Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa

The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e(-5))numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.Matthew J. Christmas, Ed Biffin and Andrew J. Low

Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium

The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.Matthew J. Christmas, Ed Biffin, Martin F. Breed & Andrew J. Low

Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2

One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species includingferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency

Direct Evidence for Dominant Bond-directional Interactions in a Honeycomb Lattice Iridate Na2IrO3

Heisenberg interactions are ubiquitous in magnetic materials and have been prevailing in modeling and designing quantum magnets. Bond-directional interactions offer a novel alternative to Heisenberg exchange and provide the building blocks of the Kitaev model, which has a quantum spin liquid (QSL) as its exact ground state. Honeycomb iridates, A2IrO3 (A=Na,Li), offer potential realizations of the Kitaev model, and their reported magnetic behaviors may be interpreted within the Kitaev framework. However, the extent of their relevance to the Kitaev model remains unclear, as evidence for bond-directional interactions remains indirect or conjectural. Here, we present direct evidence for dominant bond-directional interactions in antiferromagnetic Na2IrO3 and show that they lead to strong magnetic frustration. Diffuse magnetic x-ray scattering reveals broken spin-rotational symmetry even above Neel temperature, with the three spin components exhibiting nano-scale correlations along distinct crystallographic directions. This spin-space and real-space entanglement directly manifests the bond-directional interactions, provides the missing link to Kitaev physics in honeycomb iridates, and establishes a new design strategy toward frustrated magnetism.Comment: Nature Physics, accepted (2015

Isoprenoid emission in hygrophyte and xerophyte European woody flora: ecological and evolutionary implications

Aim The relationship between isoprenoid emission and hygrophily was investigated in woody plants of the Italian flora, which is representative of European diversity. Methods Volatile isoprenoids (isoprene and monoterpenes) were measured, or data collected from the literature, for 154 species native or endemic to the Mediterranean. The Ellenberg indicator value for moisture (EIVM) was used to describe plant hygrophily. Phylogenetic analysis was carried out at a broader taxonomic scale on 128 species, and then refined on strong isoprene emitters (Salix and Populus species) based on isoprene synthase gene sequences (IspS). Results Isoprene emitters were significantly more common and isoprene emission was higher in hygrophilous EIVM classes, whereas monoterpene emitters were more widespread and monoterpene emission was higher in xeric classes. However, when controlling for phylogeny, isoprene emission was not associated with EIVM, possibly due to the large presence of Salicaceae among hygrophilous isoprene emitters. Moreover, the distribution of isoprene emitters among EIVM classes was not related to IspS-based phylogenesis in Populus and Salix, suggesting that the gene has not undergone evolution linked to ecological pressure. In contrast, the monoterpene emission pattern is independent of phylogeny, suggesting that the evolution of monoterpenes is associated with transitions to more xeric habitats. Main conclusions Our results reveal an interesting ecological pattern linking isoprenoids and water availability. We suggest that isoprene is a trait that: (1) evolved in plants adapted to high water availability; (2) is replaced by more effective protection mechanisms, e.g. more stable isoprenoids, in plants adapting to more xeric environments; and (3) being strongly constrained by phylogeny, persists in Salicaceae adapted to more xeric environments

Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO2 compared with biomes with similar fire regimes in other continents

Vitamin K: history, metabolism, and nutrition in the horse

Vitamin K (VK) has long been known for its essential role in blood coagulation. However, over the past decade, evidence has mounted for its intrinsic and essential roles in other functions within the body, including bone metabolism, calcification, brain development and glucose metabolism. Thus, VK should no longer be considered a single-function ‘haemostasis vitamin’, but rather as a ‘multi-function vitamin’. While current research has focused on its emerging role in human nutrition, the role that VK plays in other species such as the horse has not been well described, with most of our current understanding having been extrapolated from other species, especially rodents. This review assesses the current state of knowledge of VK as it pertains to human and animal nutrition, and, where data exist, its metabolism and nutrition in the horse is explored. Future research on the roles of VK as they pertain to horses, particularly extra-hepatic functions, is necessary. Such insight will allow a greater understanding of how VK is metabolised, facilitating the development of recommendations to assist in the health, growth, and longevity of horses

Genetic variability within seagrass of the north west of Western Australia: Report of Theme 5 - Project 5.2 prepared for the Dredging Science Node

The response of seagrass species to on-going pressures such as dredging can be strongly influenced by their ability to adapt to, resist or recover from these pressures. The ability of species to adapt to a pressure, over generations, is influenced by the amount of genetic variation in a population: greater genetic diversity can enhance resistance and higher levels of gene flow between populations can enhance the rate of recovery following complete habitat loss. As seagrass are clonal plants, genetic diversity in a meadow is dependent on both the number of unique clones within the meadow, and distribution of this variation within and among meadows. Understanding the genetic diversity of seagrass meadows can provide important fundamental knowledge for the prediction of dredging impacts, by providing insights into the likelihood of recovery and the processes that may drive that recovery (vegetative regrowth, seed bank recruitment or immigration of recruits). It can also inform management, for example by providing insights into relative vulnerability to pressures, sources of recruitment populations and the importance of maintaining seed banks. However, for most seagrasses and in most parts of the world, extremely little is known about the genetic diversity and connectivity of populations..