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Austropuccinia psidii is the causal pathogen of myrtle rust disease of Myrtaceae. To gain understanding of the initial infection process, gene expression in germinating A. psidii urediniospores and in Leptospermum scoparium -inoculated leaves were investigated via analyses of RNA sequencing samples taken 24 and 48 h postinoculation (hpi). Principal component analyses of transformed transcript count data revealed differential gene expression between the uninoculated L. scoparium control plants that correlated with the three plant leaf resistance phenotypes (immunity, hypersensitive response, and susceptibility). Gene expression in the immune resistant plants did not significantly change in response to fungal inoculation, whereas susceptible plants showed differential expression of genes in response to fungal challenge. A putative disease resistance gene, jg24539.t1, was identified in the L. scoparium hypersensitive response phenotype family. Expression of this gene may be associated with the phenotype and could be important for further understanding the plant hypersensitive response to A. psidii challenge. Differential expression of pathogen genes was found between samples taken 24 and 48 hpi, but there were no significant differences in pathogen gene expression that were associated with the three different plant leaf resistance phenotypes. There was a significant decrease in the abundance of fungal transcripts encoding three putative effectors and a putative carbohydrate-active enzyme between 24 and 48 hpi, suggesting that the encoded proteins are important during the initial phase of infection. These transcripts, or their translated proteins, may be potential targets to impede the early phases of fungal infection by this wide-host-range obligate biotrophic basidiomycete., Competing Interests: The author(s) declare no conflict of interest.

Myrtaceae family includes many species with taxonomic challenges, making it one of the most complex families to identify. This study used DNA barcoding to find molecular markers for species authentication based on the Myrtaceae family's chemical composition and genetic diversity. Essential oils and genetic material were extracted from the leaves of six different species: Eugenia uniflora, E. patrisii, Myrcia splendens, Psidium guajava, P. guineense, and Psidium sp. The samples were analyzed based on compound classes and grouped into two categories. Group I included samples with high amounts of oxygenated sesquiterpenes (3.69-76.05 %) and fatty acid derivatives (0.04-43.59 %), such as E. uniflora, Myrcia splendens, and E. patrisii. Group II included samples P. guajava, P. guineense, and Psidium sp., which had a significant content of monoterpene hydrocarbons (0.69-72.35 %), oxygenated sesquiterpenes (8.06-68.1 %), phenylpropanoids (0.45-22.59 %), and sesquiterpene hydrocarbons (0.27-21.84 %). The PsbA-trnH gene sequences had a high genetic variability, allowing the species to be distinguished. A phylogenetic analysis showed two main clusters with high Bootstrap values corresponding to the subtribes Eugeniineae, Myrciinae, and Pimentinae. The results suggest a weak correlation between genetic and chemical data in these Myrtaceae species., (© 2024 Wiley-VHCA AG, Zurich, Switzerland.)

Background: Rose myrtle (Rhodomyrtus tomentosa (Ait.) Hassk), is an evergreen shrub species belonging to the family Myrtaceae, which is enriched with bioactive volatiles (α-pinene and β-caryophyllene) with medicinal and industrial applications. However, the mechanism underlying the volatile accumulation in the rose myrtle is still unclear., Results: Here, we present a chromosome-level genomic assembly of rose myrtle (genome size = 466 Mb, scaffold N50 = 43.7 Mb) with 35,554 protein-coding genes predicted. Through comparative genomic analysis, we found that gene expansion and duplication had a potential contribution to the accumulation of volatile substances. We proposed that the action of positive selection was significantly involved in volatile accumulation. We identified 43 TPS genes in R. tomentosa. Further transcriptomic and TPS gene family analyses demonstrated that the distinct gene subgroups of TPS may contribute greatly to the biosynthesis and accumulation of different volatiles in the Myrtle family of shrubs and trees. The results suggested that the diversity of TPS-a subgroups led to the accumulation of special sesquiterpenes in different plants of the Myrtaceae family., Conclusions: The high quality chromosome-level rose myrtle genome and the comparative analysis of TPS gene family open new avenues for obtaining a higher commercial value of essential oils in medical plants., (© 2024. The Author(s).)

l-Ascorbic acid (AsA, vitamin C) is a pivotal dietary nutrient with multifaceted importance in living organisms. In plants, the Smirnoff-Wheeler pathway is the primary route for AsA biosynthesis, and understanding the mechanistic details behind its component enzymes has implications for plant biology, nutritional science, and biotechnology. As part of an initiative to determine the structures of all six core enzymes of the pathway, the present study focuses on three of them in the model species Myrciaria dubia (camu-camu): GDP-d-mannose 3',5'-epimerase (GME), l-galactose dehydrogenase (l-GalDH), and l-galactono-1,4-lactone dehydrogenase (l-GalLDH). We provide insights into substrate and cofactor binding and the conformational changes they induce. The MdGME structure reveals a distorted substrate in the active site, pertinent to the catalytic mechanism. Mdl-GalDH shows that the way in which NAD+ association affects loop structure over the active site is not conserved when compared with its homologue in spinach. Finally, the structure of Mdl-GalLDH is described for the first time. This allows for the rationalization of previously identified residues which play important roles in the active site or in the formation of the covalent bond with FAD. In conclusion, this study enhances our understanding of AsA biosynthesis in plants, and the information provided should prove useful for biotechnological applications., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Premise: Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification., Methods: Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling., Results: The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented., Conclusions: We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported., (© 2024 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Austropuccinia psidii , commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis , a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 ( RTP1 ), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time., Competing Interests: The author(s) declare no conflict of interest.

Tropical fruit tree species constitute a yet untapped supply of outstanding diversity of taste and nutritional value, barely developed from the genetics standpoint, with scarce or no genomic resources to tackle the challenges arising in modern breeding practice. We generated a de novo genome assembly of the Psidium guajava, the super fruit "apple of the tropics", and successfully transferred 14,268 SNP probesets from Eucalyptus to Psidium at the nucleotide level, to detect genomic loci linked to resistance to the root knot nematode (RKN) Meloidogyne enterolobii derived from the wild relative P. guineense. Significantly associated loci with resistance across alternative analytical frameworks, were detected at two SNPs on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome to determine the order and orientation of the contigs. The P. guineense-derived resistance response to RKN and disease onset is conceivably triggered by mineral nutrients and phytohormone homeostasis or signaling with the involvement of the miRNA pathway. Hotspots of mapped resistance quantitative trait loci and functional annotation in the same genomic region of Eucalyptus provide further indirect support to our results, highlighting the evolutionary conservation of genomes across genera of Myrtaceae in the adaptation to pathogens. Marker assisted introgression of the resistance loci mapped should accelerate the development of improved guava cultivars and hybrid rootstocks., Competing Interests: The authors have declared that no competing interests exist.

In this study, the mitigative effect of Rhodomyrtus tomentosa (Ait.) Hassk fruit extract rich in phenolic compounds (RTE) on high fat diet (HFD)-induced intestinal barrier dysfunction of mice and the underlying mechanism were explored. The results revealed that RTE supplementation obviously improved gut microbiota dysbiosis induced by HFD, which was evidenced by elevated alpha diversity, suppressed Firmicutes/Bacteroidetes ratio, enriched short-chain fatty acid-producing bacteria (Odoribacter, Parabacteroides, Blautia and Akkermansia), and depleted harmful bacteria (Helicobacter, norank_f_ Desulfovibrionaceae and Mucispirillum). RTE intervention mitigated intestinal barrier dysfunction and inflammation by elevating tight junction proteins expression levels and decreasing proinflammatory cytokines levels. Furthermore, RTE administration inhibited the HFD-induced trigger of the lipopolysaccharide-toll-like receptor 4-nuclear factor kappa-B (LPS-TLR4-NF-κB) pathway in colonic tissue. Therefore, RTE supplementation may be an effective way to protect the intestinal tract in HFD-induced obese individuals., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Background and Aims: Psidium is the fourthth largest genus of Myrtaceae in the Neotropics. Psidium guajava is widely cultivated in the tropics for its edible fruit. It is commercially under threat due to the disease guava decline. Psidium cattleyanum is one of the 100 most invasive organisms in the world. Knowledge of the phylogenetic relationships within Psidium is poor. We aim to provide a review of the biology, morphology and ecology of Psidium, a phylogenetic tree, an infrageneric classification and a list of species., Methods: Morphological and geographic data were obtained by studying Psidium in herbaria and in the field between 1988 and 2020. Forty-six herbaria were visited personally. A database of approx. 6000 specimens was constructed, and the literature was reviewed. Thirty species (about a third of the species in the genus) were sampled for molecular phylogenetic inference. Two chloroplast (psbA-trnH and ndhF) and two nuclear (external transcribed spacer and internal transcribed spacer) regions were targeted. Phylogenetic trees were constructed using maximum likelihood (ML; RaxML) and Bayesian inference (BI; MrBayes)., Key Results: Psidium is a monophyletic genus with four major clades recognized as sections. Section Psidium (ten species), to which P. guajava belongs, is sister to the rest of the genus; it is widespread across the Neotropics. Section Obversifolia (six species; restricted to the Brazilian Atlantic Forest), which includes P. cattleyanum, is sister to the innermost clade composed of sister sections Apertiflora (31 species; widespread but most diverse in the Brazilian Atlantic Forest) + Mitranthes (26 species; widespread in dry forests and probably diverse in the Caribbean). Characters associated with diversification within Psidium are discussed., Conclusions: Research on pre-foliation, colleters, leaf anatomy, leaf physiology, staminal development, placentation and germination associated with the anatomy of the opercular plug is desirable. Studies are biased towards sections Psidium and Obversifolia, with other sections poorly known., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments. The continuous M. polymorpha forest stands on the island of Hawaii were differentiated into three genetic clusters, each of which grows in a distinctive environment and includes substantial genetic and phenotypic diversity. The three genetic clusters showed signatures of selection in genomic regions encompassing genes relevant to environmental adaptations, including genes associated with light utilization, oxidative stress, and leaf senescence, which are likely associated with the ecological differentiation of the species. Our demographic modeling suggested that the glaberrima cluster in wet environments maintained a relatively large population size and two clusters split: polymorpha in the subalpine zone and incana in dry and hot conditions. This ecological divergence possibly began before the species colonized the island of Hawaii. Interestingly, the three clusters recovered genetic connectivity coincidentally with a recent population bottleneck, in line with the weak reproductive isolation observed in the species. This study highlights that the degree of genetic differentiation between ecologically-diverged populations can vary depending on the strength of natural selection in the very early phases of speciation., Competing Interests: The authors have declared that no competing interests exist.

Research on terpene biosynthesis in the genus Eucalyptus (Myrtaceae) is poorly developed, but recently large numbers of terpene synthase (TPS) genes have been identified. Few of these have been characterized or their expression localized to specific tissues. A prime candidate for detailed examination of TPS gene expression is the bisexual eucalypt flower-composed of male and female reproductive organs, and vegetative tissues that may express different TPS genes. We aimed to characterize and compare the terpene profile and TPS genes expressed in anthers and gynoecia in the high oil-yielding Eucalyptus polybractea R.T. Baker. We hypothesized that gynoecia will produce greater amounts of defensive terpenes, whereas anthers will have a terpene profile that is biased towards a role in pollination. Microscopy of isolated anthers showed them to possess a single, prominent oil gland. Chemical analysis of whole floral structures at different stages of development showed total oil per unit dry mass increased as flower buds expanded, with highest concentrations in mature flower buds just prior to flower opening. The oil profile of gynoecia was dominated by the monoterpene 1,8-cineole, whereas that of isolated anthers were enriched with the monoterpene α-pinene. Through transcriptomic analysis and recombinant protein expression, we were able to identify monoterpene synthases responsible for the different profiles. Synthases for α-pinene and 1,8-cineole were expressed in each tissue type, but the relative expression of the former was higher in anthers. Sequence comparison and site-directed mutagenesis of the α-pinene synthase allowed us to identify amino acids that influence the α-pinene to β-pinene ratio of the product profile. We suggest the terpene constituents of anthers may have multiple roles including attracting pollinators through emission of volatile α-pinene, deterrence of palynivores through emission of volatile 1,8-cineole and adhesion of pollen to pollinators via the release of sticky α-pinene onto the anther surface., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.)

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two diverged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enabling their successful adaptation to biotic/abiotic stresses and arid conditions of the Australian continent.

Contaminations in sequencing data, especially in reference genomes, lead to inevitable errors in downstream analyses. Similarly, presence of contaminants in transcriptomes, misrepresents the molecular basis of various interactions. In this study, we report the presence of a large number of plant transcriptomes contaminated with RNAs encoding POU domain proteins; a family of proteins that has not been reported in plants and fungi. Besides, our findings illustrated that there are four POU domain protein-coding sequences in the reference genome of Rhodamnia argentea. It turned out that the existing foreign fragments are related to arthropods that are considered as plant pests. We also identified two contaminated draft genomes, Humulus lupulus and Cannabis sativa that contained complete rDNA sequences originating from Tetranychus species. As a result, careful screening of sequencing data before releasing them in public databases or checking existing genomes for possible contaminations is recommended.

Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed., (Crown Copyright © 2020. Published by Elsevier Inc. All rights reserved.)

The endemic tree species Calyptranthes clusiifolia (Myrtaceae) plays a relevant ecological role in the forest fragments where it has a common occurrence. In this study, we reported the development of microsatellite markers for C. clusiifolia what will allow a better understanding of the relationship between the forest fragmentation process and the genetic structure and diversity of tree populations. Seven microsatellite markers were developed using an enriched genomic library and characterized in 30 individuals (from three populations). These seven loci were polymorphic and resulted in a total of 23 alleles. The expected heterozygosity (H E ) varied from 0.14 (Caly 06) to 0.73 (Caly 22). Linkage disequilibrium between the loci (p > 0.0007) pairs was not detected. The parentage exclusion power of the first (Pe-1) and the second (Pe-2) parents were 0.6099 and 0.8548, respectively. The microsatellite markers developed are indicated for future studies of the genetic diversity in natural populations of C. clusiifolia.

Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation., (© 2020 The Authors. Evolution © 2020 The Society for the Study of Evolution.)

A phloroglucinol-terpene adduct (PTA) collection consisting of twenty-four molecules featuring three skeletons was discovered from Baeckea frutescens. Inspired by its biosynthetic hypothesis, we synthesized this PTA collection by reductive activation of stable phloroglucinol precursors into highly reactive ortho-quinone methide (o-QM) intermediates and subsequently Diels-Alder cycloaddition. We also demonstrated, for the first time, the generation process of the active o-QM by performing dynamic NMR and HPLC-MS monitoring experiments. Moreover, the PTA collection showed significant antifeedant effect toward the Plutella xylostella larvae., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Shifts in flowering time have the potential to act as strong prezygotic reproductive barriers in plants. We investigate the role of flowering time divergence in two species of mountain rose ( Metrosideros ) endemic to Lord Howe Island, Australia, a minute and isolated island in the Tasman Sea. Metrosideros nervulosa and M. sclerocarpa are sister species and have divergent ecological niches on the island but grow sympatrically for much of their range, and likely speciated in situ on the island. We used flowering time and population genomic analyses of population structure and selection, to investigate their evolution, with a particular focus on the role of flowering time in their speciation. Population structure analyses showed the species are highly differentiated and appear to be in the very late stages of speciation. We found flowering times of the species to be significantly displaced, with M. sclerocarpa flowering 53 days later than M. nervulosa . Furthermore, the analyses of selection showed that flowering time genes are under selection between the species. Thus, prezygotic reproductive isolation is mediated by flowering time shifts in the species, and likely evolved under selection, to drive the completion of speciation within a small geographical area. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood ( Corymbia hamersleyana ) and Western Gidgee ( Acacia pruinocarpa ), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa , respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes ( C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana .

Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.

Environmental conditions influence specialized plant metabolism. However, many studies aiming to understand these modulations have been conducted with model plants and/or under controlled conditions, thus not reflecting the complex interaction between plants and environment. To fully grasp these interactions, we investigated the specialized metabolism and genetic diversity of a native plant in its natural environment. We chose Myrcia bella due to its medicinal interest and occurrence in Brazilian savanna regions with diverse climate and soil conditions. An LC-HRMS-based metabolomics approach was applied to analyze 271 samples harvested across seven regions during the dry and rainy season. Genetic diversity was assessed in a subset of 40 samples using amplified fragment length polymorphism. Meteorological factors including rainfall, temperature, radiation, humidity, and soil nutrient and mineral composition were recorded in each region and correlated with chemical variation through multivariate analysis (MVDA). Marker compounds were selected using a statistically informed molecular network and annotated by dereplication against an in silico database of natural products. The integrated results evidenced different chemotypes, with variation in flavonoid and tannin content mainly linked to soil conditions. Different levels of genetic diversity and distance of populations were found to be correlated with the identified chemotypes. These observations and the proposed analytical workflow contribute to the global understanding of the impact of abiotic factors and genotype on the accumulation of given metabolites and, therefore, could be valuable to guide further medicinal exploration of native species.

A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Species radiations should be facilitated by short generation times and limited dispersal among discontinuous populations. Hawaii's hyper-diverse, landscape-dominant tree, Metrosideros, is unique among the islands' radiations for its massive populations that occur continuously over space and time within islands, its exceptional capacity for gene flow by both pollen and seed, and its extended life span (ca. >650 years). Metrosideros shows the greatest phenotypic and microsatellite DNA diversity on O'ahu, where taxa occur in tight sympatry or parapatry in mesic and montane wet forest on 2 volcanoes. We document the nonrandom distributions of 12 taxa (including unnamed morphotypes) along elevation gradients, measure phenotypes of ~6-year-old common-garden plants of 8 taxa to verify heritability of phenotypes, and examine genotypes of 476 wild adults at 9 microsatellite loci to compare the strengths of isolation across taxa, volcanoes, and distance. All 8 taxa retained their diagnostic phenotypes in the common garden. Populations were isolated by taxon to a range of degrees (pairwise FST between taxa: 0.004-0.267), and there was no pattern of isolation by distance or by elevation; however, significant isolation between volcanoes was observed within monotypic species, suggesting limited gene flow between volcanoes. Among the infraspecific taxa of Metrosideros polymorpha, genetic diversity and isolation significantly decreased and increased, respectively, with elevation. Overall, 5 of the 6 most isolated taxa were associated with highest elevations or otherwise extreme environments. These findings suggest a principal role for selection in the origin and maintenance of the exceptional diversity that occurs within continuous Metrosideros stands on O'ahu., (© The American Genetic Association 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Accurate feature annotation as well as assembly contiguity are important requisites of a modern genome assembly. They allow large-scale comparison of genomes across and within species and identification of polymorphisms, leading evolutionary and functional studies. We report an updated genome resource for Metrosideros polymorpha , the most dominant tree species in the Hawaiian native forests and a unique example of rapid and remarkable ecological diversification of woody species. Ninety-one percent of the bases in the sequence assembly (304 Mb) were organized into 11 pseudo-molecules, which would represent the chromosome structure of the species assuming the synteny to a close relative Eucalyptus Our complementary approach using manual annotation and automated pipelines identified 11.30% of the assembly to be transposable elements, in contrast to 4.1% in previous automated annotation. By increasing transcript and protein sequence data, we predicted 27,620 gene models with high concordance from the supplied evidence. We believe that this assembly, improved for contiguity, and annotation will be valuable for future evolutionary studies of M. polymorpha and closely related species, facilitating the isolation of specific genes and the investigation of genome-wide polymorphisms associated with ecological divergence., (Copyright © 2019 Izuno et al.)

Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatric eastern Australian trees: the mountain water gum (Tristaniopsis collina) and the water gum (T. laurina). Using genomic data from SNP genotyping of 480 samples, we assessed the impact of biogeographic barriers and tested for signals of range expansion. Circuit theory was used to model isolation-by-resistance across three palaeo-environment scenarios: the Last Glacial Maximum, the Holocene Climate Optimum and present-day (1950-2014). Both trees showed similar genetic structure across historically dry barriers, despite evidence of significant environmental niche differentiation and different post-glacial habitat shifts. Tristaniopsis collina exhibits the signature of serial founder effects consistent with recent or rapid range expansion, whilst T. laurina has genetic patterns consistent with long-term persistence in geographically isolated populations despite occupying a broader bioclimatic niche. We found the minor influence of isolation-by-resistance on both species, though other unknown factors appear to shape genetic variation. We postulate that specialized recruitment traits (adapted to flood-disturbance regimes) rather than habitat availability limited post-glacial range expansion in T. laurina. Our findings indicate that niche breadth does not always facilitate range expansion through colonization and migration across barriers, though it can promote long-term persistence in situ.

Many species occur across environmental gradients and it is expected that these species will exhibit some signals of adaptation as heterogeneous environments and localized gene flow may facilitate local adaptation. While riparian zones can cross climate gradients, many of which are being impacted by climate change, they also create microclimates for the vegetation, reducing environmental heterogeneity. Species with differing distributions in these environments provide an opportunity to investigate the importance of genetic connectivity in influencing signals of adaptation over relatively short geographical distance. Association analysis with genomic data was used to compare signals of selection to climate variables in two species that have differing distributions along a river traversing a climate gradient. Results demonstrate links between connectivity, standing genetic variation, and the development of signals of selection. In the restricted species, the combination of high gene flow in the middle and lower catchment and occurrence in a microclimate created along riverbanks likely mitigated the development of selection to most climatic variables. In contrast the more widely distributed species with low gene flow showed a stronger signal of selection. Together these results strengthen our knowledge of the drivers and scale of adaptation and reinforce the importance of connectivity across a landscape to maintain adaptive potential of plant species., Competing Interests: The authors declare no conflict of interest.

Jaboticaba is a grape-like fruit that accumulates high levels of anthocyanins in the peel and is proposed as a good source of functional pigments. However, the molecular mechanisms underlying anthocyanin accumulation in jaboticaba peel remains to be elucidated. In this study, we employed RNA-seq technique to compare the transcriptomic differences between green-colored and black-colored jaboticaba peels. Over 5 million high-quality reads were assembled into 62,190 unigenes with an average length of 737 bp, 29,320 (47.15%) of them were annotated by public databases. 2152 unigenes were found to be differentially expressed (830 upregulated and 1322 downregulated). Gene ontology analysis and pathway enrichment annotation revealed that 18 differentially expressed genes encode phenylalanine ammonialyase, 4-coumaroyl:CoA-ligase, chalcone synthase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, anthocyanidin synthase, UDP-glucose: flavonoid 3-O-glucosyltransferase, glutathione S-transferase, Cytochrome b5 were associated with anthocyanin biosynthesis. Additionally, 54 differentially expressed transcription factors were identified. Furthermore, the expression of genes involved in biosynthesis and signal transduction of ethylene and abscisic acid were negatively and positively correlated with that of anthocyanin pathway genes and anthocyanin accumulation, respectively. Quantitative reverse transcription PCR analysis of candidate genes showed trends similar to those in the RNA-seq analysis. McMYB, a homolog of AtMYB113, induced anthocyanin accumulation in tobacco leaves when co-infiltrated PsbHLH3. These results will contribute to further understanding of the molecular mechanisms regulating anthocyanin accumulation in jaboticaba peel., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.

Background: Isoprene is a five-carbon chemical that is an important starting material for the synthesis of rubber, elastomers, and medicines. Although many plants produce huge amounts of isoprene, it is very difficult to obtain isoprene directly from plants because of its high volatility and increasing environmental regulations. Over the last decade, microorganisms have emerged as a promising alternative host for efficient and sustainable bioisoprene production. Isoprene synthase (IspS) has received much attention for the conversion of isoprene from dimethylallyl diphosphate (DMAPP). Herein, we isolated a highly expressible novel IspS gene from Metrosideros polymorpha (MpIspS), which was cloned and expressed in Escherichia coli, using a plant cDNA library and characterized its molecular and biochemical properties., Results: The signal sequence deleted MpIspS was cloned and expressed in E. coli as a 65-kDa monomer. The maximal activity of the purified MpIspS was observed at pH 6.0 and 55 °C in the presence of 5 mM Mn 2+ . The K m , k cat , and k cat /K m for DMAPP as a substrate were 8.11 mM, 21 min - 1 , and 2.59 mM - 1  min - 1 , respectively. MpIspS was expressed along with the exogenous mevalonate pathway to produce isoprene in E. coli. The engineered cells produced isoprene concentrations of up to 23.3 mg/L using glycerol as the main carbon source., Conclusion: MpIspS was expressed in large amounts in E. coli, which led to increased enzymatic activity and resulted in isoprene production in vivo. These results demonstrate a new IspS enzyme that is useful as a key biocatalyst for bioisoprene production in engineered microbes.

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9-10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes.

Heimia myrtifolia is an important medicinal plant with several pharmacologically active alkaloids and is also used as an ornamental landscape plant. The purpose of this study is to complete and characterize the chloroplast (cp) genome of H. myrtifolia and compare genomic features to other Myrtales species' cp genomes. The analysis showed that H. myrtifolia has a total length of 159,219 bp with a typical quadripartite structure containing two identical inverted repeats (IRs) of 25,643 bp isolated by one large single copy (LSC) of 88,571 bp and one small single copy (SSC) of 18,822 bp. The H. myrtifolia cp genome contains 129 genes with eight ribosomal RNAs, 30 transfer RNAs, and 78 protein coding genes, in which 17 genes are duplicated in two IR regions. The genome organization including gene type and number and guanine-cytosine (GC) content is analyzed among the 12 cp genomes in this study. Approximately 255 simple sequence repeats (SSRs) and 16 forward, two reverses, and two palindromic repeats were identified in the H. myrtifolia cp genome. By comparing the whole H. myrtifolia cp genome with 11 other Myrtales species, the results showed that the sequence similarity was high between coding regions while sequence divergence was high between intergenic regions. By employing the full cp genomes for phylogenetic analysis, structural and sequence differences were characterized between H. myrtifolia and 11 Myrtales species illustrating what patterns are common in the evolution of cp genomes within the Myrtales. The first entire cp genome in the genus Heimia provides a valuable resource for further studies in these medicinally and ornamentally important taxa., Competing Interests: The authors declare no conflict of interest.

The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the "CAP clade"), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent pollen shifts and position in the latitudinal gradient support the selective role of harmomegathy, the mechanism by which pollen grains accommodate their volume in response to water loss.

Camu-camu [Myrciaria dubia (Kunth) McVaugh] is currently an important and promising fruit species grown in the Peruvian Amazon, as well as in Brazil, Colombia, and Bolivia. The species is valued for its high content of fruit-based vitamin C. Large plantations have been established only in the last two decades, and a substantial part of the production is still obtained by collecting fruits from the wild. Domestication of the species is at an early stage; most farmers cultivate the plants without any breeding, or only through a simple mass selection process. The main objective of the study was to characterize morphological and genetic variation within and among cultivated and natural populations of camu-camu in the Peruvian Amazon. In total, we sampled 13 populations: ten wild in the Iquitos region, and three cultivated in the Pucallpa region in the Peruvian Amazon. To assess the genetic diversity using seven microsatellite loci, we analyzed samples from ten individual trees per each population (n = 126). Morphological data was collected from five trees from each population (n = 65). The analysis did not reveal statistically significant differences for most of the morphological descriptors. For wild and cultivated populations, the observed heterozygosity was 0.347 and 0.404 (expected 0.516 and 0.506), and the fixation index was 0.328 and 0.200, respectively. Wild populations could be divided into two groups according to the UPGMA and STRUCTURE analysis. In cultivated populations, their approximate origin was determined. Our findings indicate a high genetic diversity among the populations, but also a high degree of inbreeding within the populations. This can be explained by either the isolation of these populations from each other or the low number of individuals in some populations. This high level of genetic diversity can be explored for the selection of superior individuals for further breeding.

Background: Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes., Results: We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps., Conclusions: These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

The ability of plants to maintain an intact water transport system in leaves under drought conditions is intimately linked to survival and can been be seen as adaptive in shaping species climatic limits. Large differences in leaf hydraulic vulnerability to drought are known among species from contrasting climates, yet whether this trait varies among populations within a single species and, furthermore, whether it is altered by changes in growth conditions, remain unclear. We examined intraspecific variation in both leaf water transport capacity (Kleaf) and leaf hydraulic vulnerability to drought (P50leaf) among eight populations of Corymbia calophylla (R. Br.) K.D. Hill & L.A.S. Johnson (Myrtaceae) from both cool and warm climatic regions grown reciprocally under two temperature treatments representing the cool and warm edge of the species distribution. Kleaf did not vary between cool and warm-climate populations, nor was it affected by variable growth temperature. In contrast, population origin and growth temperature independently altered P50leaf. Using data pooled across growth temperatures, cool-climate populations showed significantly higher leaf hydraulic vulnerability (P50leaf = -3.55 ± 0.18 MPa) than warm-climate populations (P50leaf = -3.78 ± 0.08 MPa). Across populations, P50leaf decreased as population home-climate temperature increased, but was unrelated to rainfall and aridity. For populations from both cool and warm climatic regions, P50leaf was lower under the warmer growth conditions. These results provide evidence of trait plasticity in leaf hydraulic vulnerability to drought in response to variable growth temperature. Furthermore, they suggest that climate, and in particular temperature, may be a strong selective force in shaping intraspecific variation in leaf hydraulic vulnerability to drought., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance. In the present work, we reported the complete cp genome of feijoa. The feijoa cp genome is a circular molecule of 159,370 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC 88,028 bp) and a Small Single Copy region (SSC 18,598 bp) separated by Inverted Repeat regions (IRs 26,372 bp). The genome structure, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. When compared to other cp genome sequences of Myrtaceae, feijoa showed closest relationship with pitanga (Eugenia uniflora L.). Furthermore, a comparison of pitanga synonymous (Ks) and nonsynonymous (Ka) substitution rates revealed extremely low values. Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of three Myrtoideae clades.

Two different techniques for genomic DNA fragmentation before microsatellite-enriched library construction-restriction enzyme (NlaIII and MseI) digestion and sonication-were compared to examine their effects on simple sequence repeat (SSR) detection using high-throughput sequencing. Tens of thousands of SSR regions from 5 species of the plant family Myrtaceae were detected when the output of individual samples was >1 million paired-end reads. Comparison of the two DNA fragmentation techniques showed that restriction enzyme digestion was superior to sonication for identification of heterozygous genotypes, whereas sonication was superior for detection of various SSR flanking regions with both species-specific and common characteristics. Therefore, choosing the most suitable DNA fragmentation method depends on the type of analysis that is planned.

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the relative position of Myrtus communis, the placement of the Blepharocalyx group, the absence of generic endemism in the Caribbean, and the paraphyletism of the former Pimenta group. Distinct calibration approaches affect biogeography interpretation, increasing the number of necessary long distance dispersal events in the topology with older nodes. It is hypothesised that biological intrinsic factors such as modifications of embryo type and polyploidy might have played a role in accelerating shifts of diversification rates in Neotropical lineages. Future perspectives include formal subtribal classification, standardization of fossil calibration approaches and better links between diversification shifts and trait evolution., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Myrciaria dubia (camu-camu) is an Amazon tree that produces a tart fruit with high vitamin C content. It is probably the fruit with the highest vitamin C content among all Brazilian fruit crops and it can be used to supplement daily vitamin C dose. This property has attracted the attention of consumers and, consequently, encouraged fruit farmers to produce it. In order to identify and select potential accessions for commercial exploitation and breeding programs, M. dubia has received considerable research attention. The identification and characterization of genetic diversity, as well as identification of the population structure of accessions preserved in germplasm banks are fundamental for the success of any breeding program. The objective of this study was to evaluate the genetic variability of 10 M. dubia populations obtained from the shores of Reis Lake, located in the municipality of Caracaraí, Roraima, Brazil. Fourteen polymorphic inter simple sequence repeat (ISSR) markers were used to study the population genetic diversity, which resulted in 108 identified alleles. Among the 14 primers, GCV, UBC810, and UBC827 produced the highest number of alleles. The study illustrated the suitability and efficiency of ISSR markers to study the genetic diversity of M. dubia accessions. We also revealed the existence of high genetic variability among both accessions and populations that can be exploited in future breeding programs and conservation activities of this species.

Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high-altitude cluster was much smaller. A F ST -based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments., (© 2017 John Wiley & Sons Ltd.)

Nitrogen (N) fertilization is necessary to sustain productivity in eucalypt plantations, but it can increase the risk of greenhouse gas emissions. However, the response of soil greenhouse gas emissions to N fertilization might be influenced by soil characteristics, which is of great significance for accurately assessing greenhouse gas budgets and scientific fertilization in plantations. We conducted a two-year N fertilization experiment (control [CK], low N [LN], middle N [MN] and high N [HN] fertilization) in two eucalypt plantations with different soil characteristics (higher and lower soil organic carbon sites [HSOC and LSOC]) in Guangxi, China, and assessed soil-atmosphere greenhouse gas exchanges. The annual mean fluxes of soil CO2, CH4, and N2O were separately 153-266 mg m-2 h-1, -55 --40 μg m-2 h-1, and 11-95 μg m-2 h-1, with CO2 and N2O emissions showing significant seasonal variations. N fertilization significantly increased soil CO2 and N2O emissions and decreased CH4 uptake at both sites. There were significant interactions of N fertilization and SOC level on soil CO2 and N2O emissions. At the LSOC site, the annual mean flux of soil CO2 emission was only significantly higher than the CK treatment in the HN treatment, but, at the HSOC site, the annual mean flux of soil CO2 emission was significantly higher for both the LN (or MN) and HN treatments in comparison to the CK treatment. Under the CK and LN treatments, the annual mean flux of N2O emission was not significantly different between HSOC and LSOC sites, but under the HN treatment, it was significantly higher in the HSOC site than in the LSOC site. Correlation analysis showed that changes in soil CO2 and N2O emissions were significantly related to soil dissolved organic carbon, ammonia, nitrate and pH. Our results suggested significant interactions of N fertilization and soil characteristics existed in soil-atmosphere greenhouse gas exchanges, which should be considered in assessing greenhouse gas budgets and scientific fertilization strategies in eucalypt plantations., Competing Interests: The authors have declared that no competing interests exist.

Background: The present study evaluated the variability of cambuci fruit (Campomanesia phaea) cultivated in São Paulo State in the towns of Mogi das Cruzes, Paraibuna, Paranapiacaba and Rio Grande da Serra, and characterized it at different maturity stages with respect to size, firmness, soluble solids content, titratable acidity, phenolic content, ethylene production, respiration rate and in vitro antioxidant capacity., Results: Ripe fruit from the same locality, Paraibuna, showed large variations in size and acidity. Ripe fruit from different towns showed significant variation of total phenolics and, consequently, variation in antioxidant capacity. During maturation, the phenolic content and firmness decreased from unripe to ripe stages. The total soluble solids/titratable acidity ratio can be used as a parameter to differentiate cambuci at different maturity stages. However, the decrease in firmness combined with the absence of an ethylene climacteric peak does not allow us to conclude whether cambuci is climacteric or non-climacteric., Conclusion: Genetic and soil composition studies are needed to assess the reasons for the differences found among fruit from the same location, as well as the variability among fruit harvested in four localities. The best parameters for assessing the maturity stages of cambuci comprise the rounding of its corners and its firmness because the more mature the pulp, the softer is the fruit. © 2016 Society of Chemical Industry., (© 2016 Society of Chemical Industry.)

Cambuci (Campomanesia phaea) belongs to the Myrtaceae family and is native to the Atlantic Forest of Brazil. It has ecological and social appeal but is exposed to problems associated with environmental degradation and expansion of agricultural activities in the region. Comprehensive studies on this species are rare, making its conservation and genetic improvement difficult. Thus, it is important to develop research activities to understand the current situation of the species as well as to make recommendations for its conservation and use. This study was performed to characterize the cambuci accessions found in the germplasm bank of Coordenadoria de Assistência Técnica Integral using inter-simple sequence repeat markers, with the goal of understanding the plant's population structure. The results showed the existence of some level of genetic diversity among the cambuci accessions that could be exploited for the genetic improvement of the species. Principal coordinate analysis and discriminant analysis clustered the 80 accessions into three groups, whereas Bayesian model-based clustering analysis clustered them into two groups. The formation of two cluster groups and the high membership coefficients within the groups pointed out the importance of further collection to cover more areas and more genetic variability within the species. The study also showed the lack of conservation activities; therefore, more attention from the appropriate organizations is needed to plan and implement natural and ex situ conservation activities.

Myrcia lundiana Kiaersk. is a tree of the family Myrtaceae found in tropical and subtropical areas of the southern hemisphere that produces essential oil. The aim of this study was to characterize the genetic diversity of M. lundiana plants from a native population of Parque Nacional de Itabaiana, using inter-simple sequence repeat molecular markers. Thirty-five primers were tested, 20 of which were polymorphic, resulting in 135 polymorphic and informative bands. Results of the cluster analysis, obtained using the unweighted pair group method with arithmetic mean, grouped plants into three clusters: Cluster I - MLU001, MLU002, MLU003, MLU004, MLU005, MLU006, MLU018, MLU019, MLU020, MLU021, MLU022; MLU008, MLU011, MLU012, MLU014, MLU015, MLU017, MLU026, and MLU028; Cluster II - MLU007, MLU009, MLU010, MLU013, and MLU016; and Cluster III - MLU023, MLU024, MLU025, and MLU027. Jaccard similarity coefficients for pair-wise comparisons of plants ranged between 0.15 and 0.87. MLU014 and MLU015 presented low genetic diversity, with a similarity index of 0.87. Conversely, MLU007 and MLU019 presented high diversity, with a similarity index of 0.15. According to the structure analysis, three distinct clusters were formed. Genetic diversity of M. lundiana plants was intermediate, and expansion of its genetic diversity is necessary. MLU026 and MLU028 are the most suitable for selection in breeding programs, since they clearly represent all of the diversity present in these plants. Moreover, these results provide important information on the existing genetic variability, highlighting the importance of Parque Nacional de Itabaiana for the conservation of this species.

Intraspecific hybrid zones involving long-lived woody species are rare and can provide insights into the genetic basis of early-diverging traits in speciation. Within the landscape-dominant Hawaiian tree, Metrosideros polymorpha, are morphologically distinct successional varieties, incana and glaberrima, that dominate new and old lava flows, respectively, below 1200 me on volcanically active Hawai'i Island, with var. glaberrima also extending to higher elevations and bogs. Here, we use morphological measurements on 86 adult trees to document the presence of an incana-glaberrima hybrid zone on the 1855 Mauna Loa lava flow on east Hawai'i Island and parent-offspring analysis of 1311 greenhouse seedlings from 71 crosses involving 72 adults to estimate heritabilities and genetic correlations among vegetative traits. Both the variation in adult leaf pubescence at the site and the consistency between adult and offspring phenotypes suggest the presence of two hybrid classes, F1s and var. incana backcrosses, as would be expected on a relatively young lava flow. Nine nuclear microsatellite loci failed to distinguish parental and hybrid genotypes. All four leaf traits examined showed an additive genetic basis with moderate to strong heritabilities, and genetic correlations were stronger for the more range-restricted var. incana. The differences between varieties in trait values, heritabilities and genetic correlations, coupled with high genetic variation within but low genetic variation between varieties, are consistent with a multi-million-year history of alternating periods of disruptive selection in contrasting environments and admixture in ephemeral hybrid zones. Finally, the contrasting genetic architectures suggest different evolutionary trajectories of leaf traits in these forms.

Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.

Metrosideros polymorpha, a dominant tree species in the Hawaiian Islands, shows an extreme phenotypic polymorphism both across gradients of climatic/edaphic conditions and within populations, making it a potentially useful model species for evolutionary study. In order to understand how the phenotypic diversity is maintained within populations as well as across populations, we examined the diversities of several leaf and stem functional traits across five elevations and two soil substrates on the volcanic mountain of Mauna Loa, on the island of Hawaii. Leaf dry mass per area (LMA), a key leaf functional trait, was particularly focused on and analyzed in relation to its underlying components-namely, tissue LMA and trichome LMA (LMA = tissue LMA + trichome LMA). Across populations, tissue LMA increased linearly with elevation while trichome LMA showed unimodal patterns with elevation, which were better correlated with temperature and rainfall, respectively. Substantial phenotypic variations were also found within populations. Interestingly, the variations of tissue LMA were often negatively correlated to trichome LMA within populations, which contrasts with the cross-populations pattern, where a strong positive correlation between tissue LMA and trichome LMA was found. This suggests that phenotypic variations within populations were substantially influenced by local ecological processes. Soil depth (an indicator of local water availability) and tree size (an indicator of colonized timing) modestly explained the within-population variations, implying other local environmental factors and/or random processes are also important in local phenotypic diversity. This study provides an insight about how phenotypic diversity of plant species is maintained from local to landscape levels.

We assessed the transferability of 120 EST-derived Eucalyptus microsatellite primers to Campomanesia adamantium and C. pubescens. Both species are berry trees native to the Brazilian Cerrado, and population genetic information is poor. Twelve markers were used to analyze the genetic variability of four sampled populations. Regarding DNA extraction, we sampled leaf tissues from two populations of each species (80 individuals). Of the 120 primers evaluated, 87 did not amplify any PCR products, and 21 rendered nonspecific amplification. Twelve primers were successfully transferred, providing a low combined probability of genetic identity for both species (5.718 x 10(-10) for C. adamantium; 1.182 x 10(-11) for C. pubescens) and a high probability of paternity exclusion (0.99939 for C. adamantium; 0.99982 for C. pubescens). The average number of alleles in the polymorphic loci was 6.8 for C. adamantium and 7.8 for C. pubescens, ranging from 2 to 16 alleles per locus. The observed heterozygosity values for C. adamantium and C. pubescens were 0.504 and 0.503, respectively, and the expected heterozygosity values for C. adamantium and C. pubescens were 0.517 and 0.579, respectively. The populations exhibited structured genetic variability with qP values of 0.105 for C. adamantium and 0.249 for C. pubescens. Thus, we concluded that these 12 microsatellite markers, transferred from Eucalyptus, were efficient for population genetic studies of C. adamantium and C. pubescens.

We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Background: Micro RNAs are a class of small non coding RNAs of 20-24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing., Results: In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements., Conclusions: The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.