Analyzing sorbitol biosynthesis using a metabolic network flux model of a lichenized strain of the green microalga .

a unicellular terrestrial microalga found either free-living or in association with lichenized fungi, protects itself from desiccation by synthesizing and accumulating low-molecular-weight carbohydrates such as sorbitol. The metabolism of this algal species and the interplay of sorbitol biosynthesis with its growth, light absorption, and carbon dioxide fixation are poorly understood. Here, we used a recently available genome assembly for to develop a metabolic flux model and analyze the alga's metabolic capabilities, particularly, for sorbitol biosynthesis.

Chromosome-Level Genome Assembly of the Australian Rainforest Tree Rhodamnia argentea (Malletwood).

Myrtaceae are a large family of woody plants, including hundreds that are currently under threat from the global spread of a fungal pathogen, Austropuccinia psidii (G. Winter) Beenken, which causes myrtle rust. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth.

Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus and provides insights into plastid gene degeneration.

The orchid genus R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect.

Plastid phylogenomics clarifies broad-level relationships in (Orchidaceae) and provides insights into range evolution of Australasian section .

The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only section with a center of diversity in Australasia is sect. .

The AusTraits plant dictionary.

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources.

The origin and speciation of orchids.

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c.

Re-assessment of type material of Broth. and descriptions of four new taxa (Bryophyta, Plagiotheciaceae) from Australasia.

A re-examination of the original collection of described by Brotherus in 1916 indicated that this material is not homogeneous. Re-examination of the diagnosis of this species and morphological analysis supports that two separate taxa should be distinguished - Plagiotheciumnovae-seelandiaevar.novae-seelandiae and P.

Genome-wide CRISPR screening identifies a role for ARRDC3 in TRP53-mediated responses.

Whole-genome screens using CRISPR technologies are powerful tools to identify novel tumour suppressors as well as factors that impact responses of malignant cells to anti-cancer agents. Applying this methodology to lymphoma cells, we conducted a genome-wide screen to identify novel inhibitors of tumour expansion that are induced by the tumour suppressor TRP53. We discovered that the absence of Arrestin domain containing 3 (ARRDC3) increases the survival and long-term competitiveness of MYC-driven lymphoma cells when treated with anti-cancer agents that activate TRP53.

Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification.

Premise: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear.

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data.

hybpiper-nf and paragone-nf: Containerization and additional options for target capture assembly and paralog resolution.

Premise: The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog groups are computationally efficient and broadly applicable to non-model organisms, especially in the absence of a known species tree.

Beauveria australis finds a new host in French dung beetles introduced to Australia.

Exotic dung beetles have been introduced to Australia for over 50 years to mitigate issues caused by dung produced by livestock. This study aims at identifying fungi affecting a beetle colony and investigating their source. Fungal hyphae emerging from the cuticle of dead beetles were cultured and a multigene phylogeny showed that Beauveria bassiana and B.

Reproductive Strategies and Population Genetic Structure in Two Dryland River Floodplain Plants, and .

Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems, life history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies that allow plants to persist.

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods.

Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant-pollinator networks.

Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant-pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations.

Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics.

Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia's orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships, divergence times and range evolution in Pterostylidinae (Orchidoideae), the second largest subtribe in the Australian orchid flora, comprising the genera and .

Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia.

The Australasian biogeographic realm is a major centre of diversity for orchids, with every subfamily of the Orchidaceae represented and high levels of endemism at the species rank. It is hypothesised that there is a commensurate diversity of viruses infecting this group of plants. In this study, we have utilised high-throughput sequencing to survey for viruses infecting greenhood orchids (Pterostylidinae) in New South Wales and the Australian Capital Territory.

Polyploidy but Not Range Size Is Associated With Seed and Seedling Traits That Affect Performance of Species.

Ploidy and species range size or threat status have been linked to variation in phenotypic and phenological seed and seedling traits, including seed size, germination rate (speed) and seedling stature. There is surprisingly little known about the ecological outcomes of relationships between ploidy, key plant traits and the drivers of range size. Here we determined whether ploidy and range size in , a genus of shrubs that includes many threatened species, are associated with variation in seed and seedling traits that might limit the regeneration performance of obligate seeders in fire-prone systems.

Long-read assemblies reveal structural diversity in genomes of organelles - an example with .

Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, , using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure.

The evolution and biogeographic history of epiphytic thalloid liverworts.

Among liverworts, the epiphytic lifestyle is not only present in leafy forms but also in thalloid liverworts, which so far has received little attention in evolutionary and biogeographical studies. Metzgeria, with about 107 species worldwide, is the only genus of thalloid liverworts that comprises true epiphytes. In the present study, we provide the first comprehensive molecular phylogeny, including estimated divergence times and ancestral ranges of this genus.

Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding.

Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures.

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

Premise: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery.