Biology subjects

Lu-Irving, P.

Publications and source records attributed to Lu-Irving, P..

5 recordsLinked to original sources

bioRxiv2025

Tangled evolutionary history: genetically divergent taxa and hybrids characterise lantana invasions in Australia

Aimto investigate population genomics and phylogeography in invasive lantana, including its taxonomy, spatial distribution, and patterns of morphological and genetic variation across the Australian continent. Locationthe main area invaded by lantana on the Australian continent, i.e., coastal and subcoastal eastern Australia from northern Queensland to southern New South Wales up to approximately 100 km inland, across 22 degrees latitude. The native range of lantana in the Americas was also represented. Methodswe used DArTseq to generate genome-wide single nucleotide polymorphism (SNP) data for >600 individuals representing the native and Australian invaded ranges of lantana. We analysed data from >20,000 SNPs to identify distinct genetic clusters, and test the extent to which they corresponded with taxonomic descriptions and morphotype concepts used in lantana biological control. Genome sizes were estimated for a small representative subset of individuals using flow cytometry. We used MaxEnt to estimate habitat suitability for different lantana genetic clusters, and compared these predictions with observed patterns in biological control agent host-specificity. Resultsinvasive lantana in Australia consisted of several divergent genetic clusters of most likely tetraploid individuals. Gene flow between genetic clusters was limited, consistent with the notion that multiple species introductions and/or hybridisation events were part of the invasion history. Two widespread, homogeneous genetic clusters were found to be dominant in Australia; two other genetic clusters with more limited distributions were identified with potential for future spread. Biological control agent host preferences were consistent with identified genetic clusters. Main conclusionstreating invasive lantana as a single taxon may be counterproductive for effective management. Comprehensive taxonomic revision is needed to enable more precise identification of invasive taxa. Improved identification will support improved management, particularly if using biological control.

evolutionary biology↗

bioRxiv2024

Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data

Technological advances have propelled DNA sequencing of non-model organisms, making sequencing more accessible and cost effective, which has also increased the availability of raw data in public repositories. However, contamination is a significant concern, and the use and reuse of sequencing data requires quality control and curation. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp assembly anchored to 11 chromosomes (2n = 22). The R. argentea genome will inform conservation efforts for Myrtaceae species threatened by the global spread of the fungal disease myrtle rust. We observed contamination in the sequencing data and further investigation revealed an arthropod source. Here, we demonstrate the feasibility of assembling a high-quality gapless telomere-to-telomere mite genome using contaminated host plant sequencing data. The mite exhibits genome streamlining and has a 35 Mbp genome (68.6% BUSCO completeness) on two chromosomes, capped with a novel TTTGG telomere sequence. Phylogenomic analysis suggests that it is a previously unsequenced eriophyoid mite. Despite its unknown identity, this complete nuclear genome provides a valuable resource to investigate invertebrate genome reduction. This study emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of two species, including a tree that faces substantial conservation challenges, contributing to broader biodiversity initiatives. SignificanceThe genomes of Rhodamnia argentea and an associated eriophyoid mite, which contaminated the tree raw sequencing data, were assembled for the first time. We generated valuable chromosome-level genomic resources for the conservation of myrtle rust impacted tree species, pest genomics, and understanding genome streamlining. The research underscores the growing prevalence of sequencing experiments in non-model organisms while emphasising the importance of quality control and curation of sequencing data.

genomics↗

bioRxiv2021

Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs complete. We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 Duplicated BUSCO genes suggest almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

genomics↗

bioRxiv2017

Variation in the oxidative burst in response to wounding and bacterial infection among native and invading genotypes of yellow starthistle (Centaurea solstitialis)

O_LIPremise of the study: Invasive plants may leave enemies behind when they colonize a new habitat, allowing selection to favor increased investment in growth and/or reproduction over defensive traits. Previous studies have identified reduced diversity of potential bacterial pathogens and evolutionary increases in growth and reproduction in invading populations of yellow starthistle (Centaurea solstitialis). This study leverages a recently developed high-throughput assay of immune function to test for evidence of a trade-off between increased growth and defense against bacterial pathogens in yellow starthistles invasion of California (USA).\nC_LIO_LIMethods: Seven bacterial strains were cultured from infected leaf tissue in the native range. Healthy leaf tissue from five native European collections and six invading collections were exposed to these native bacterial strains. A standardized assay of peroxidase activity was used measure the oxidative burst immune response to pathogen recognition by the leaf. Immune responses were compared to plant growth within and between ranges to assess evidence for a trade-off.\nC_LIO_LIKey Results: Plant genotypes from the native range demonstrated a higher immune response to bacterial strains than did invading genotypes, consistent with a trade-off with plant growth across regions. The same trade-off was also apparent across genotypes from the native range, but not across genotypes from the invaded range.\nC_LIO_LIConclusions: Our results provide evidence that increased growth in a highly invasive plant species may come at a cost to immune function, consistent with the hypothesis that escape from enemies can provide opportunities for shifts in resource allocation that favor the proliferation of non-native species.\nC_LI

plant biology↗

bioRxiv2017

Escape from bacterial diversity: potential enemy release in invading yellow starthistle (Centaurea solstitialis) microbiomes

O_LIInvasive species could benefit from introduction to locations with favorable species interactions. Microbiomes are an important source of interactions that vary across regions. We examine whether bacterial communities could explain more favorable microbial interactions in highly invasive populations of yellow starthistle.\nC_LIO_LIWe sequenced amplicons of prokaryotic 16S rRNA genes to characterize bacterial community composition in the phyllosphere, ectorhizosphere, and endorhizosphere of plants from seven invading populations in California, USA and eight native populations in Europe. We tested for differentiation of microbiomes by geography, plant compartment, and plant genotype.\nC_LIO_LIBacterial communities differed significantly between native and invaded ranges within plant compartments, with consistently lower diversity in plants from the invaded range. Genera containing known plant pathogens also showed lower diversity in invaded range plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbial differences between ranges.\nC_LIO_LIOur findings reveal changes in the composition and diversity of bacterial interactions in invading plants, consistent with observations of altered soil interactions in this invasion. These results call for further study of the sources of variation in microbiomes and the potential for bacteria to facilitate invasion success.\nC_LI

plant biology↗