Biology subjects

Bragg, J. G.

Publications and source records attributed to Bragg, J. G..

8 recordsLinked to original sources

bioRxiv2025

Genome assembly of Spinifex sericeus provides insights into repetitive content and haplotype variation in a dioecious coastal grass

Spinifex sericeus (beach spinifex) is a perennial, dioecious grass native to coastal ecosystem of Oceania that has an important role in dune stability. We present a near telomere-to-telomere, haplotype-resolved nuclear genome alongside complete organelle genomes of S. sericeus. The nuclear genome is highly repeat-rich, dominated by long terminal repeat (LTR) retrotransposons. Comparative analysis of the two haplotypes reveals extensive structural variation and high levels of duplication that are suggestive of active and expanding LTRs that may drive genome evolution and expansion in this species. The chloroplast genome exhibits heteroplasmy, having two distinct circular configurations spanning 138 kbp each. The complex mitochondrial genome consists of a large linear component spanning 1.85 Mbp and a small circular 134 kbp component. These genomic resources provide a foundation for advancing research on sex determination and stress adaptation in grasses, and well as practical applications in crop improvement and genetically informed coastal dune restoration. Significance statementThe reference genome of Spinifex sericeus provides a foundational resource for understanding adaptations to the harsh coastal dune environment, including saline conditions, extreme temperatures, and drought. The genome enables comparative studies within Poaceae, where current reference genomes are dominated by crop species, and supports conservation and restoration efforts for coastal ecosystem management.

genomics↗

bioRxiv2025

Genomic prediction of disease resistance provides a path to marker assisted restoration in a wetland foundation tree species

Tree species worldwide are under threat from non-native pathogens that impact forests and the ecosystem services they provide. Myrtle rust, caused by Austropuccinia psidii, is one example, first detected in Australia in 2010. This fungal pathogen infects immature tissue from a wide range of Myrtaceae hosts, including the wetland foundation species Melaleuca quinquenervia. Durable restoration action for this species would preferentially incorporate disease resistant individuals. Our aim for this study was to provide a molecular assay to identify and select resistant individuals and seed lots for restoration. We conducted artificial inoculation of a panel of seedlings and measured their immune responses to myrtle rust. We then performed whole genome sequencing (3.2M common SNPs) and conducted a Genome Wide Association Study (N = 492), which revealed clusters of significantly associated SNPs in three chromosomal regions, including clusters of putative R genes. Associated SNPs were filtered to a panel of 1,049 for a highly accurate genomic prediction model (R = 0.83). This provides a relatively inexpensive approach to identifying resistant individuals or seed lots for restoration and a template for managing myrtle rust impacts while maintaining population genetic diversity.

plant biology↗

bioRxiv2024

Genomics and resistance assays inform the management of two tree species being devastated by the invasive myrtle rust pathogen

Myrtle rust is a plant disease caused by the invasive fungal pathogen Austropuccinia psidii (G. Winter) Beenken, which has a global host list of 480 species. It was detected in Australia in 2010 and has caused the rapid decline of native Myrtaceae species, including rainforest trees Rhodamnia rubescens (Benth.) Miq. (scrub turpentine) and Rhodomyrtus psidioides (G.Don) Benth. (native guava). Ex situ collections of these species have been established, with the goal of preserving remaining genetic variation. Analysis of reduced representation sequencing (DArTseq; n = 444 for R. rubescens and n = 301 for R. psidioides) showed genetic diversity is distributed along a latitudinal gradient across the range of each species. A panel of samples of each species (n = 27 for R. rubescens and n = 37 for R. psidioides) were resequenced at genome scale, revealing large historical e]ective population sizes, and little variation among individuals in inferred levels of deleterious load. In Rhodamnia rubescens, experimental assays (n = 297) identified individuals that are putatively resistant to myrtle rust. This highlights two important points: there are tangible pathways to recovery for species that are highly susceptible to rust via a genetically informed breeding program, and there is a critical need to act quickly before more standing diversity is lost.

genomics↗

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↗

bioRxiv2023

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

BackgroundThe coastal wetland tree species Melaleuca quinquenervia (Cav.) S.T.Blake (Myrtaceae), commonly named the broad-leaved paperbark, is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are still presented in their haploid, collapsed state, the full allelic diversity of the NLR gene family has not been widely published for outcrossing tree species. ResultsWe assembled a chromosome-level pseudo-phased genome for M. quinquenervia and describe the full allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains. ConclusionsWe anticipate that the high quality of the genome for M. quinquenervia will provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.

genomics↗

bioRxiv2021

Genomic constraints to drought adaptation

Global shifts in climate and precipitation patterns are altering the diversity and structure of forests. The ability for species to adapt is especially difficult for long lived foundation species with unknown genetic and trait diversity. We harnessed genomic, physiological, and climate data to determine adaptation constraints. We used denovo assembly and 6.5 million genomic variants with drought related traits from 432 individuals sourced from across the complete range of the foundation tree species Corymbia calophylla. We found genomic variants determining traits predominantly in gene regulatory regions. The ability for populations to adapt was limited by within population genetic diversity associated with traits, and epistatic interactions within traits and pleiotropic interactions among traits. Nevertheless, we could accurately predict adaptive traits using genomic and climate data to guide reforestation. Our study indicated that some populations may contain variation sufficient for the species to adapt to the effects of drought, while other populations will need increased variability from those sources.

evolutionary biology↗

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

Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change

As species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions. Eucalyptus melliodora is a foundation species of a critically endangered community in Australia that is a target for restoration. We examined patterns of genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining gene flow up to 500 km and associations with environmental variables. Climate chamber studies revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Overall our results suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model to E. melliodora restoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration.

genomics↗