Background: Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specifc basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specifc basecaller models. We also evaluate accuracy gains from ONT’s improved fowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.

Results: Basecalling with ONT Guppy 5 and 6 super-accurate gave almost identical results, attaining read accuracies of 91.96% and 94.15%. Guppy’s plant-specifc model gave highly mixed results, attaining read accuracies of 91.47% and 96.18%. Species-specifc basecalling models improved read accuracy, attaining 93.24% and 95.16% read accuracies. R10.4 sequencing kits also improve sequencing accuracy, attaining read accuracies of 95.46% (super-accurate) and 96.87% (species-specifc).

Conclusions: The use of a single mixed-species basecaller model, such as ONT Guppy super-accurate, may be reducing the accuracy of nanopore sequencing, due to conflicting genome biology within the training dataset and study species. Training of single-species and genome-specifc basecaller models improves read accuracy. Studies that aim to do large-scale long-read genotyping would primarily benefit from training their own basecalling models. Such studies could use sequencing accuracy gains and improving bioinformatics tools to improve study outcomes.

This dataset includes molecular data and associated metadata supporting the analysis of Prostanthera volucris (Lamiaceae) as a new, distinct species in the Central Tablelands. Samples of 3 taxa for this study were collected from across New South Wales, Australia.

Analysis code can be found at https://github.com/rpodonnell/ASB_PEC

Micromorphological investigations and morphometric analyses of median laminal cells in Ectropothecium Mitt. and its relatives in Hypnales confirmed the presence of protuberances in some taxa. Differences in form and size of protuberances were diagnostic and statistically significant in some taxa. Combined cpDNA (rpL32-trnL, trnH-,em>psbA, and trnSGG) and ITS1-5.8S-ITS2 nDNA sequence data were well-suited to examine evolutionary relationships of Ectropothecium. All analyses recovered Ectropothecium as paraphyletic and supported sister relationships of Ectropothecium and Vesicularia (Müll.Hal.) Müll.Hal. Analyses of molecular and combined data supported the monophyly of Australasian Ectropothecium, with the inclusion of Trachythecium verrucosum (A.Jaeger) M.Fleisch. in Ectropothecium. These latter analyses also recovered Ectropothecium and Vesicularia as sisters.

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate signifcant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

The Australian and New Guinean everlasting paper daisy genus Xerochrysum, widely grown around the world as Strawflower, Everlasting or Immortelle, was recently revised. The first and type species, Xerochrysum bracteatum, was described in 1803 as Xeranthemum bracteatum from a plant cultivated in the Empress Joséphine's garden at Malmaison. During our project, we learned that Xerochrysum was naturalised in St. Helena, the place of Napoleón Bonaparte's last exile, and is presumed to have been introduced by him. We conducted genetic analyses to test the derivation of the St. Helena plants. Comparisons with some colourful hybrid cultivars and naturally occurring populations in Australia found the St. Helena plants to be most similar to Xerochrysum bracteatum s. str. of the Sydney Basin. The St. Helena plants were without admixture of another species as would be expected if they were more recently escaped ornamental cultivars. Our results support the conclusion that the St. Helena Xerochrysum were introduced during Napoleón's exile, likely as a reminder of his wife's garden.