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Improved understanding of mosquito-plant feeding interactions can reveal insights into the ecological dynamics of pathogen transmission. In wild malaria vectors Anopheles gambiae s.l. and An. funestus group surveyed in selected dryland ecosystems of Kenya, we found a low level of plant feeding (2.8%) using biochemical cold anthrone test but uncovered 14-fold (41%) higher rate via DNA barcoding targeting the chloroplast rbcL gene. Plasmodium falciparum positivity was associated with either reduced or increased total sugar levels and varied by mosquito species. Gut analysis revealed the mosquitoes to frequently feed on acacia plants (~ 89%) (mainly Vachellia tortilis) in the family Fabaceae. Chemical analysis revealed 1-octen-3-ol (29.9%) as the dominant mosquito attractant, and the sugars glucose, sucrose, fructose, talose and inositol enriched in the vegetative parts, of acacia plants. Nutritional analysis of An. longipalpis C with high plant feeding rates detected fewer sugars (glucose, talose, fructose) compared to acacia plants. These results demonstrate (i) the sensitivity of DNA barcoding to detect plant feeding in malaria vectors, (ii) Plasmodium infection status affects energetic reserves of wild anopheline vectors and (iii) nutrient content and olfactory cues likely represent potent correlates of acacia preferred as a host plant by diverse malaria vectors. The results have relevance in the development of odor-bait control strategies including attractive targeted sugar-baits., (© 2024. The Author(s).)

Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to understand the factors that influence the development of dark heartwood, a comparative analysis was conducted on the microstructure, substance composition, differential gene expression, and metabolite profiles in the sapwood (SW), transition zone (TZ), and heartwood (HW) of two distinct clones, SR14 and SR25. A microscopic examination revealed that heartwood color variations are associated with an increased substance content within the ray parenchyma cells. A substance analysis indicated that the levels of starches, sugars, and lignin were more abundant in SP compared to HW, while the concentrations of phenols, flavonoids, and terpenoids were found to be higher in HW than in SP. Notably, the dark heartwood of the SR25 clone exhibited greater quantities of phenols and flavonoids compared to the SR14 clone, suggesting that these compounds are pivotal to the color distinction of the heartwood. An integrated analysis of transcriptome and metabolomics data uncovered a significant accumulation of sinapyl alcohol, sinapoyl aldehyde, hesperetin, 2', 3, 4, 4', 6'-peptahydroxychalcone 4'-O-glucoside, homoeriodictyol, and (2S)-liquiritigenin in the heartwood of SR25, which correlates with the up-regulated expression of CCRs ( evm . TU . Chr3 . 1751 , evm . TU . Chr4 . 654_667 , evm . TU . Chr4 . 675 , evm . TU . Chr4 . 699 , and evm . TU . Chr4 . 704 ), COMTs ( evm . TU . Chr13 . 3082 , evm . TU . Chr13 . 3086 , and evm . TU . Chr7 . 1411 ), CADs ( evm . TU . Chr10 . 2175 , evm . TU . Chr1 . 3453 , and evm . TU . Chr8 . 1600 ), and HCTs ( evm . TU . Chr4 . 1122 , evm . TU . Chr4 . 1123 , evm . TU . Chr8 . 1758 , and evm . TU . Chr9 . 2960 ) in the TZ of A . melanoxylon . Furthermore, a marked differential expression of transcription factors (TFs), including MYBs , AP2/ERFs , bHLHs , bZIPs , C2H2s , and WRKYs , were observed to be closely linked to the phenols and flavonoids metabolites, highlighting the potential role of multiple TFs in regulating the biosynthesis of these metabolites and, consequently, influencing the color variation in the heartwood. This study facilitates molecular breeding for the accumulation of metabolites influencing the heartwood color in A . melanoxylon , and offers new insights into the molecular mechanisms underlying heartwood formation in woody plants.

The Acacia koa S-adenosylmethionine (SAM) synthetase was identified from transcriptome data and cloned into the T 7 -expression vector pEt14b. Assays indicate a thermoalkaliphic enzyme which tolerates conditions up to pH 10.5, 55 °C and 3 M KCl. In vitro examples of plant SAM-synthetase activity are scarce, however this study provides supporting evidence that these extremophilic properties may actually be typical for this plant enzyme. Enzyme kinetic constants (K m  = 1.44 mM, K cat  = 1.29 s -1 , V max 170 μM. min -1 ) are comparable to nonplant SAM-synthetases except that substrate inhibition was not apparent at 10 mM ATP/L-methionine. Methods were explored in this study to reduce feedback inhibition, which is known to limit SAM-synthetase activity in vitro. Four single-point mutation variants of the Acacia koa SAM-synthetase were produced, each with varying degrees of reduced reaction rate, greater sensitivity to product inhibition and loss of thermophilic properties. Although an enhanced mutant was not produced, this study describes the first mutagenesis of a plant SAM-synthetase. Overcoming feedback inhibition was accomplished by the addition of organic solvent to enzyme assays. Acetonitrile, methanol or dimethylformamide, when included as 25% of the assay volume, improved total SAM production by 30-65%., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Masson SAS.. All rights reserved.)

Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and regulatory mechanism of heartwood during wood development remain largely unclear. In this study, both microscopic observation and content determination proved that total amount of starches decreased and phenolics and flavonoids increased gradually from sapwood (SW) to HW. We also obtained the metabolite profiles of 10 metabolites related to phenolics and flavonoids during HW formation by metabolomics. Additionally, we collected a comprehensive overview of genes associated with the biosynthesis of sugars, terpenoids, phenolics, and flavonoids using RNA-seq. A total of ninety-one genes related to HW formation were identified. The transcripts related to plant hormones, programmed cell death (PCD), and dehydration were increased in transition zone (TZ) than in SW. The results of RT-PCR showed that the relative expression level of genes and transcription factors was also high in the TZ, regardless of the horizontal or vertical direction of the trunk. Therefore, the HW formation took place in the TZ for A. melanoxylon from molecular level, and potentially connected to plant hormones, PCD, and cell dehydration. Besides, the increased expression of sugar and terpenoid biosynthesis-related genes in TZ further confirmed the close connection between terpenoid biosynthesis and carbohydrate metabolites of A. melanoxylon. Furthermore, the integrated analysis of metabolism data and RNA-seq data showed the key transcription factors (TFs) regulating flavonoids and phenolics accumulation in HW, including negative correlation TFs (WRKY, MYB) and positive correlation TFs (AP2, bZIP, CBF, PB1, and TCP). And, the genes and metabolites from phenylpropanoid and flavonoid metabolism and biosynthesis were up-regulated and largely accumulated in TZ and HW, respectively. The findings of this research provide a basis for comprehending the buildup of metabolites and the molecular regulatory processes of HW formation in A. melanoxylon., (© 2024. The Author(s).)

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2023.)

Natural selection for plant species in heterogeneous environments creates genetic variation for traits such as cold tolerance. While physiological or molecular analyses have been used to evaluate stress tolerance adaptations, combining these approaches may provide deeper insight. Acacia koa (koa) occurs from sea level to 2300 m in Hawai'i, USA. At high elevations, natural koa populations have declined due to deforestation, and freeze tolerance is a limiting factor for tree regeneration. We used physiology and molecular analyses to evaluate cold tolerance of koa populations from low (300-750 m), middle (750-1500 m), and high elevations (1500-2100 m). Half of the seedlings were cold acclimated by exposure to progressively lowered air temperatures for eight weeks (from 25.6/22.2°C to 8/4°C, day/night). Using the whole plant physiology-freezing test and koa C-repeat Binding Factor CBF genes, our results indicated that koa can be cold-acclimated when exposed to low, non-freezing temperatures. Seedlings from high elevations had consistently higher expression of Koa CBF genes associated with cold tolerance, helping to explain variation in cold-hardy phenotypes. Evaluation of the genetic background of 22 koa families across the elevations with low coverage RNA sequencing indicated that high elevation koa had relatively low values of heterozygosity, suggesting that adaptation is more likely to arise in the middle and low elevation sources. This physiology and molecular data for cold tolerance of koa across the elevation gradient of the Hawaiian Islands provides insights into natural selection processes and may help to support guidelines for conservation and seed transfer in forest restoration efforts., (© 2023 The Authors. Physiologia Plantarum published by John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.)

The introduced species Acacia saligna is a very promiscuous host as it can be efficiently nodulated with a wide range diversity of rhizobia taxa, including both fast and slow-growing strains. Fourteen nitrogen (N)-fixing bacteria were isolated from root nodules of wild Acacia saligna growing in distinct geographic locations in Morocco and were examined for their symbiotic efficiency and phenotypic properties. Multivariate tools, such as principal component analysis (PCA) and hierarchical clustering analysis (HCA), were used to study the correlation between phenotypic and symbiotic variables and discriminate and describe the similarities between different isolated bacteria with respect to all the phenotypic and symbiotic variables. Phenotypic characterization showed a variable response to extreme temperature, salinity and soil pH. At the plant level, the nodulation, nitrogen fixation, and the shoot and root dry weights were considered. The obtained results show that some of the tested isolates exhibit remarkable tolerances to the studied abiotic stresses while showing significant N 2 fixation, indicating their usefulness as effective candidates for the inoculation of acacia trees. The PCA also allowed showing the isolates groups that present a similarity with evaluated phenotypic and symbiotic parameters. The genotypic identification of N 2 -fixing bacteria, carried out by the 16S rDNA approach, showed a variable genetic diversity among the 14 identified isolates, and their belonging to three different genera, namely Agrobacterium, Phyllobacterium and Rhizobium., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1 T , B. betae PL7HG1 T , B. ganzhouense CCBAU 51670  T , B. cytisi CTAW11 T and B. rifense CTAW71 T ) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14AB T (=LMG 31415  T  = SARCC-753  T ) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Acacia melanoxylon (blackwood) is a valuable wood with excellent-quality heartwood extensively utilized worldwide. The main aim of this study was to confirm the horizontal and vertical variation and provide estimated values of genetic gains and clonal repeatabilities for improving breeding program of A. melanoxylon . Six blackwood clones at 10 years old were analyzed in Heyuan and Baise cities in China. Stem trunk analysis was conducted for sample trees to explore the differences between heartwood and sapwood. The heartwood radius (HR), heartwood area (HA), and heartwood volume (HV) in heartwood properties decreased as tree height (H) in growth traits increased, and the HV = 1.2502 DBH (diameter at breast height) 1.7009 model can accurately estimate the heartwood volume. Furthermore, G × E analysis showed that the heritabilities of the eleven indices, including DBH, DGH (diameter at ground height), H, HR, SW (sapwood width), BT (bark thickness), HA, SA (sapwood area), HV, HRP (heartwood radius percentage), HAP (heartwood area percentage), and HVP (heartwood volume percentage) were between 0.94 and 0.99, and repeatabilities of the eleven indices were between 0.74 and 0.91. Clonal repeatability of DBH (0.91), DGH (0.88), and H (0.90) in growth traits, HR (0.90), HVP (0.90), and HV (0.88) in heartwood properties were slightly higher than for SA (0.74), SW (0.75), HAP (0.75), HRP (0.75), and HVP (0.75). These data also implied that the growth characteristics of heartwood and sapwood of blackwood clones were less affected by the environment and had substantial heritability.

Three bacterial strains, 1AS11 T , 1AS12 and 1AS13, members of the new symbiovar salignae and isolated from root nodules of Acacia saligna grown in Tunisia, were characterized using a polyphasic approach. All three strains were assigned to the Rhizobium leguminosarum complex on the basis of rrs gene analysis. Phylogenetic analysis based on 1734 nucleotides of four concatenated housekeeping genes ( recA , atpD , glnII and gyrB ) showed that the three strains were distinct from known rhizobia species of the R. leguminosarum complex and clustered as a separate clade within this complex. Phylogenomic analysis of 92 up-to-date bacterial core genes confirmed the unique clade. The digital DNA-DNA hybridization and blast-based average nucleotide identity values for the three strains and phylogenetically related Rhizobium species ranged from 35.9 to 60.0% and 87.16 to 94.58 %, which were lower than the 70 and 96% species delineation thresholds, respectively. The G+C contents of the strains were 60.82-60.92 mol% and the major fatty acids (>4 %) were summed feature 8 (57.81 %; C 18 : 1  ω7 c ) and C 18 : 1  ω7 c 11-methyl (13.24%). Strains 1AS11 T , 1AS12 and 1AS13 could also be differentiated from their closest described species ( Rhizobium indicum , Rhizobium laguerreae and Rhizobium changzhiense ) by phenotypic and physiological properties as well as fatty acid content. Based on the phylogenetic, genomic, physiological, genotypic and chemotaxonomic data presented in this study, strains 1AS11 T , 1AS12 and 1AS13 represent a new species within the genus Rhizobium and we propose the name Rhizobium acaciae sp. nov. The type strain is 1AS11 T (=DSM 113913 T =ACCC 62388 T ).

Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes., Competing Interests: The authors have declared that no competing interests exist.

Biochemical markers such as protein are very important to determine genetic diversity among plant species in a given population which in turn is very important for breeders and farmers as they can then easily select the most appropriate variety to grow in a given locality. In this connection, the present study is aimed to evaluate genetic diversity in Acacia modesta germplasm through Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) technique. About 40 genotypes were subjected to SDS-PAGE analysis where a total of 12 polypeptide bands were observed in electrophoretogram. Out of which 16.67% were monomorphic while the remaining 83.33% were polymorphic. Variation found in B-2, 4, 5, 6, 7, 8, 9, 10, 11 and 12, were 20, 22.50, 32.50, 10, 2.50, 22.50, 15, 5, 2.50 and 75% respectively. Locus contribution toward genetic disagreement was 83.33%. Cluster analysis sorted all the genotypes into 9 clusters. The genotypes in one cluster were identical regarding protein profiling and showed less intra-specific genetic variation whereas differences were find from other genotypes.

Novel approaches to combating antibiotic resistance are needed given the ever-continuing rise of antibiotic resistance and the scarce discovery of new antibiotics. Little is known about the colonization dynamics and the role of intrinsic plant-food characteristics in this process. We sought to determine whether plant fiber could alter colonization dynamics by antibiotic-resistant bacteria in the gut. We determined that ingestion of antibiotics in mice markedly enhanced gut colonization by a pathogenic extended-spectrum beta-lactamase-producing Escherichia coli strain of human origin, E. coli JJ1886 (ST131- H 30Rx). Furthermore, ingestion of soluble acacia fiber before and after antibiotic exposure significantly reduced pathogenic E. coli colonization. 16S rRNA analysis and ex vivo cocultures demonstrated that fiber protected the microbiome by serving as a prebiotic, which induced native gut E. coli to inhibit pathogenic E. coli via colicin M. Fiber may be a useful prebiotic with which to administer antibiotics to protect human and livestock gut microbiomes against colonization from antibiotic-resistant, pathogenic bacteria. IMPORTANCE A One Health-based strategy-the concept that human health and animal health are interconnected with the environment-is necessary to determine the drivers of antibiotic resistance from food to the clinic. Moreover, humans can ingest antibiotic-resistant bacteria on food and asymptomatically, or "silently," carry such bacteria in the gut long before they develop an opportunistic extraintestinal infection. Here, we determined that fiber-rich foods, in particular acacia fiber, may be a new, promising, and inexpensive prebiotic to administer with antibiotics to protect the mammalian (i.e., human and livestock) gut against such colonization by antibiotic-resistant, pathogenic bacteria.

Black wattle (Acacia mearnsii) has great economic value as a commercial source of tannins, timber and a source of firewood for local and international markets. It has been suggested that to maximize the genetic gain of A. mearnsii plantations in South Africa, the gene pool that exist within ICFR needs to be broadened via introduction of new genotypes with diverse traits. In this work, 282 A. mearnsii samples sourced from the ICFR breeding program were genotyped using 11 cross-species SSR markers. Our results showed low to moderate genetic differentiation (F ST ) among the six breeding subpopulations, with positive inbreeding (F IS ) values that could be attributed to an historical inbreeding event. Low levels of relatedness could however indicate some mechanism of inbreeding avoidance. The effects from a recent supplementation of genetic material from two native Australian populations were observed through genetic structuring analyses. Analysis of molecular variance (AMOVA) revealed that significant genetic variation was mainly distributed within populations (75%) and among individuals (23%). The results provide significant information on A. mearnsii population genetic diversity and structure, which can be used for conservation of the current subpopulations and future tree improvement programs., (© 2021. The Botanical Society of Japan.)

Background and Aims: Invasive species may undergo rapid evolution despite very limited standing genetic diversity. This so-called genetic paradox of biological invasions assumes that an invasive species has experienced (and survived) a genetic bottleneck and then underwent local adaptation in the new range. In this study, we test how often Australian acacias (genus Acacia), one of the world's most problematic invasive tree groups, have experienced genetic bottlenecks and inbreeding., Methods: We collated genetic data from 51 different genetic studies on Acacia species to compare genetic diversity between native and invasive populations. These studies analysed 37 different Acacia species, with genetic data from the invasive ranges of 11 species, and data from the native range for 36 species (14 of these 36 species are known to be invasive somewhere in the world, and the other 22 are not known to be invasive)., Key Results: Levels of genetic diversity are similar in native and invasive populations, and there is little evidence of invasive populations being extensively inbred. Levels of genetic diversity in native range populations also did not differ significantly between species that have and that do not have invasive populations., Conclusion: We attribute our findings to the impressive movement, introduction effort and human usage of Australian acacias around the world., (© The Author(s) 2021. 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.)

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 .

Members of genus Acacia comprises of trees used as fuelwood, timber and fodder. Moreover, some parts of plants are also used for their therapeutic properties. The development and applications of breeding and biotechnological tools are advancing at a significantly fast rate. Molecular markers and genomics offer vital information with regard to the inherited variation. The aim of this study to complied and discussed the developments in molecular maker technology, genomics and genetic engineering concerning genus Acacia. Overall, this information will be useful to gain awareness about the crucial trees in the genus Acacia from breeding and a biotechnological perspective.

Clonality may provide reproductive assurance for many threatened plants while limiting sexual reproductive success either through energetic tradeoffs or because clones are self-incompatible. Most stands of the Australian arid-zone plant Acacia carneorum, flower annually but low seed set and an absence of sexual recruitment now suggest that this species and other, important arid-zone ecosystem engineers may have low genotypic diversity. Indeed, our recent landscape-scale genetic study revealed that stands are typically monoclonal, with genets usually separated by kilometers. An inability to set sexually produced seed or a lack of genetically diverse mates may explain almost system-wide reproductive failure. Here, using microsatellite markers, we genotyped 100 seeds from a rare fruiting stand (Middle-Camp), together with all adult plants within it and its 4 neighboring stands (up to 5 km distant). As expected, all stands surveyed were monoclonal. However, the Middle-Camp seeds were generated sexually. Comparing seed genotypes with the single Middle-Camp genotype and those of genets from neighboring and other regional stands (n = 26), revealed that 73 seeds were sired by the Middle-Camp genet. Within these Middle-Camp seeds we detected 19 genotypes in proportions consistent with self-fertilization of that genet. For the remaining 27 seeds, comprising 8 different genotypes, paternity was assigned to the nearest neighboring stands Mallee and Mallee-West, approximately 1 km distant. Ironically, given this species' vast geographic range, a small number of stands with reproductively compatible near neighbors may provide the only sources of novel genotypes., (© The American Genetic Association. 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Age-dependent changes in plant defense against herbivores are widespread, but why these changes exist remains a mystery. We explored this question by examining a suite of traits required for the interaction between swollen thorn acacias (genus Vachellia ) and ants of the genus Pseudomyrmex In this system, plants provide ants with refuge and food in the form of swollen stipular spines, protein-lipid-rich "Beltian" bodies, and sugar-secreting extrafloral nectaries-the "swollen thorn syndrome." We show that this syndrome develops at a predictable time in shoot development and is tightly associated with the temporal decline in the microRNAs miR156 and miR157 and a corresponding increase in their targets-the SPL transcription factors. Growth under reduced light intensity delays both the decline in miR156/157 and the development of the swollen thorn syndrome, supporting the conclusion that these traits are controlled by the miR156-SPL pathway. Production of extrafloral nectaries by Vachellia sp. that do not house ants is also correlated with a decline in miR156/157, suggesting that this syndrome evolved by co-opting a preexisting age-dependent program. Along with genetic evidence from other model systems, these findings support the hypothesis that the age-dependent development of the swollen thorn syndrome is a consequence of genetic regulation rather than a passive developmental pattern arising from developmental constraints on when these traits can develop., Competing Interests: The authors declare no conflict of interest.

Premise of the Study: Knowledge about the introduction history (source(s), number and size of introduction events) of an invasive species is a crucial prerequisite to understand invasion success and to facilitate effective and sustainable management approaches, especially for effective biological control. We investigated the introduction history of the Australian legume tree Acacia dealbata in South Africa. Results of this study will not only provide critical information for the management of this species in South Africa, but will also broaden our overall knowledge on the invasion ecology of this globally important invasive tree., Methods: We used nuclear microsatellite markers to compare the genetic diversity and structure between 42 native Australian and 18 invasive South African populations and to test different and competing introduction scenarios using Approximate Bayesian Computation analyses., Key Results: Australian populations were characterized by two distinct genetic clusters, while South African populations lacked any clear genetic structure and showed significantly lower levels of genetic diversity compared to native range populations. South African populations were also genetically divergent from native populations and the most likely introduction scenario indicated an unknown source population., Conclusions: Although we cannot definitely prove the cause of the observed genetic novelty/diversification in South African Acacia dealbata populations, it cannot be attributable to insufficient sampling of native populations. Our study highlights the complexity of unravelling the introduction histories of commercially important alien species., (© 2019 Botanical Society of America.)

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

This experiment aimed to investigate the role of 24-epibrassinolide (EBL) against NaCl - induced salinity stress in Acacia gerrardii Benth. NaCl (200 mM) imparted deleterious effects on the growth and chlorophyll contents of A. gerrardii, but foliar application of EBL (1.0 mg/l; each plant received 2.5 ml) mitigated the negative effect considerably. NaCl reduced chlorophyll content but this was significantly ameliorated by the application of EBL. EBL reduced significantly NaCl - induced oxidative stress hence protect membranes and also improved the relative water content significantly by 6.6% as compared with control. Nitrate reductase activity declined after NaCl treatment but EBL application sustained its activity under normal and stressed conditions. Exogenous application of EBL significantly improved the activity of superoxide dismutase, catalase and the enzymes of the ascorbate-glutathione pathway thereby protecting the photosynthetic electron transport chain and other metabolic processes in A. gerrardii from NaCl - induced oxidative stress.

The influence of geographic range on species persistence has long been of interest and there is a need for a better understanding of the genetic consequences for species with restricted distributions, particularly with the increasing rate of global species extinctions. However, the genetic effects of restricted range are often confounded by the impacts of population distribution. We compared chloroplast and nuclear genetic diversity and differentiation in two acacias, the restricted, patchily distributed Acacia atkinsiana and the widespread, semi-continuously distributed A. ancistrocarpa. Lower intra-population diversity and higher differentiation between populations were seen in A. atkinsiana compared to its widespread congener, A. ancistrocarpa. There was little evidence of geographical influences on population genetic structure in A. ancistrocarpa whereas A. atkinsiana exhibited nuclear genetic structure with isolation by distance, differentiation of near-coastal populations from those in the ranges, and differentiation of peripheral populations from those in the centre of the distribution. These results are consistent with expectations of the effect of geographic range and population distribution on genetic diversity, but indicate that distribution of populations rather than geographic range has influenced the observed genetic structure. The contrasting patterns observed here demonstrate that conservation approaches for species management and ecological restoration need to consider the distribution of populations in geographically restricted species., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: This study was funded by Rio Tinto (http://www.riotinto.com/). This does not alter our adherence to PLOS ONE policies on sharing data and materials.

The chemical composition of Acacia catechu, Schinopsis balansae, and Acacia mearnsii proanthocyanidins has been determined using a novel analytical approach that rests on the concerted use of quantitative (31)P NMR and two-dimensional heteronuclear NMR spectroscopy. This approach has offered significant detailed information regarding the structure and purity of these complex and often elusive proanthocyanidins. More specifically, rings A, B, and C of their flavan-3-ol units show well-defined and resolved absorbance regions in both the quantitative (31)P NMR and HSQC spectra. By integrating each of these regions in the (31)P NMR spectra, it is possible to identify the oxygenation patterns of the flavan-3-ol units. At the same time it is possible to acquire a fingerprint of the proanthocyanidin sample and evaluate its purity via the HSQC information. This analytical approach is suitable for both the purified natural product proanthocyanidins and their commercial analogues. Overall, this effort demonstrates the power of the concerted use of these two NMR techniques for the structural elucidation of natural products containing labile hydroxy protons and a carbon framework that can be traced out via HSQC.

Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Acacia farnesiana is a shrub widely distributed in soils heavily polluted with arsenic in Mexico. However, the mechanisms by which this species tolerates the phytotoxic effects of arsenic are unknown. This study aimed to investigate the tolerance and bioaccumulation of As by A. farnesiana seedlings exposed to high doses of arsenate (AsV) and the role of peroxidases (POX) and glutathione S-transferases (GST) in alleviating As-stress. For that, long-period tests were performed in vitro under different AsV treatments. A. farnesiana showed a remarkable tolerance to AsV, achieving a half-inhibitory concentration (IC50) of about 2.8 mM. Bioaccumulation reached about 940 and 4380 mg As·kg(-1) of dry weight in shoots and roots, respectively, exposed for 60 days to 0.58 mM AsV. Seedlings exposed to such conditions registered a growth delay during the first 15 days, when the fastest As uptake rate (117 mg kg(-1) day(-1)) occurred, coinciding with both the highest rate of lipid peroxidation and the strongest up-regulation of enzyme activities. GST activity showed a strong correlation with the As bioaccumulated, suggesting its role in imparting AsV tolerance. This study demonstrated that besides tolerance to AsV, A. farnesiana bioaccumulates considerable amounts of As, suggesting that it may be useful for phytostabilization purposes.

Ants are prominent seed dispersal agents in many ecosystems, and dispersal distances are small in comparison with vertebrate dispersal agents. However, the distance and distribution of ant-mediated dispersal in arid/semi-arid environments remains poorly explored. We used microsatellite markers and parentage assignment to quantify the distance and distribution of dispersed seeds of Acacia karina, retrieved from the middens of Iridomyrmex agilis and Melophorus turneri perthensis. From parentage assignment, we could not distinguish the maternal from each parent pair assigned to each seed, so we applied two approaches to estimate dispersal distances, one conservative (CONS), where the parent closest to the ant midden was considered to be maternal, and the second where both parents were deemed equally likely (EL) to be maternal, and used both distances. Parentage was assigned to 124 seeds from eight middens. Maximum seed dispersal distances detected were 417 m (CONS) and 423 m (EL), more than double the estimated global maximum. Mean seed dispersal distances of 40 m (±5.8 SE) (CONS) and 79 m (±6.4 SE) (EL) exceeded the published global average of 2.24 m (±7.19 SD) by at least one order of magnitude. For both approaches and both ant species, seed dispersal was predominantly (44-84% of all seeds) within 50 m from the maternal source, with fewer dispersal events at longer distances. Ants in this semi-arid environment have demonstrated a greater capacity to disperse seeds than estimated elsewhere, which highlights their important role in this system, and suggests significant novel ecological and evolutionary consequences for myrmecochorous species in arid/semi-arid Australia.

Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 174,233 bp in size, comprising inverted repeats of 38,225 bp and single-copy regions of 92,798 bp and 4,985 bp [corrected]. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex.

Background and Aims: Understanding patterns of pollen dispersal and variation in mating systems provides insights into the evolutionary potential of plant species and how historically rare species with small disjunct populations persist over long time frames. This study aims to quantify the role of pollen dispersal and the mating system in maintaining contemporary levels of connectivity and facilitating persistence of small populations of the historically rare Acacia woodmaniorum., Methods: Progeny arrays of A. woodmaniorum were genotyped with nine polymorphic microsatellite markers. A low number of fathers contributed to seed within single pods; therefore, sampling to remove bias of correlated paternity was implemented for further analysis. Pollen immigration and mating system parameters were then assessed in eight populations of varying size and degree of isolation., Key Results: Pollen immigration into small disjunct populations was extensive (mean minimum estimate 40 % and mean maximum estimate 57 % of progeny) and dispersal occurred over large distances (≤1870m). Pollen immigration resulted in large effective population sizes and was sufficient to ensure adaptive and inbreeding connectivity in small disjunct populations. High outcrossing (mean tm = 0·975) and a lack of apparent inbreeding suggested that a self-incompatibility mechanism is operating. Population parameters, including size and degree of geographic disjunction, were not useful predictors of pollen dispersal or components of the mating system., Conclusions: Extensive long-distance pollen dispersal and a highly outcrossed mating system are likely to play a key role in maintaining genetic diversity and limiting negative genetic effects of inbreeding and drift in small disjunct populations of A. woodmaniorum. It is proposed that maintenance of genetic connectivity through habitat and pollinator conservation will be a key factor in the persistence of this and other historically rare species with similar extensive long-distance pollen dispersal and highly outcrossed mating systems., (© The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Despite the normally strong link between geographic proximity and relatedness of recently diverged taxa, truly puzzling biogeographic anomalies to this expectation exist in nature. Using a dated phylogeny, population genetic structure and estimates of ecological niche overlap, we tested the hypothesis that two geographically very disjunct, but morphologically very similar, island endemics (Acacia heterophylla from Réunion Island and A. koa from the Hawaiian archipelago) are the result of dispersal between these two island groups, rather than independent colonization events from Australia followed by convergent evolution. Our genetic results indicated that A. heterophylla renders A. koa paraphyletic and that the former colonized the Mascarene archipelago directly from the Hawaiian Islands ≤ 1.4 million yr ago. This colonization sequence was corroborated by similar ecological niches between the two island taxa, but not between A. melanoxylon from Australia (a sister, and presumed ancestral, taxon to A. koa and A. heterophylla) and Hawaiian A. koa. It is widely accepted that the long-distance dispersal of plants occurs more frequently than previously thought. Here, however, we document one of the most exceptional examples of such dispersal. Despite c. 18 000 km separating A. heterophylla and A. koa, these two island endemics from two different oceans probably represent a single taxon as a result of recent extreme long-distance dispersal., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

This study was directed at the understanding of the function of CCoAOMT isolated from Acacia auriculiformis x Acacia mangium. Full length cDNA of the Acacia hybrid CCoAOMT (AhCCoAOMT) was 1024-bp long, containing 750-bp coding regions, with one major open reading frame of 249 amino acids. On the other hand, full length genomic sequence of the CCoAOMT (AhgflCCoAOMT) was 2548 bp long, containing three introns and four exons with a 5' untranslated region (5'UTR) of 391 bp in length. The 5'UTR of the characterized CCoAOMT gene contains various regulatory elements. Southern analysis revealed that the Acacia hybrid has more than three copies of the CCoAOMT gene. Real-time PCR showed that this gene was expressed in root, inner bark, leaf, flower and seed pod of the Acacia hybrid. Downregulation of the homologous CCoAOMT gene in tobacco by antisense (AS) and intron-containing hairpin (IHP) constructs containing partial AhCCoAOMT led to reduction in lignin content. Expression of the CCoAOMT in AS line (pART-HAS78-03) and IHP line (pART-HIHP78-06) was reduced respectively by 37 and 75% compared to the control, resulting in a decrease in the estimated lignin content by 24 and 56%, respectively. AhCCoAOMT was found to have altered not only S and G units but also total lignin content, which is of economic value to the pulp industry. Subsequent polymorphism analysis of this gene across eight different genetic backgrounds each of A. mangium and A. auriculiformis revealed 47 single nucleotide polymorphisms (SNPs) in A. auriculiformis CCoAOMT and 30 SNPs in A. mangium CCoAOMT.

Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo- and paleo-endemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo- and paleo-endemism, useful to the conservation decision-making process.

Motivation: Rich collections of biodiversity information such as spatial distributions, species descriptions and trait data are now synthesized in publicly available online sources such as GBIF. Also phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. We demonstrate with PhyloJIVE that any phylogenetic tree can be linked to online biodiversity data in the browser. This evolutionary view of biodiversity data is demonstrated in a case study that suggests that this approach may be useful to scientists and non-experts users.

Organogenesis is an important process for plant regeneration by tissue or cell mass differentiation to regenerate a complete plant. MicroRNAs (miRNAs) play an essential role in regulating plant development by mediating target genes at transcriptional and post-transcriptional levels, but the diversity of miRNAs and their potential roles in organogenesis of Acacia crassicarpa have rarely been investigated. In this study, approximately 10 million sequence reads were obtained from a small RNA library, from which 189 conserved miRNAs from 57 miRNA families, and 7 novel miRNAs from 5 families, were identified from A. crassicarpa organogenetic tissues. Target prediction for these miRNAs yielded 237 potentially unique genes, of which 207 received target Gene Ontology annotations. On the basis of a bioinformatic analysis, one novel and 13 conserved miRNAs were selected to investigate their possible roles in A. crassicarpa organogenesis by qRT-PCR. The stage-specific expression patterns of the miRNAs provided information on their possible regulatory functions, including shoot bud formation, modulated function after transfer of the culture to light, and regulatory roles during induction of organogenesis. This study is the first to investigate miRNAs associated with A. crassicarpa organogenesis. The results provide a foundation for further characterization of miRNA expression profiles and roles in the regulation of diverse physiological pathways during adventitious shoot organogenesis of A. crassicarpa.

Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity because of the effects of inbreeding and genetic drift. Across the globe, terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance and a lack of evidence of recent genetic bottlenecks suggest long-term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology., (© 2013 John Wiley & Sons Ltd.)

Background: The influence of introduction history and post-introduction dynamics on genetic diversity and structure has been a major research focus in invasion biology. However, genetic diversity and structure in the invasive range can also be affected by human-mediated processes in the native range prior to species introductions, an aspect often neglected in invasion biology. Here we aim to trace the native provenance of the invasive tree Acacia pycnantha by comparing the genetic diversity and structure between populations in the native Australian range and the invasive range in South Africa. This approach also allowed us to explore how human actions altered genetic structure before and after the introduction of A. pycnantha into South Africa. We hypothesized that extensive movement and replanting in A. pycnantha's Australian range prior to its introduction to South Africa might result in highly admixed genotypes in the introduced range, comparable genetic diversity in both ranges, and therefore preclude an accurate determination of native provenance(s) of invasive populations., Results: In the native range Bayesian assignment tests identified three genetic clusters with substantial admixture and could not clearly differentiate previously identified genetic entities, corroborating admixture as a result of replantings within Australia. Assignment tests that included invasive populations from South Africa indicated similar levels of admixture compared to Australian populations and a lack of genetic structure. Invasive populations of A. pycnantha in South Africa are as genetically diverse as native populations, and could not be assigned to particular native range regions., Conclusions: Our results indicate that the genetic structure of A. pycnantha in Australia has been greatly altered through various planting initiatives. Specifically, there is little geographic structure and high levels of admixture. While numerous introduction history scenarios may explain the levels of admixture observed in South Africa, planting records of A. pycnantha in Australia suggest that populations were probably already admixed before propagules were introduced to South Africa. These findings have important implications for the management of invasive A. pycnantha populations in South Africa, especially for classical biological control, and more broadly, for studies that aim to understand the evolutionary dynamics of the invasion process.

Background: Repeated colonisation of novel host-plants is believed to be an essential component of the evolutionary success of phytophagous insects. The relative timing between the origin of an insect lineage and the plant clade they eat or reproduce on is important for understanding how host-range expansion can lead to resource specialisation and speciation. Path and stepping-stone sampling are used in a Bayesian approach to test divergence timing between the origin of Acacia and colonisation by thrips. The evolution of host-plant conservatism and ecological specialisation is discussed., Results: Results indicated very strong support for a model describing the origin of the common ancestor of Acacia thrips subsequent to that of Acacia. A current estimate puts the origin of Acacia at approximately 6 million years before the common ancestor of Acacia thrips, and 15 million years before the origin of a gall-inducing clade. The evolution of host conservatism and resource specialisation resulted in a phylogenetically under-dispersed pattern of host-use by several thrips lineages., Conclusions: Thrips colonised a diversity of Acacia species over a protracted period as Australia experienced aridification. Host conservatism evolved on phenotypically and environmentally suitable host lineages. Ecological specialisation resulted from habitat selection and selection on thrips behavior that promoted primary and secondary host associations. These findings suggest that delayed and repeated colonisation is characterised by cycles of oligo- or poly-phagy. This results in a cumulation of lineages that each evolve host conservatism on different and potentially transient host-related traits, and facilitates both ecological and resource specialisation.

Background and Aims: Understanding the introduction history of invasive plant species is important for their management and identifying effective host-specific biological control agents. However, uncertain taxonomy, intra- and interspecific hybridization, and cryptic speciation may obscure introduction histories, making it difficult to identify native regions to explore for host-specific agents. The overall aim of this study was to identify the native source populations of Acacia pycnantha, a tree native to south-eastern Australia and invasive in South Africa, Western Australia and Portugal. Using a phylogeographical approach also allowed an exploration of the historical processes that have shaped the genetic structure of A. pycnantha in its native range., Methods: Nuclear (nDNA) and plastid DNA sequence data were used in network and tree-building analyses to reconstruct phylogeographical relationships between native and invasive A. pycnantha populations. In addition, mismatch distributions, relative rates and Bayesian analyses were used to infer recent demographic processes and timing of events in Australia that led to population structure and diversification., Key Results: The plastid network indicated that Australian populations of A. pycnantha are geographically structured into two informally recognized lineages, the wetland and dryland forms, whereas the nuclear phylogeny showed little geographical structure between these two forms. Moreover, the dryland form of A. pycnantha showed close genetic similarity to the wetland form based on nDNA sequence data. Hybrid zones may explain these findings, supported here by incongruent phylogenetic placement of some of these taxa between nuclear and plastid genealogies., Conclusions: It is hypothesized that habitat fragmentation due to cycles of aridity inter-dispersed with periods of abundant rainfall during the Pleistocene (approx. 100 kya) probably gave rise to native dryland and wetland forms of A. pycnantha. Although the different lineages were confined to different ecological regions, we also found evidence for intraspecific hybridization in Victoria. The invasive populations in Portugal and South Africa represent wetland forms, whereas some South African populations resemble the Victorian dryland form. The success of the biological control programme for A. pycnantha in South Africa may therefore be attributed to the fact that the gall-forming wasp Trichilogaster signiventris was sourced from South Australian populations, which closely match most of the invasive populations in South Africa.

Acacia mangium and A. mangium × A. auriculiformis hybrids have gained an increasing interest in reafforestation programs under the humid tropical conditions, mainly for pulpwood production. This is due to their impressive growth on acid and degraded soils, as well as their capability to restore soil fertility thanks to their natural nitrogen-fixing ability. It is crucial to develop efficient methods for improving the genetic quality and the mass production of the planting stocks of these species. In this regard, in vitro micropropagation is well suited to overcome the limitations of more conventional techniques for mass propagating vegetatively selected juvenile, mature, or even transgenic genotypes. Micropropagation of A. mangium either from seeds or from explants collected from outdoors is initiated on Murashige and Skoog (MS) basal medium supplemented with 4.4 μM BA. Microshoot cultures produced by axillary budding are further developed and maintained by regular subcultures every 60 days onto fresh MS culture medium added with 2.2 μM BA + 0.1 μM NAA. This procedure enhances the organogenic capacity for shoot multiplication by axillary budding, with average multiplication rates of 3-5 every 2 months, as well as for adventitious rooting. The rooting is initiated on Schenk and Hildebrandt culture medium containing 4 μM IAA. The maintenance of shoot cultures in total darkness for 3 weeks increases the rooting rates reaching more than 70%. The hybrid A. mangium × A. auriculiformis genotypes are subcultured at 2-month intervals with an average multiplication rate of 3 and rooting rates of 95-100% on a half-strength MS basal medium containing 1.1 μM NAA. The rooted microshoots are transferred to ex vitro controlled conditions for acclimatization and further growth, prior to transfer to the field, or use as stock plants for cost-effective and true-to-type mass production by rooted cuttings.

Background: Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids., Results: We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100%) compared to the traditional in vitro approach (44%). Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50%) of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively., Conclusion: We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely related species, we converted most SNPs to successful assays. We also demonstrated that Illumina GoldenGate genotyping together with manual clustering can provide high quality genotypes for a non-model species like Acacia. These SNPs markers are not only important for linkage map construction, but will be very useful for hybrid discrimination and genetic diversity assessment of natural germplasms in the future.

Colchicine-induced neoautotetraploid genotypes of Acacia mangium were cloned and planted in mixture with a set of diploid clones in an orchard in southern Vietnam. Following good general flowering, open-pollinated seed was collected from trees of both cytotypes and microsatellite markers were used to determine the breeding system as characterised by the proportion of outcrosses in young seedling progeny. As predicted from the literature, the progeny of diploid clones were predominantly outcrossed (t(m) = 0.97). In contrast, the progeny of the tetraploid clones were almost entirely selfs (t(m) = 0.02; 3 of 161 seedlings assayed were tetraploid outcrosses and there were no triploids). Segregation at loci heterozygous in the tetraploid mothers followed expected ratios, indicating sexual reproduction rather than apomixis. Post-zygotic factors are primarily responsible for divergence of the breeding systems. Commonly, less than 1 % of Acacia flowers mature as a pod, and after mixed pollination, diploid outcrossed seed normally develops at the expense of selfs. Selfs of the tetraploid trees appear to express less genetic load and have a higher probability of maturing. However, this does not fully explain the observed deficiency of outcross tetraploid progeny. Presumably, there are cytogenetic reasons which remain to be investigated. In nature, selfing would increase the probability of establishment of neotetraploids irrespective of cytotype frequency in the population. Breeders need to review their open-pollinated breeding and seed production strategies. It remains to be seen whether this is an ephemeral problem, with strong fertility selection restoring potential for outcrossing over generations.

Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h(T(cpSSR))=0.903-0.948) and population differentiation (G(ST(RFLP))=0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G(ST(cpSSR))=0.392; R(ST)=0.673; R(ST)>R(ST) (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.

The ability of an invasive species to establish and spread to new areas may depend on its ability to tolerate a broad range of environmental conditions. Due to climate change, increasing occurrences of extreme events such as droughts are expected in the Mediterranean region and invasive species may expand if they cope with water stress. Limited information is available on the responses of Acacia longifolia, one of the most aggressive plant species in Portuguese coastal sand dune ecosystems, to prolonged water stress. In this study, we exposed A. longifolia plants from two distinct populations, one from the wet (northern) and another from the dry (southern) climate regions of Portugal, to drought conditions, and monitored morphological, physiological and biochemical responses. One-month-old seedlings were submitted to three different water treatments which involved watering twice a week, every 7 days and every 10 days, respectively, for three months, under controlled conditions. Overall, the progressive drought stress significantly affected most of the growth parameters considered, except the root:shoot ratio. Water stress also increased the uptake of ions (Ca²⁺, Mg²⁺, K⁺ and Na⁺) and N concentration. On the contrary, the C/N ratio decreased under water stress conditions. Isotopic analysis did not reveal significant differences in δ¹³C with water treatments but the same pattern was not observed in δ¹⁵N values. Compared with the wet climate population, the dry climate population showed somewhat differing responses to water stress, indicating a genetic difference between populations. These results provide insights into limitations and opportunities for establishment of A. longifolia in a drought-prone scenario., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)

Acacia saligna is a species complex that has become invasive in a number of countries worldwide where it has caused substantial environmental and economic impacts. Understanding genetic and other factors contributing to its success may allow managers to limit future invasions of closely related species. We used three molecular markers to compare the introduced range (South Africa) to the native range (Western Australia). Nuclear markers showed that invasive populations are divergent from native populations and most closely related to a cultivated population in Western Australia. We also found incongruence between nuclear and chloroplast data that, together with the long history of cultivation of the species, suggest that introgressive hybridization (coupled with chloroplast capture) may have occurred within A. saligna. While we could not definitively prove introgression, the genetic distance between cultivated and native A. saligna populations was comparable to known interspecific divergences among other Acacia species. Therefore, cultivation, multiple large-scale introductions and possibly introgressive hybridization have rapidly given rise to the divergent genetic entity present in South Africa. This may explain the known global variation in invasiveness and inaccuracy of native bioclimatic models in predicting potential distributions., (© 2012 Blackwell Publishing Ltd.)

MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.

Background and Aims: The ecological, evolutionary and genetic bases of population differentiation in a variable environment are often related to the selection pressures that plants experience. We compared differences in several growth- and defence-related traits in two isolated populations of Acacia raddiana trees from sites at either end of an extreme environmental gradient in the Negev desert., Methods: We used random amplified polymorphic DNA (RAPD) to determine the molecular differences between populations. We grew plants under two levels of water, three levels of nutrients and three levels of herbivory to test for phenotypic plasticity and adaptive phenotypic plasticity., Key Results: The RAPD analyses showed that these populations are highly genetically differentiated. Phenotypic plasticity in various morphological traits in A. raddiana was related to patterns of population genetic differentiation between the two study sites. Although we did not test for maternal effects in these long-lived trees, significant genotype × environment (G × E) interactions in some of these traits indicated that such plasticity may be adaptive., Conclusions: The main selection pressure in this desert environment, perhaps unsurprisingly, is water. Increased water availability resulted in greater growth in the southern population, which normally receives far less rain than the northern population. Even under the conditions that we defined as low water and/or nutrients, the performance of the seedlings from the southern population was significantly better, perhaps reflecting selection for these traits. Consistent with previous studies of this genus, there was no evidence of trade-offs between physical and chemical defences and plant growth parameters in this study. Rather, there appeared to be positive correlations between plant size and defence parameters. The great variation in several traits in both populations may result in a diverse potential for responding to selection pressures in different environments.

Background: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15-35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem., Results: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species., Conclusions: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses suggest an evolutionary mechanism for miRNA targets on the basis of the length of their 5' and 3' UTRs and their cellular roles. The results obtained can be used to better understand the roles of small RNAs during lignin biosynthesis and for the development of gene constructs for silencing of specific genes involved in monolignol biosynthesis with minimal effect on plant fitness and viability. For the first time, small RNAs were proven to play an important regulatory role during lignin biosynthesis in A. mangium.