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Degnan RM, McTaggart AR, Shuey LS, Pame LJS, Smith GR, Gardiner DM, Nock V, Soffe R, Sale S, Garrill A, Carroll BJ, Mitter N, Sawyer A. Exogenous double-stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta. Mol Plant Pathol 2023; 24:191-207. [PMID: 36528383 PMCID: PMC9923395 DOI: 10.1111/mpp.13286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/01/2023]
Abstract
Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems.
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Affiliation(s)
- Rebecca M. Degnan
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alistair R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Louise S. Shuey
- Queensland Department of Agriculture and FisheriesEcosciences PrecinctDutton ParkQueenslandAustralia
| | - Leny Jane S. Pame
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Volker Nock
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
| | - Rebecca Soffe
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- Present address:
School of EngineeringRMIT UniversityMelbourneVictoriaAustralia
| | - Sarah Sale
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Ashley Garrill
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Bernard J. Carroll
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Anne Sawyer
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
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Wilson JD, Bond JE, Harvey MS, Ramírez MJ, Rix MG. Correlation with a limited set of behavioral niches explains the convergence of somatic morphology in mygalomorph spiders. Ecol Evol 2023; 13:e9706. [PMID: 36636427 PMCID: PMC9830016 DOI: 10.1002/ece3.9706] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Understanding the drivers of morphological convergence requires investigation into its relationship with behavior and niche space, and such investigations in turn provide insights into evolutionary dynamics, functional morphology, and life history. Mygalomorph spiders (trapdoor spiders and their kin) have long been associated with high levels of morphological homoplasy, and many convergent features can be intuitively associated with different behavioral niches. Using genus-level phylogenies based on recent genomic studies and a newly assembled matrix of discrete behavioral and somatic morphological characters, we reconstruct the evolution of burrowing behavior in the Mygalomorphae, compare the influence of behavior and evolutionary history on somatic morphology, and test hypotheses of correlated evolution between specific morphological features and behavior. Our results reveal the simplicity of the mygalomorph adaptive landscape, with opportunistic, web-building taxa at one end, and burrowing/nesting taxa with structurally modified burrow entrances (e.g., a trapdoor) at the other. Shifts in behavioral niche, in both directions, are common across the evolutionary history of the Mygalomorphae, and several major clades include taxa inhabiting both behavioral extremes. Somatic morphology is heavily influenced by behavior, with taxa inhabiting the same behavioral niche often more similar morphologically than more closely related but behaviorally divergent taxa, and we were able to identify a suite of 11 somatic features that show significant correlation with particular behaviors. We discuss these findings in light of the function of particular morphological features, niche dynamics within the Mygalomorphae, and constraints on the mygalomorph adaptive landscape relative to other spiders.
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Affiliation(s)
- Jeremy D. Wilson
- Biodiversity and Geosciences ProgramQueensland Museum Collections and Research CentreHendraQueenslandAustralia
| | - Jason E. Bond
- Department of Entomology and NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Mark S. Harvey
- Collections and ResearchWestern Australian MuseumWelshpoolWestern AustraliaAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Martín J. Ramírez
- Museo Argentino de Ciencias NaturalesConsejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - Michael G. Rix
- Biodiversity and Geosciences ProgramQueensland Museum Collections and Research CentreHendraQueenslandAustralia
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Jaya FR, Tanner JC, Whitehead MR, Doughty P, Keogh JS, Moritz CC, Catullo RA. Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone. Mol Ecol 2022; 31:4527-4543. [PMID: 35780470 PMCID: PMC9542136 DOI: 10.1111/mec.16597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022]
Abstract
When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which probably reduces attractiveness to females. Integrating population genomic data, mitochondrial sequencing, morphology and behavioural approaches provides an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.
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Affiliation(s)
- Frederick R. Jaya
- Australian Institute for Microbiology and InfectionUniversity of Technology SydneyUltimoNew South WalesAustralia
| | - Jessie C. Tanner
- Centre for Evolutionary Biology, School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
| | | | - Paul Doughty
- Western Australian MuseumPerthWestern AustraliaAustralia
| | - J. Scott Keogh
- Centre for Biodiversity Analysis, Ecology & Evolution, Research School of BiologyAustralian National UniversityActonAustralian Capital TerritoryAustralia
| | - Craig C. Moritz
- Centre for Biodiversity Analysis, Ecology & Evolution, Research School of BiologyAustralian National UniversityActonAustralian Capital TerritoryAustralia
| | - Renee A. Catullo
- Centre for Evolutionary Biology, School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Centre for Biodiversity Analysis, Ecology & Evolution, Research School of BiologyAustralian National UniversityActonAustralian Capital TerritoryAustralia
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Nargar K, O’Hara K, Mertin A, Bent SJ, Nauheimer L, Simpson L, Zimmer H, Molloy BPJ, Clements MA. Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics. Front Plant Sci 2022; 13:912089. [PMID: 35845679 PMCID: PMC9277221 DOI: 10.3389/fpls.2022.912089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia's orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships, divergence times and range evolution in Pterostylidinae (Orchidoideae), the second largest subtribe in the Australian orchid flora, comprising the genera Pterostylis and Achlydosa. Phylogenetic analysis of 75 plastid genes provided well-resolved and supported phylogenies. Intrageneric relationships in Pterostylis were clarified and monophyly of eight of 10 sections supported. Achlydosa was found to not form part of Pterostylidinae and instead merits recognition at subtribal level, as Achlydosinae. Pterostylidinae were inferred to have originated in eastern Australia in the early Oligocene, coinciding with the complete separation of Australia from Antarctica and the onset of the Antarctic Circumpolar Current, which led to profound changes in the world's climate. Divergence of all major lineages occurred during the Miocene, accompanied by increased aridification and seasonality of the Australian continent, resulting in strong vegetational changes from rainforest to more open sclerophyllous vegetation. The majority of extant species were inferred to have originated in the Quaternary, from the Pleistocene onwards. The rapid climatic oscillations during the Pleistocene may have acted as important driver of speciation in Pterostylidinae. The subtribe underwent lineage diversification mainly within its ancestral range, in eastern Australia. Long-distance dispersals to southwest Australia commenced from the late Miocene onwards, after the establishment of the Nullarbor Plain, which constitutes a strong edaphic barrier to mesic plants. Range expansions from the mesic into the arid zone of eastern Australia (Eremaean region) commenced from the early Pleistocene onwards. Extant distributions of Pterostylidinae in other Australasian regions, such as New Zealand and New Caledonia, are of more recent origin, resulting from long-distance dispersals from the Pliocene onwards. Temperate eastern Australia was identified as key source area for dispersals to other Australasian regions.
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Affiliation(s)
- Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Kate O’Hara
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Allison Mertin
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Stephen J. Bent
- DATA61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Heidi Zimmer
- Centre for Australian National Biodiversity Research (Joint Venture Between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Brian P. J. Molloy
- Allan Herbarium, Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (Joint Venture Between Parks Australia and CSIRO), Canberra, ACT, Australia
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McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt‐Lebuhn AN, Baker WJ, Forest F, Jackson CJ. New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Appl Plant Sci 2021; 9:APS311420. [PMID: 34336399 PMCID: PMC8312740 DOI: 10.1002/aps3.11420] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE 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.
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Affiliation(s)
- Todd G. B. McLay
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
- Centre for Australian National Biodiversity ResearchCSIROCanberraAustralia
| | - Joanne L. Birch
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Bee F. Gunn
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Weixuan Ning
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Jennifer A. Tate
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lars Nauheimer
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Elizabeth M. Joyce
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Lalita Simpson
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Chris J. Jackson
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
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Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets. Appl Plant Sci 2021; 9:APS311441. [PMID: 34336402 PMCID: PMC8312746 DOI: 10.1002/aps3.11441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 05/24/2023]
Abstract
PREMISE Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.
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Affiliation(s)
- Lars Nauheimer
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Nicholas Weigner
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Elizabeth Joyce
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Charles Clarke
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Cairns Botanic GardensCollins AvenueEdge HillQueensland4870Australia
| | - Katharina Nargar
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- National Research Collections AustraliaCommonwealth Industrial and Scientific Research Organisation (CSIRO)GPO Box 1700CanberraAustralian Capital Territory2601Australia
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