Massey Research Online - Browsing by Author "Lockhart PJ"

Browsing by Author "Lockhart PJ"

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Comparative Analyses of Complete Peronosporaceae (Oomycota) Mitogenome Sequences-Insights into Structural Evolution and Phylogeny.
(Oxford University Press on behalf of the Society for Molecular Biology and Evolution, 2022-04-19) Winkworth RC; Neal G; Ogas RA; Nelson BCW; McLenachan PA; Bellgard SE; Lockhart PJ
Members of the Peronosporaceae (Oomycota, Chromista), which currently consists of 25 genera and approximately 1,000 recognized species, are responsible for disease on a wide range of plant hosts. Molecular phylogenetic analyses over the last two decades have improved our understanding of evolutionary relationships within Peronosporaceae. To date, 16 numbered and three named clades have been recognized; it is clear from these studies that the current taxonomy does not reflect evolutionary relationships. Whole organelle genome sequences are an increasingly important source of phylogenetic information, and in this study, we present comparative and phylogenetic analyses of mitogenome sequences from 15 of the 19 currently recognized clades of Peronosporaceae, including 44 newly assembled sequences. Our analyses suggest strong conservation of mitogenome size and gene content across Peronosporaceae but, as previous studies have suggested, limited conservation of synteny. Specifically, we identified 28 distinct syntenies amongst the 71 examined isolates. Moreover, 19 of the isolates contained inverted or direct repeats, suggesting repeated sequences may be more common than previously thought. In terms of phylogenetic relationships, our analyses of 34 concatenated mitochondrial gene sequences resulted in a topology that was broadly consistent with previous studies. However, unlike previous studies concatenated mitochondrial sequences provided strong support for higher-level relationships within the family.
Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health.
(Elsevier B.V., 2023-09-15) Hulme PE; Beggs JR; Binny RN; Bray JP; Cogger N; Dhami MK; Finlay-Smits SC; French NP; Grant A; Hewitt CL; Jones EE; Lester PJ; Lockhart PJ
One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.
Estimation of quantitative genetic parameters for dry matter yield and vegetative persistence-related traits in a white clover training population
(Wiley Periodicals LLC on behalf of Crop Science Society of America, 2022-11-21) Ehoche OG; Arojju SK; Cousins G; O'Connor JR; Maw B; Tate JA; Lockhart PJ; Jahufer MZZ; Griffiths AG; Resende Jr M
White clover (Trifolium repens L.), an economically important forage legume in temperate pastures, provides quality herbage and plant-available nitrogen. Enhancing breeding efforts to improve dry matter (DM) yield and vegetative persistence will increase on-farm value of this forage. To increase genetic gain for such traits, breeding tools like genomic selection have proven to be highly valuable in other crops. However, its success relies on a sufficiently large training population and key fundamentals of selective breeding, that is, presence of additive variation. We investigated quantitative genetic parameters for spring DM yield and vegetative persistence in a white clover training population comprising 200 half-sibling (HS) families. This population was established in a replicated cattle-grazed, mixed-sward field trial at two contrasting locations and assessed for spring DM yield and stolon-related vegetative persistence traits over a 3-yr period. The additive variation and genotype × environment interactions, comprising the effects from year, season, and location were significant (P <.05) for most traits. Narrow-sense heritability for all traits ranged from low (.13; post-summer stolon branches) to high (.73; leaf size) and there was a positive phenotypic correlation (.28) between spring DM yield and stolon number. These results indicate that both spring DM yield and persistence can be concurrently improved through selective breeding in the current population. We also demonstrated that applying a high selection pressure produces the highest predicted genetic gain. There is, however, a trade-off between genetic gain and diversity in the population for the long-term success of a breeding program.
Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia
(John Wiley and Sons Ltd, 2020-12) Ahmed I; Lockhart PJ; Agoo EMG; Naing KW; Nguyen DV; Medhi DK; Matthews PJ
As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).
Genetic Rescue and the Plight of Ponui Hybrids
(Frontiers Media S.A., 2021-01-15) Undin M; Lockhart PJ; Hills SFK; Castro I; Vernesi C
Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.
Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar
(Centers for Disease Control and Prevention, 2021-11) Aung HL; Nyunt WW; Fong Y; Biggs PJ; Winkworth RC; Lockhart PJ; Yeo TW; Hill PC; Cook GM; Aung ST
Multidrug resistance is a major threat to global elimination of tuberculosis (TB). We performed phenotypic drug-susceptibility testing and whole-genome sequencing for 309 isolates from 342 consecutive patients who were given a diagnosis of TB in Yangon, Myanmar, during July 2016‒June 2018. We identified isolates by using the GeneXpert platform to evaluate drug-resistance profiles. A total of 191 (62%) of 309 isolates had rifampin resistance; 168 (88%) of these rifampin-resistant isolates were not genomically related, indicating the repeated emergence of resistance in the population, rather than extensive local transmission. We did not detect resistance mutations to new oral drugs, including bedaquiline and pretomanid. The current GeneXpert MTB/RIF system needs to be modified by using the newly launched Xpert MTB/XDR cartridge or line-probe assay. Introducing new oral drugs to replace those currently used in treatment regimens for multidrug-resistant TB will also be useful for treating TB in Myanmar.
Integrated transcriptome and proteome analyses reveal potential mechanisms in Stipa breviflora underlying adaptation to grazing
(John Wiley and Sons Australia, Ltd on behalf of Chinese Grassland Society and Lanzhou University, 2024-03-14) Liu Y; Sun S; Zhang Y; Song M; Tian Y; Lockhart PJ; Zhang X; Xu Y; Dang Z; Matthew C
Background: Long-term overgrazing has led to severe degradation of grasslands, posing a significant threat to the sustainable use of grassland resources. Methods: Based on the investigation of changes in functional traits and photosynthetic physiology of Stipa breviflora under no grazing, moderate grazing, and heavy grazing treatments, the changes in expression patterns of genes and proteins associated with different grazing intensities were assessed through integrative transcriptomic and proteomic analyses. Results: Differentially expressed genes and proteins were identified under different grazing intensities. They were mainly related to RNA processing, carbon metabolism, and secondary metabolite biosynthesis. These findings suggest that long-term grazing leads to molecular phenotypic plasticity, affecting various biological processes and metabolic pathways in S. breviflora. Correlation analysis revealed low correlation between the transcriptome and the proteome, indicating a large-scale regulation of gene expression at the posttranscriptional and translational levels during the response of S. breviflora to grazing. The expression profiles of key genes and proteins involved in photosynthesis and phenylpropanoid metabolism pathways suggested their synergistic response to grazing in S. breviflora. Conclusions: Our study provides insight into the adaptation mechanisms of S. breviflora to grazing and provides a scientific basis for the development of more efficient grassland protection and utilization practices.
Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji.
(Frontiers Media S.A., 2022-12-20) Pipite A; Lockhart PJ; McLenachan PA; Christi K; Kumar D; Prasad S; Subramani R; Moyer CL
Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.
Leech breach: a first record of the invasive freshwater leech Helobdella europaea (Hirudinea: Glossiphoniidae) in Fiji
(CSIRO Publishing, 2023-07-03) Rashni B; Brown KT; McLenachan PA; Lockhart PJ; Southgate PC; Lal MM; Calver M
Context: The freshwater flat leech Helobdella europaea Kutschera, 1987 is a small annelid indigenous to South America. This invasive species feeds on the haemolymph of host aquatic invertebrates, with occurrences reported from Europe, USA, Taiwan, North Africa, Hawai'i, Australia and New Zealand. A large number of individuals were discovered in the Ba River catchment, Fiji, during a 2015-2020 freshwater biodiversity survey, raising concerns of potential impacts on endemic Fijian aquatic invertebrate fauna and ecosystem integrity. Aims: To facilitate assessments of its spread and ethology, this study employed morphological and phylogenetic analyses for verification of taxonomic identity. Methods: Phylogenetic trees were constructed using a 658 bp fragment of the mitochondrial DNA cox1 (COI) gene. The first complete mitochondrial genome sequence of H. europaea was also determined using selective multiple displacement amplification and Oxford Nanopore Technology to provide a reference for future comparative analyses and source tracking of spread to other regions. Key results: Morphological and COI analyses identified all Fijian leech specimens collected (n = 16) as H. europaea, reporting the first occurrence of this species on a south-west Pacific Island. The complete mitochondrial genome was sequenced. Conclusions: Confirmation of its presence in Fiji is a national biosecurity concern and will guide the Biosecurity Authority of Fiji and national agencies in further ecosystem assessment and response strategies. Implications: With the complete mitochondrial genome of H. europaea now available, transmission pathway traceability is possible in other regions where this species may be detected.
Mixed Mating in a Multi-Origin Population Suggests High Potential for Genetic Rescue in North Island Brown Kiwi, Apteryx mantelli
(Frontiers Media S.A., 2021-08-10) Undin M; Lockhart PJ; Hills SFK; Armstrong DP; Castro I; Berger-Tal O
Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi Apteryx mantelli population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future Apteryx reinforcement translocations, a potential that is currently under utilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.
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 VM
Increasing 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.
RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna.
(John Wiley and Sons, Inc., 2024-03-01) Dang Z; Li J; Liu Y; Song M; Lockhart PJ; Tian Y; Niu M; Wang Q; Varshney R
Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.
The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the "kauri killing" Phytophthora in New Zealand
(PLOS, 2021-05-21) Winkworth RC; Bellgard SE; McLenachan PA; Lockhart PJ; Blair JE
Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0-304.4 years and 95% HPDs of 206.9-414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.
Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences
(MDPI (Basel, Switzerland), 2021-11-02) Dang Z; Jia Y; Tian Y; Li J; Zhang Y; Huang L; Liang C; Lockhart PJ; Matthew C; Li FY; Hobza R
Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin-Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.

Browsing by Author "Lockhart PJ"

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