Journal Articles
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Item Comparative analysis of plastid genomes from allopolyploid Tragopogon miscellus and its diploid parents(John Wiley and Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands, 2025-09-15) Mukhtar U; Newmarch SC; Winkworth RC; Soltis PS; Soltis DE; Tate JA; Wang X-QTragopogon is a model system for the study of recent, recurrent, and reciprocal allopolyploid formation. Recent research has focused on the fates of nuclear genes duplicated in the allopolyploid T. miscellus relative to the parental diploids, T. dubius and T. pratensis. In contrast, little attention has been given to organellar genomes, which interact with the duplicated nuclear genomes via their gene products. Here we reconstructed plastid genomes (plastomes) for representatives of these three species to investigate their structure and variability among natural and synthetic allopolyploids. Genomic libraries were Illumina-sequenced for several individuals of the allopolyploid T. miscellus and its diploid parents. Whole plastomes were assembled from skimmed data with comparative analyses used to quantify structural and nucleotide variation. Tragopogon plastomes have a typical quadripartite structure and are similar in size to those of other Asteraceae. The 12 plastomes were highly similar, sharing ~99.5%–100% identity. In all but one case, the plastome sequence for each of the polyploids was most similar to that of its expected maternal parent. The exception involved a polyploid that unexpectedly had a T. dubius plastome type, likely as the result of backcrossing with its presumed paternal parent. Such backcrossing events may have contributed to the demise of this polyploid population. Plastome sequences can be used to infer the maternal origins of polyploids as well as investigate ongoing population-level dynamics. More fully assessing plastome variation across the geographic distribution of polyploids and their diploid progenitors may provide additional insights into polyploid formation, population dynamics, and subsequent evolution.Item Evolutionary relationships in Santalales inferred using target capture with Angiosperms353, focusing on Australasian Santalaceae sensu lato(CSIRO Publishing, Australia, 2025-08) Anderson BM; Edlund M; James SA; Lepschi BJ; Nickrent DL; Sultan A; Tate JA; Petersen G; Murphy DThe angiosperm order Santalales comprises more than 2500 species, most of which are hemi- or holoparasitic on other plants, and derive water and nutrients via specialised structures that attach to host roots or stems. The parasitic lifestyle has affected the morphology and genomes of these plants, and classification of the order has been difficult, with outstanding questions about membership of and relationships between families in the order. We chose to focus on improving phylogenetic sampling in the broadly circumscribed Santalaceae sens. lat., with emphasis on Australasian members of Amphorogynaceae and Viscaceae as part of the Genomics for Australian Plants Initiative. We used target capture with the Angiosperms353 bait set to generate a dataset of 318 nuclear loci × 195 samples, including publicly available data from other Santalales families. Phylogenetic inferences using maximum likelihood concatenation and a summary coalescent approach were largely congruent and resolved relationships between most families, agreeing with much of the previous work on the order. Some relationships that have been difficult to resolve remained so, such as branching order among some families in Olacaceae sens. lat. and Santalaceae sens. lat. Denser sampling in Amphorogynaceae and Viscaceae provided new insights into species-level relationships in genera such as Leptomeria and Choretrum, and allowed testing of recent phylogenetic work in Korthalsella. Our new phylogenetic hypothesis is consistent with one origin of root hemiparasitism, two origins of holoparasitism and five origins of aerial parasitism in the order. Although Angiosperms353 was successful, some phylogenetic bias in gene recovery suggests that future studies may benefit from more specific baits and deeper sequencing, especially for Viscaceae.Item Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand(Elsevier Inc, USA, 2026-01) Ning W; Meudt HM; Nicolas AN; Plunkett GM; Heenan PB; Lee WG; Tate JAGenera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in Azorella (Apiaceae) sections Schizeilema and Stilbocarpa that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6x and 10x), and assess the biogeography of the New Zealand Azorella species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two Azorella sections in New Zealand likely resulted from different biogeographic events from South America − one to the subantarctic islands (section Stilbocarpa) and a second to the South Island (section Schizeilema). In addition, within section Schizeilema, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand Azorella and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.Item Sequence data support greater taxonomic diversity and a complicated history of hybridisation in New Zealand’s sun orchids - Thelymitra (Orchidaceae)(Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2025-06-26) Jones HR; Lehnebach CA; Tate JAThelymitra, commonly known as sun orchids, is a genus of orchids present in New Zealand (NZ), known for their radially symmetrical and brightly coloured flowers. A long history of nomenclatural changes, and a recent and rapid circumscription of Australian (AU) taxa has left our understanding of this genus in NZ lagging. In this study we report two phylogenies of NZ Thelymitra species, based on nuclear (LFY) and plastid (ycf1) sequence data. The phylogenies identify support for several taxa currently only known by tag-names as being distinct from those that are currently described both in NZ and AU, as well as evidence supporting an extensive history of hybrid speciation in this genus in NZ, which had been hypothesised previously for six species. This work has also found evidence for species complexes within NZ Thelymitra that need further molecular and taxonomic work to fully resolve species boundaries. In this study we also demonstrate a novel application of nanopore sequencing of amplicons, that enables the recovery of multiple sequence copies in allopolyploid taxa without the prior need for cloning.Item Simple and Efficient Transformation and Gene Editing of Marchantia polymorpha Spores(Wiley Periodicals LLC, 2025-05-27) Yorker RM; Deroles SC; Zhou Y; Tate JA; Davies KM; Albert NWMarchantia polymorpha (Marchantia) has become a model species for liverwort studies, owing to its rapid growth in vitro, ease of propagation, simple genetics, small genome, haploid-dominant life cycle, and because it is amenable to genetic transformation. Efficient transformation provides a foundation for many molecular and genetic analyses. The protocol described here is a simple and robust procedure for transforming Marchantia for a variety of applications, including gene overexpression and CRISPR genome editing. This simplified Agrobacterium tumefaciens-mediated transformation protocol targets spores, using common Agrobacterium strains GV3101 or EHA105, and overcomes challenges experienced in other methods. Spores are sterilized and distributed over sterile filter papers, which effectively retain spores and regenerating spores (known as sporelings). This approach enables the sporelings to be transferred to different agar growth media at different stages of transformation. A critical feature is preculturing the spores with acetosyringone (AS) prior to co-cultivation with Agrobacterium. This treatment profoundly enhances the transformation rate, particularly for Agrobacterium strain GV3101. GV3101 is preferred for its rapid growth rate, simple transformation, and lack of a recombinase (recA), stabilizing plasmids. The protocol is suitable for transforming Marchantia with constructs for CRISPR gene editing. Editing efficiency can be increased by introducing a heat-shock treatment during the transformation procedure, which increases the proportion of plants with larger edited sectors, facilitating mutant identification and propagation. Constructs and strategies for both overexpression and multiplex genome editing with sgRNA arrays using new and existing vectors are described. Using this spore transformation protocol for CRISPR gene editing, we routinely achieve 60% to 70% mutation rates, significantly reducing the effort required to generate and isolate mutants for functional analyses.Item Rhododendron diversity conservation in global botanic gardens: A case study of Maddenia species(Cambridge University Press on behalf of Fauna & Flora International, 2024-11-04) Hu L; MacKay M; Gardiner SE; Tate JAEffective ex situ conservation of plants in botanic gardens requires sufficient wild accessions to represent wild diversity. In Rhododendron L. (Ericaceae), c. 64% of the taxa are threatened or require field investigation. As a case study of the analysis of ex situ conservation gaps we used ecogeographical representation as a proxy for genetic representation in ex situ collections of the 65 taxa of Rhododendron subsection Maddenia. We compiled the first list profiling both wild distributions and ex situ wild collections of all taxa in subsection Maddenia. Our results reveal that 55 Maddenia taxa are in cultivation. Of the 18 threatened taxa all are in cultivation but nine require further collection to capture adequate wild diversity. There are 12 Data Deficient taxa: These await further field investigation of wild populations and nine of them require wild collections to conserve genetic diversity. The UK, the USA, Australia, New Zealand and China are the top five countries holding ex situ collections of subsection Maddenia; in these countries nearly 66% of the ex situ sites hold > 86% of the global living collections of subsection Maddenia. We recommend that wild collections of endemic species of subsection Maddenia should be established in all 10 countries of origin and that data should be shared internationally for metacollections. In addition to proposing priorities, our case study highlights the challenges facing data and collection management to help achieve effective ex situ conservation for Rhododendron species.Item Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover.(Springer Nature, 2025-01-23) Ehoche OG; Arojju SK; Jahufer MZZ; Jauregui R; Larking AC; Cousins G; Tate JA; Lockhart PJ; Griffiths AGGenomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from -0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100-120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28-124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.Item Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)(Elsevier Inc., 2024-11-22) Meudt HM; Pearson S; Ning W; Prebble JM; Tate JAIsland and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent radiation centred in New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these Myosotis species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from Aotearoa New Zealand and Australia, which is ∼ 2-3 × more taxon sampling and ∼ 80-120 × more molecular data than previously published for Myosotis. Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of Myosotis.Item Understanding Rhododendron intraspecific compatibility in botanic garden collections for species conservation(CSIRO Publishing, 2024-09-19) Hu L; Gardiner SE; Tate JA; MacKay MB; Nolan RContext Controlled pollination is an important technique for maintaining intraspecific diversity in integrated plant conservation practices, particularly in genera such as Rhododendron, where open pollination usually produces hybrids with unknown paternal lineages. Aims This study investigated the capacity for viable seed set from self- and intraspecific cross-pollination for Rhododendron taxa in different categories of the International Union for Conservation of Nature (IUCN) Red List, to guide conservation management of threatened species in botanic garden collections. Methods The following five taxa of subsection Maddenia were studied: R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), R. nuttallii (Near Threatened), and R. excellens (Vulnerable). Controlled pollination was performed on selected garden accessions, and seed germination was tested at an alternating temperature regime of 15/25°C, 8 h photoperiod, and ~6 μmol m−2 s−1 photosynthetic photon flux density (PPFD). Key results Intraspecific compatibilities varied among different taxa and between self- and outcross treatments. X-ray images for Rhododendron seeds showed low capacity to predict seed germination. Neither X-ray scan nor fungicide (Ridomil) treatment showed any adverse impact on seed germination, which has positive implications for seed-banking and subsequent raising of Rhododendron seedlings. Conclusions Controlled intraspecific pollination can be used to maintain diversity of ex situ accessions for selected Rhododendron species. However, the zero or low compatibility demonstrated in some species, such as R. excellens, suggests that these species may require a different approach. Implications Intraspecific pollination should be evaluated for each Rhododendron species before a propagation program is initiated in ex situ conservation.Item Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.(Frontiers Media S.A., 2022-01-09) Pearson SM; Griffiths AG; Maclean P; Larking AC; Hong SW; Jauregui R; Miller P; McKenzie CM; Lockhart PJ; Tate JA; Ford JL; Faville MJ; Xie W; Rodriguez VMIncreasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.