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Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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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 New targets acquired: Improving locus recovery from the Angiosperms353 probe set(Botanical Society of America, 14/06/2021) McLay T; Birch J; Gunn B; Ning W; Tate J; Nauheimer L; Joyce E; Simpson L; Schmidt-Lebuhn A; Baker W; Forest F; Jackson CPREMISE: 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. METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.