plants within a single species, which is observable as "chemotypes". Understanding the molecular basis of chemotypic variation will help explain how such variation is maintained in natural populations as well as allowing focussed breeding for those terpenes sought by industry. The leaves of the medicinal tea tree, Melaleuca alternifolia, are used to produce terpinen-4-ol rich tea tree oil, but there are six naturally occurring chemotypes; three cardinal chemotypes (dominated by terpinen-4-ol, terpinolene and 1,8-cineole, respectively) and three intermediates. It has been predicted that three distinct terpene synthases could be responsible for the maintenance of chemotypic variation in this species. RESULTS: We isolated and characterised the most abundant terpene synthases (TPSs) from the three cardinal chemotypes of M. alternifolia. Functional characterisation of these enzymes shows that they produce the dominant compounds in the foliar terpene profile of all six chemotypes. Using RNA-Seq, we investigated the expression of these and 24 additional putative terpene synthases in young leaves of all six chemotypes of M. alternifolia. CONCLUSIONS: Despite contributing to the variation patterns observed, variation in gene expression of the three TPS genes is not enough to explain all variation for the maintenance of chemotypes. Other candidate terpene synthases as well as other levels of regulation must also be involved. The results of this study provide novel insights into the complexity of terpene biosynthesis in natural populations of a non-model organism.The research was funded by the Australian Research Council (ARC) Discovery Program (DP14101755), the Australian Government Rural Industries Research and Development Corporation (RIRDC) and the Australia Tea Tree Industry Association (ATTIA). Grants from the Go8-DAAD Research Scheme and a Humboldt Research Award from the Alexander von Humboldt Foundation to WJF underpinned this collaborative research. Each of the funding bodies granted the funds based on a research proposal. They had no influence over the experimental design, data analysis or interpretation, or writing the manuscript

Mosaic eucalypts : chemical variation and differential gene expression within a eucalyptus melliodora and a eucalyptus sideroxylon tree

Mosaic Eucalyptus trees provide unparalleled natural experiments to understand how plants control the synthesis of chemical defences against herbivorous insects and mammals. In natural eucalypt mosaics, different branches on a single tree show vastly different leaf chemical profiles (chemotypes) and thus vastly different responses to herbivores (resistant or susceptible). I have been working with two such mosaic eucalypts (E. melliodora and E. sideroxylon), where the leaves of the resistant chemotype have a different terpene profile compared with the leaves of the susceptible ecotype. Chemotypic variation of terpenes is under strong genetic control and the terpene biosynthetic pathway is well described, however little is known about the genetic control over genes within this pathway, especially the terpene synthase gene family (the last step in the pathway). The overall aim of my thesis is to explore the genetic variation, particularly in the terpene biosynthetic pathway that accompanies the chemical variation in these two mosaics and propose a mechanism for the development of mosaic eucalypts. The key outcomes of my thesis were: 1. Despite being found in a number of recognisable species of Myrtaceae, high foliar concentrations of the terpene 1,8 cineole is unlikely to have been present in the common ancestor to this family. 2. There is a chemotype associated with the leaves resistant to herbivory that is distinct to that of the leaves susceptible to herbivory. These chemotypes differ in monoterpenes, sesquiterpenes and formylated phloroglucinol compounds (FPCs). 3. The number of genes differentially regulated between the leaves of the two branches of the E. melliodora mosaic is very similar to the number of genes differentially regulated between functionally different tissues in the same organism (e.g. roots and flowers). 4. There are biosynthetic pathways with no genes differentially regulated between the leaves of the two branches, however we found that the entire pathway is differentially regulated. 5. There are many terpene synthases expressed in the leaves of the mosaics that produce the same terpenes, suggesting there may be another role for terpenes in eucalypts besides defence within the leaf. In summary, I have investigated the chemical differences between resistant and susceptible leaves within the mosaics, and found many genetic differences that could contribute to development and maintenance of mosaicism. The conclusions from this work can be applied more broadly to terpene chemotypes in all plants, which many industries rely heavily upon

Vitamin D and COVID-19: state of the art

Introdução: recentemente observou-se níveis, significativamente, menores de 25(OH)D em pacientes com PCR positivo para SARS-CoV-2 em comparação com pacientes negativos. Um estudo sobre envelhecimento reiterou que durante a atual pandemia, a suplementação adequada de vitamina D, especialmente, em pessoas mais velhas, pode ser benéfica para populações vulneráveis. Objetivo: apresentar e discutir os aspectos envolvidos na relação entre a vitamina D e a COVID-19. Material e Método: trata-se de um estudo de revisão do estado da arte no qual buscou-se nas bases de dados Medline, Lilacs e Scielo, os estudos sobre a temática a partir de 2019, em língua portuguesa, inglesa e espanhola, utilizando-se os descritores: vitamina D; imunidade; deficiência vitamínica; pandemia. Desenvolvimento: estudos observacionais mostraram uma ligação consistente entre deficiência de vitamina D e suscetibilidade às infecções respiratórias agudas. Em relação ao COVID-19, um dos estudos mostrou que a chance de infecção com o vírus, é três vezes maior para indivíduos com deficiência de vitamina D e a probabilidade de desenvolver quadro grave nesses pacientes, é cerca de cinco vezes maior do que em outros. Considerações finais: No contexto da COVID-19, alguns estudos mostram benefícios em relação a níveis adequados ou suplementação desse hormônio na melhora ou impedimento da gravidade da doença, sendo um tratamento com potencial exitoso no que se refere ao Coronavírus.Introduction: recently, significantly lower levels of 25(OH)D were observed in patients with positive PCR for SARS-CoV-2 compared to negative patients. An aging study reiterated that during the current pandemic, adequate vitamin D supplementation, especially in older people, may be beneficial for vulnerable populations. Objective: to present and discuss the aspects involved in the relationship between vitamin D and COVID-19. Material and Method: this is a state- of-the-art review study in which Medline, Lilacs and Scielo databases were searched for studies on the subject from 2019, in Portuguese, English and Spanish, using up the descriptors: vitamin D; immunity; vitamin deficiency; pandemic. Development: Observational studies have shown a consistent link between vitamin D deficiency and susceptibility to acute respiratory infections. Regarding COVID-19, one of the studies showed that the chance of infection with the virus is three times greater for individuals with vitamin D deficiency and the probability of developing a serious condition in these patients is about five times greater than in others. Final considerations: In the context of COVID-19, some of the studies show benefits in relation to adequate levels or supplementation of this hormone in improving or preventing the severity of the disease, being a potentially successful treatment with regard to the Coronavirus

The evolution of foliar terpene diversity in Myrtaceae

Plant terpenes play many roles in natural systems, from altering plant-animal interactions, to altering the local abiotic environment. Additionally, many industries depend on terpenes. For example, commercially used essential oils, including tea tree oi