ORCID Profile
0000-0001-6587-8875
Current Organisation
Queensland University of Technology
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Palaeontology (incl. Palynology) | Phylogeny and Comparative Analysis | Evolutionary Biology | Horticultural Production | Genomics | Animal Systematics and Taxonomy | Horticultural Crop Protection (Pests, Diseases and Weeds)
Expanding Knowledge in the Earth Sciences | Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity of environments not elsewhere classified | Environmentally Sustainable Plant Production not elsewhere classified | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Publisher: Elsevier BV
Date: 06-2008
DOI: 10.1016/J.TPLANTS.2008.03.004
Abstract: Many emerging invasive species display evidence of rapid adaptation. Contemporary genetic studies demonstrate that adaptation to novel environments can occur within 20 generations or less, indicating that evolutionary processes can influence invasiveness. However, the source of genetic or epigenetic variation underlying these changes remains uncharacterised. Here, we review the potential for rapid adaptation from standing genetic variation and from new mutations, and examine four types of evolutionary change that might promote or constrain rapid adaptation during the invasion process. Understanding the source of variation that contributes to adaptive evolution in invasive plants is important for predicting future invasion scenarios, identifying candidate genes involved in invasiveness, and, more generally, for understanding how populations can evolve rapidly in response to novel and changing environments.
Publisher: Wiley
Date: 22-05-2013
DOI: 10.1111/EVO.12136
Abstract: Adaptation to replicate environments is often achieved through similar phenotypic solutions. Whether selection also produces convergent genomic changes in these situations remains largely unknown. The variable groundsel, Senecio lautus, is an excellent system to investigate the genetic underpinnings of convergent evolution, because morphologically similar forms of these plants have adapted to the same environments along the coast of Australia. We compared range-wide patterns of genomic ergence in natural populations of this plant and searched for regions putatively affected by natural selection. Our results indicate that environmental adaptation followed complex genetic trajectories, affecting multiple loci, implying both the parallel recruitment of the same alleles and the ergence of completely different genomic regions across geography. An analysis of the biological functions of candidate genes suggests that adaptation to coastal environments may have occurred through the recruitment of different genes participating in similar processes. The relatively low genetic convergence that characterizes the parallel evolution of S. lautus forms suggests that evolution is more constrained at higher levels of biological organization.
Publisher: Wiley
Date: 05-02-2008
Publisher: Public Library of Science (PLoS)
Date: 26-08-2015
Publisher: Wiley
Date: 07-02-2023
DOI: 10.1111/JEN.13101
Abstract: The Queensland fruit fly, Bactrocera tryoni , is an economically important pest insect of horticultural crops in Australia, damaging a wide variety of fruits and vegetables. To study the B. tryoni –fruit interaction, we conducted a transcriptomic investigation of B. tryoni larvae feeding on three ripening stages of tomato fruit, which had been previously shown to influence larval performance. Fruit fly larval survival in immature tomato fruit is very poor, which we hypothesized to be due to the effect of tomato fruit toxins which are mostly expressed in green fruit. We found 2709 transcripts differentially expressed in larvae feeding on the three ripening stages. The transcript expression pattern was most ergent between larvae feeding in immature fruit compared with fully ripe fruit, with intermediate expression in larvae feeding in colour‐break fruit. Gene Set Enrichment Analysis showed that larvae fed in immature fruit had a higher number of depleted GO terms in comparison with larvae fed on fully ripe fruit, particularly GO terms associated with larval development, metabolism and basic cellular functions. Enriched GO terms in larvae fed on fully ripe fruit showed the opposite pattern, with a greater number of enriched terms related to larval growth and detoxification processes. We concluded that poor larval survival in immature‐green fruit is likely because the substrate offers a very poor diet for larvae, which limits normal developmental functions. By contrast, in colour‐break and fully ripe fruit the substrate allows normal development, including the expression of metabolically costly detoxification mechanisms.
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.GENE.2015.03.074
Abstract: Changes in water quality parameters such as pH and salinity can have a significant effect on productivity of aquaculture species. Similarly, relative osmotic pressure influences various physiological processes and regulates expression of a number of osmoregulatory genes. Among those, carbonic anhydrase (CA) plays a key role in systemic acid-base balance and ion regulation. Redclaw crayfish (Cherax quadricarinatus) are unique in their ability to thrive in environments with naturally varied pH levels, suggesting unique adaptation to pH stress. To date, however, no studies have focused on identification and characterisation of CA or other osmoregulatory genes in C. quadricarinatus. Here, we analysed the redclaw gill transcriptome and characterized CA genes along with a number of other key osmoregulatory genes that were identified in the transcriptome. We also examined patterns of gene expression of these CA genes when exposed to three pH treatments. In total, 72,382,710 paired end Illumina reads were assembled into 36,128 contigs with an average length of 800bp. Approximately 37% of contigs received significant BLAST hits and 22% were assigned gene ontology terms. Three full length CA isoforms cytoplasmic CA (ChqCAc), glycosyl-phosphatidylinositol-linked CA (ChqCAg), and β-CA (ChqCA-beta) as well as two partial CA gene sequences were identified. Both partial CA genes showed high similarity to ChqCAg and appeared to be duplicated from the ChqCAg. Full length coding sequences of Na(+)/K(+)-ATPase, V-type H(+)-ATPase, sarcoplasmic Ca(+)-ATPase, arginine kinase, calreticulin and Cl(-) channel protein 2 were also identified. Only the ChqCAc gene showed significant differences in expression across the three pH treatments. These data provide valuable information on the gill expressed CA genes and their expression patterns in freshwater crayfish. Overall our data suggest an important role for the ChqCAc gene in response to changes in pH and in systemic acid-base balance in freshwater crayfish.
Publisher: Wiley
Date: 25-05-2013
DOI: 10.1111/MEC.12311
Abstract: Instances of parallel ecotypic ergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel ergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has ersified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic ersity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic ergence in face of gene flow.
Publisher: Wiley
Date: 22-04-2013
DOI: 10.1111/MEC.12277
Abstract: Invasive species provide excellent study systems to evaluate the ecological and evolutionary processes that contribute to the colonization of novel environments. While the ecological processes that contribute to the successful establishment of invasive plants have been studied in detail, investigation of the evolutionary processes involved in successful invasions has only recently received attention. In particular, studies investigating the genomic and gene expression differences between native and introduced populations of invasive species are just beginning and are required if we are to understand how plants become invasive. In the current issue of Molecular Ecology, Hodgins et al. (2013) tackle this unresolved question, by examining gene expression differences between native and introduced populations of annual ragweed, Ambrosia artemisiifolia. The study identifies a number of potential candidate genes based on gene expression differences that may be responsible for the success of annual ragweed in its introduced range. Furthermore, genes involved in stress response are over-represented in the differentially expressed gene set. Future experiments could use functional studies to test whether changes in gene expression at these candidate genes do in fact underlie changes in growth characteristics and reproductive output observed in this and other invasive species.
Publisher: Springer Science and Business Media LLC
Date: 08-2014
Publisher: Wiley
Date: 11-2010
DOI: 10.3732/AJB.1000300
Abstract: Microsatellite loci were developed to characterize genetic variation and population sub ision in Khaya senegalensis (Desr.) A. Juss. (Meliaceae). • Microsatellite loci were identified from genomic DNA sequences generated using the 454 GS-FLX titanium platform. Primers were designed for 67 tri- and tetranucleotide repeats, of which 20 were selected for 2 multiplexes based on lification success and band size. Eleven of these loci showed polymorphism in two populations of Khaya senegalensis and lified in in iduals from across the species range. • These new microsatellite loci will be useful for investigation of the evolutionary and conservation genetics of Khaya senegalensis.
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/BT04208
Abstract: Post-germination buoyancy has been proposed to reduce seedling establishment in hibious plants if seeds germinate under flooded conditions. We tested this hypothesis in two hibious species, Helmholtzia glaberrima (Hook.) and Philydrum lanuginosum (Banks & Sol.). We tested whether seed germination was affected by different levels of inundation, whether seedlings germinating underwater floated and whether seedlings established after prolonged floatation at rates comparable to seedling establishment in waterlogged soil. Germination underwater and in waterlogged soil was similar for both species. Seeds germinating underwater exhibited post-germination buoyancy and established at similar rates to seedlings in waterlogged soil. The results demonstrated that if seeds germinated underwater, post-germination buoyancy conferred the potential to avoid inundation and promote establishment, when waters recede and/or in areas of high soil moisture that are not submerged. More generally, this finding showed that post-germination buoyancy can promote seedling dispersal and the deposition of seedlings in conditions more favourable for establishment if seeds germinate under flooded conditions or in permanent wetlands.
Publisher: Oxford University Press (OUP)
Date: 07-10-2010
DOI: 10.1093/AOB/MCQ201
Publisher: Wiley
Date: 30-11-2010
Publisher: Springer Science and Business Media LLC
Date: 02-11-2016
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.MARGEN.2014.08.004
Abstract: In this study we undertook deep sequencing of the blood cockle, Anadara trapezia, transcriptome to generate genomic resources for future functional genomics analyses. Over 27 million high quality paired end reads were assembled into 75024 contigs. Of these contigs, 29013 (38.7%) received significant BLASTx hits and gene ontology (GO) terms were assigned to 13718 of these sequences. This resource will facilitate physiological genomic studies to test the gene expression response of A. trapezia to various environmental stresses.
Publisher: Cold Spring Harbor Laboratory
Date: 31-08-2023
DOI: 10.1101/2023.08.30.555036
Abstract: Background : Lineage theory suggests that the development of traits associated with reproductive isolation coupled with traits associated with ecological differentiation are essential for the maintenance of sympatric lineages. However, the relative importance of these factors has rarely been tested simultaneously. Bactrocera tryoni and B. neohumeralis are a tephritid fruit fly species pair that have significant overlap in geographic range and host use, with time of male mating the only known difference in their mating systems. Using this system, we tested the relative importance of ecological differentiation versus assortative mating in sympatric lineage maintenance. Results : Genome-wide SNP analyses found strong genetic differentiation between the species with no evidence for hybridization in the field. Most outlier SNPs were restricted to narrow regions towards the centromeres and telomeres of chromosomes. Enrichment of annotation terms indicated an overabundance of genes with the abnormal neuroanatomy term. Terms of interest associated with sleep and circadian rhythm, potentially important to the allochronic reproductive barrier, were non-enriched. Ecological data found no evidence for ecological ergence or competitive displacement between the two species based on significant positive correlations between species numbers trapped at different times of the year, trapped in different habitats within a region, or when reared from fruit. Conclusions : Our study highlights the significance of assortative mating over ecological differentiation for sympatric lineage maintenance of the B. tryoni/B. neohumeralis sibling pair. The paper represents one of the most well-characterized ex les of the importance of genomic ergence in the coexistence of two closely related species.
Publisher: Elsevier BV
Date: 11-2009
Publisher: Wiley
Date: 18-09-2019
DOI: 10.1002/ECE3.5633
Publisher: Public Library of Science (PLoS)
Date: 06-10-2015
Publisher: Wiley
Date: 04-05-2018
DOI: 10.1002/ECE3.4044
Publisher: Elsevier BV
Date: 10-2019
DOI: 10.1016/J.TOXICON.2019.07.002
Abstract: Sea anemone venoms have long been recognised as a rich source of peptides with interesting pharmacological and structural properties. Our recent transcriptomic studies of the Australian sea anemone Actinia tenebrosa have identified a novel 13-residue peptide, U-AITx-Ate1. U-AITx-Ate1 contains a single disulfide bridge and bears no significant homology to previously reported amino acid sequences of peptides from sea anemones or other species. We have produced U-AITx-Ate1 using solid-phase peptide synthesis, followed by oxidative folding and purification of the folded peptide using reversed-phase high-performance liquid chromatography. The solution structure of U-AITx-Ate1 was determined based on two-dimensional nuclear magnetic resonance spectroscopic data. Diffusion-ordered NMR spectroscopy revealed that U-AITx-Ate1 was monomeric in solution. Perturbations in the 1D
Publisher: MDPI AG
Date: 08-01-2018
Publisher: Wiley
Date: 10-2010
DOI: 10.3732/AJB.1000254
Abstract: Cynodon species are multiple-use grasses that display varying levels of adaptation to biotic and abiotic stress. Previously identified EST-SSR primers were characterized and multiplexed to assess the level of genetic ersity present within a collection of almost 1200 Cynodon accessions from across Australia. • Two multiplex reactions were developed comprising a total of 16 EST-SSR markers. All SSR markers lified across different Cynodon species and different levels of ploidy. The number of alleles ranged from one to eight per locus and the total number of alleles for the germplasm collection was 79. • The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic ersity in Cynodon grasses.
Publisher: MDPI AG
Date: 10-01-2020
Abstract: Small-for-gestational-age (SGA) infants are fetuses that have not reached their genetically programmed growth potential. Low birth weight predisposes these infants to an increased risk of developing cardiovascular, metabolic and neurodevelopmental conditions in later life. However, our understanding of how this pathology occurs is currently incomplete. Previous research has focused on understanding the transcriptome, epigenome and bacterial signatures separately. However, we hypothesise that interactions between moderators of gene expression are critical to understanding fetal growth restriction. Through a review of the current literature, we identify that there is evidence of modulated expression/methylation of the placental genome and the presence of bacterial DNA in the placental tissue of SGA infants. We also identify that despite limited evidence of the interactions between the above results, there are promising suggestions of a relationship between bacterial signatures and placental function. This review aims to summarise the current literature concerning fetal growth from multiple avenues and propose a novel relationship between the placental transcriptome, methylome and bacterial signature that, if characterised, may be able to improve our current understanding of the placental response to stress and the aetiology of growth restriction.
Publisher: Elsevier BV
Date: 08-2007
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/BT03064
Abstract: The distribution of genetic variation among five isolated sites of the riparian species Helmholtzia glaberrima (J.D.Hook) was examined in Toloona Creek (28�13′S, 153�07′E) by using dominant lified fragment length polymorphism (AFLP) markers. From the 137 fragments assessed, analysis of molecular variance (AMOVA) showed that most genetic variability occurred within sites (68%), although high (32%) variation also occurred among sites. Highly significant pairwise θ estimates among all s led sites suggest that gene flow is restricted in H. glaberrima. Levels of within-site ersity were intermediate and significantly different across the s led sites. Significant levels of linkage disequilibrium were detected at all sites except TC3. Differences in linkage disequilibrium and genetic ersity among the sites suggest that sites may have been founded by different numbers of colonists. Mantel tests found no correlation between geographic and genetic distance and significant levels of linkage disequilibrium were detected at the total site level, supporting a non-equilibrium model of population structure. The observed pattern of non-equilibrium population structure and genetic variation in H. glaberrima are best explained by a classical metapopulation model.
Publisher: Elsevier BV
Date: 12-2015
Publisher: MDPI AG
Date: 09-04-2020
DOI: 10.3390/MD18040202
Abstract: This review examines the current state of knowledge regarding toxins from anthozoans (sea anemones, coral, zoanthids, corallimorphs, sea pens and tube anemones). We provide an overview of venom from phylum Cnidaria and review the ersity of venom composition between the two major clades (Medusozoa and Anthozoa). We highlight that the functional and ecological context of venom has implications for the temporal and spatial expression of protein and peptide toxins within class Anthozoa. Understanding the nuances in the regulation of venom arsenals has been made possible by recent advances in analytical technologies that allow characterisation of the spatial distributions of toxins. Furthermore, anthozoans are unique in that ecological roles can be assigned using tissue expression data, thereby circumventing some of the challenges related to pharmacological screening.
Publisher: Hindawi Limited
Date: 12-01-2015
DOI: 10.1111/ANU.12211
Publisher: Springer Science and Business Media LLC
Date: 22-09-2015
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/BT10181
Abstract: We examined evolutionary relationships, hybridisation and genetic ersity in species of Dacrydium (Podocarpaceae) in Remote Oceania, where it is restricted to New Caledonia and Fiji. We used cpDNA sequence (trnL–trnF) data to construct a phylogeny and estimate taxon ergence by using a relaxed molecular clock approach. The phylogeny was verified using allozymes, which were also used to investigate genetic ersity of all species and the hybridisation dynamics of two endangered species, D. guillauminii and D. nidulum. Our results suggested that Dacrydium species in Remote Oceania form a monophyletic group that arose and ersified within the last 20 million years through long-distance dispersal and a range of speciation mechanisms. Whereas we detected no hybridisation between the Fijian species D. nausoriense and D. nidulum, we confirmed hybridisation between D. guillauminii and D. araucarioides in New Caledonia and determined introgression to be assymetric from the widespread D. araucarioides into the rare, restricted-range species D. guillauminii. In addition, D. guillauminii had lower genetic ersity than did the other species of Dacrydium studied, which had genetic ersity similar to that of other gymnosperms. Our results provided evidence for the recent and complex ersification of Dacrydium in Remote Oceania. In addition, low genetic ersity of and introgression from D. araucarioides, are of grave concern for the conservation of D. guillauminii.
Publisher: Springer Science and Business Media LLC
Date: 27-07-2012
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.TREE.2008.10.007
Abstract: Biological invasions are caused by human-mediated extra-range dispersal and, unlike natural extra-range dispersal, are often the result of multiple introductions from multiple sources to multiple locations. The processes and opportunities that result in propagules moving from one area to another can be used more broadly to differentiate all types of extra-range dispersal. By examining key properties of dispersal pathways (notably propagule pressure, genetic ersity and the potential for simultaneous movement of coevolved species), the establishment and evolutionary trajectories of extra-range dispersal can be better understood. Moreover, elucidation of the mechanistic properties of dispersal pathways is crucial for scientists and managers who wish to assist, minimise or prevent future movements of organisms.
Publisher: MDPI AG
Date: 12-12-2019
DOI: 10.3390/MD17120701
Abstract: Serine proteases play pivotal roles in normal physiology and a spectrum of patho-physiological processes. Accordingly, there is considerable interest in the discovery and design of potent serine protease inhibitors for therapeutic applications. This led to concerted efforts to discover versatile and robust molecular scaffolds for inhibitor design. This investigation is a bioprospecting study that aims to isolate and identify protease inhibitors from the cnidarian Actinia tenebrosa. The study isolated two Kunitz-type protease inhibitors with very similar sequences but quite ergent inhibitory potencies when assayed against bovine trypsin, chymostrypsin, and a selection of human sequence-related peptidases. Homology modeling and molecular dynamics simulations of these inhibitors in complex with their targets were carried out and, collectively, these methodologies enabled the definition of a versatile scaffold for inhibitor design. Thermal denaturation studies showed that the inhibitors were remarkably robust. To gain a fine-grained map of the residues responsible for this stability, we conducted in silico alanine scanning and quantified in idual residue contributions to the inhibitor’s stability. Sequences of these inhibitors were then used to search for Kunitz homologs in an A. tenebrosa transcriptome library, resulting in the discovery of a further 14 related sequences. Consensus analysis of these variants identified a rich molecular ersity of Kunitz domains and expanded the palette of potential residue substitutions for rational inhibitor design using this domain.
Publisher: MDPI AG
Date: 29-06-2021
Abstract: Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails.
Publisher: Wiley
Date: 15-12-2016
DOI: 10.1111/NPH.13789
Abstract: Plants have evolved many strategies to protect themselves from attack, including peptide toxins that are ribosomally synthesized and thus adaptable directly by genetic polymorphisms. Certain toxins in Clitoria ternatea (butterfly pea) are cyclic cystine‐knot peptides of c . 30 residues, called cyclotides, which have co‐opted the plant's albumin‐1 gene family for their production. How butterfly pea albumin‐1 genes were commandeered and how these cyclotides are utilized in defence remain unclear. The role of cyclotides in host plant ecology and biotechnological applications requires exploration. We characterized the sequence ersity and expression dynamics of precursor and processing proteins implicated in butterfly pea cyclotide biosynthesis by expression profiling through RNA‐sequencing ( RNA ‐seq). Peptide‐enriched extracts from various organs were tested for activity against insect‐like membranes and the model nematode Caenorhabditis elegans . We found that the evolution and deployment of cyclotides involved their ersification to exhibit different chemical properties and expression between organs facing different defensive challenges. Cyclotide‐enriched fractions from soil‐contacting organs were effective at killing nematodes, whereas similar enriched fractions from aerial organs contained cyclotides that exhibited stronger interactions with insect‐like membrane lipids. Cyclotides are employed as versatile and combinatorial mediators of defence in C. ternatea and have specialized to affect different classes of attacking organisms.
Publisher: Canadian Science Publishing
Date: 07-2008
DOI: 10.1139/B08-063
Abstract: To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa s led broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae Haemodoraceae and Pontederiaceae are also sister taxa. Our s ling of Philydraceae includes all three or four genera in the family we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.
Publisher: Cold Spring Harbor Laboratory
Date: 10-12-2022
DOI: 10.1101/2022.12.08.518931
Abstract: ShK from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in actinarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni , characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T . stephensoni . We identified ten SA8 genes in two clusters and six SA8 genes in five clusters for T. stephensoni and A. tenebrosa , respectively. Nine SA8 T. stephensoni genes were found in a single cluster and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. Our results provide the first demonstration that SA8 is a unique gene family in actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T . stephensoni .
Publisher: Elsevier BV
Date: 08-2015
DOI: 10.1016/J.MARGEN.2015.03.004
Abstract: We undertook deep sequencing of gill transcriptomes from two freshwater crayfish, Cherax cainii and Cherax destructor, in order to generate genomic resources for future genomics research. Over 83 and 100 million high quality (quality score (Q)≥30) paired-end Illumina reads (150 bp) were assembled into 147,101 and 136,622 contigs in C. cainii and C. destructor, respectively. A total of 24,630 and 23,623 contigs received significant BLASTx hits and allowed the identification of multiple gill expressed candidate genes associated with pH and salinity balance. These functionally annotated transcripts will provide a resource to facilitate comparative genomic research in the genus Cherax, and in particular allow insights into respiratory and osmoregulatory physiology of this group of animals.
Publisher: Springer Science and Business Media LLC
Date: 26-09-2014
Publisher: Springer Science and Business Media LLC
Date: 12-05-2020
DOI: 10.1038/S41598-020-64597-X
Abstract: Seed production can be improved if genetic selection is applied to key reproductive traits when a substantial amount additive genetic variation is present that can be exploited in a selective breeding program. Despite the commercial importance of reproductive traits to the seed production sector currently, few quantitative genetic studies have been conducted to address these traits in farmed penaeid shrimp culture lines. Here, we investigated genetic parameters for a number of key reproductive traits that directly impact nauplii production in Pacific white shrimp ( P. vannamei ) hatcheries in China. Our objectives were to determine the additive genetic variance associated with reproductive traits, and to anticipate any potential impacts on reproductive performance when selecting for increased body weight by assessing genetic correlations between post-spawning body weight and specific female reproductive traits. Data were collected on 595 females from 78 full-sib families over 30 days, with a total of 1,113 spawning events recorded. Traits studied included: body weight after spawning (WAS), number of eggs per spawn (NE), number of nauplii per spawn (NN), egg hatching rate per spawn (HR), number of eggs produced relative to female weight (g) (FE), and spawn frequency over 30 days (SF). Estimated heritability was high for WAS ( h 2 = 0.64 ± 0.10) and moderate for NE (0.26 ± 0.07), NN (0.18 ± 0.06), and SF (0.15 ± 0.06), respectively. In contrast, h 2 for HR (0.04 ± 0.03) and FE (0.05 ± 0.04) were low. The genetic correlations between growth trait (WAS) with NE, NN and SF were 0.93 ± 0.10, 0.84 ± 0.10, and 0.57 ± 0.18, respectively. While the genetic correlation between WAS and HR was low (0.02 ± 0.33), a negative genetic correlation was found between WAS and FE (−0.50 ± 0.27). Overall, we concluded that it is possible to improve the key female reproductive traits (i.e. NE, NN, and SF) in cultured white shrimp lines via genetic selection, but not for HR or FE. The genetic relationship between the growth trait and reproductive traits predicts that selection on fast growth would increase the production in the seed sector, with little or no compromise on the eggs quality.
Publisher: Public Library of Science (PLoS)
Date: 05-09-2014
Publisher: Public Library of Science (PLoS)
Date: 10-08-2011
Publisher: Springer Science and Business Media LLC
Date: 02-02-2017
DOI: 10.1038/SREP41458
Abstract: Wound healing and regeneration in cnidarian species, a group that forms the sister phylum to Bilateria, remains poorly characterised despite the ability of many cnidarians to rapidly repair injuries, regenerate lost structures, or re-form whole organisms from small populations of somatic cells. Here we present results from a fully replicated RNA-Seq experiment to identify genes that are differentially expressed in the sea anemone Calliactis polypus following catastrophic injury. We find that a large-scale transcriptomic response is established in C. polypus , comprising an abundance of genes involved in tissue patterning, energy dynamics, immunity, cellular communication, and extracellular matrix remodelling. We also identified a substantial proportion of uncharacterised genes that were differentially expressed during regeneration, that appear to be restricted to cnidarians. Overall, our study serves to both identify the role that conserved genes play in eumetazoan wound healing and regeneration, as well as to highlight the lack of information regarding many genes involved in this process. We suggest that functional analysis of the large group of uncharacterised genes found in our study may contribute to better understanding of the regenerative capacity of cnidarians, as well as provide insight into how wound healing and regeneration has evolved in different lineages.
Publisher: MDPI AG
Date: 14-07-2021
Abstract: Sea anemones vary immensely in life history strategies, environmental niches and their ability to regenerate. While the sea anemone Nematostella vectensis is the starlet of many key regeneration studies, recent work is emerging on the erse regeneration strategies employed by other sea anemones. This manuscript will explore current molecular mechanisms of regeneration employed by non-model sea anemones Exaiptasia diaphana (an emerging model species for coral symbiosis studies) and Calliactis polypus (a less well-studied species) and examine how these species compare to the model sea anemone N. vectensis. We summarize the field of regeneration within sea anemones, within the greater context of phylum Cnidaria and in other invertebrate models of regeneration. We also address the current knowledge on two key systems that may be implemented in regeneration: the innate immune system and developmental pathways, including future aspects of work and current limitations.
Publisher: Wiley
Date: 11-09-2007
DOI: 10.1111/J.1469-8137.2007.02217.X
Abstract: Hybridization between native and invasive species can have several outcomes, including enhanced weediness in hybrid progeny, evolution of new hybrid lineages and decline of hybridizing species. Whether there is a decline of hybridizing species largely depends on the relative frequencies of parental taxa and the viability of hybrid progeny. Here, the in idual- and population-level consequences of hybridization between the Australian native Senecio pinnatifolius and the exotic Senecio madagascariensis were investigated with lified fragment length polymorphism (AFLP) markers, and this information was used to estimate the annual loss of viable seeds to hybridization. A high frequency (range 8.3-75.6%) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations. A hybridization advantage was observed for S. madagascariensis, where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Calculations indicated that S. pinnatifolius would produce less viable seed than S. madagascariensis, if hybridization was frequency dependent and S. madagascariensis reached a frequency of between 10 and 60%. For this native-exotic species pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. As a result of asymmetric hybridization, S. pinnatifolius would appear to be under threat if S. madagascariensis increases numerically in areas of contact.
Publisher: MDPI AG
Date: 10-05-2022
Abstract: The larvae of frugivorous tephritid fruit flies feed within fruit and are global pests of horticulture. With the reduced use of pesticides, alternative control methods are needed, of which fruit resistance is one. In the current study, we explicitly tested for phenotypic evidence of induced fruit defences by running concurrent larval survival experiments with fruit on or off the plant, assuming that defence induction would be stopped or reduced by fruit picking. This was accompanied by RT-qPCR analysis of fruit defence and insect detoxification gene expression. Our fruit treatments were picking status (unpicked vs. picked) and ripening stage (colour break vs. fully ripe), our fruit fly was the polyphagous Bactrocera tryoni, and larval survival was assessed through destructive fruit s ling at 48 and 120 h, respectively. The gene expression study targeted larval and fruit tissue s les collected at 48 h and 120 h from picked and unpicked colour-break fruit. At 120 h in colour-break fruit, larval survival was significantly higher in the picked versus unpicked fruit. The gene expression patterns in larval and plant tissue were not affected by picking status, but many putative plant defence and insect detoxification genes were upregulated across the treatments. The larval survival results strongly infer an induced defence mechanism in colour-break tomato fruit that is stronger/faster in unpicked fruits however, the gene expression patterns failed to provide the same clear-cut treatment effect. The lack of conformity between these results could be related to expression changes in uns led candidate genes, or due to critical changes in gene expression that occurred during the uns led periods.
Publisher: Wiley
Date: 09-2014
DOI: 10.1111/MEC.12880
Abstract: In male tephritid fruit flies of the genus Bactrocera, feeding on secondary plant compounds (sensu lato male lures = methyl eugenol, raspberry ketone and zingerone) increases male mating success. Ingested male lures alter the male pheromonal blend, normally making it more attractive to females and this is considered the primary mechanism for the enhanced mating success. However, the male lures raspberry ketone and zingerone are known, across a erse range of other organisms, to be involved in increasing energy metabolism. If this also occurs in Bactrocera, then this may represent an additional benefit to males as courtship is metabolically expensive and lure feeding may increase a fly's short-term energy. We tested this hypothesis by performing comparative RNA-seq analysis between zingerone-fed and unfed males of Bactrocera tryoni. We also carried out behavioural assays with zingerone- and cuelure-fed males to test whether they became more active. RNA-seq analysis revealed, in zingerone-fed flies, up-regulation of 3183 genes with homologues transcripts to those known to regulate intermale aggression, pheromone synthesis, mating and accessory gland proteins, along with significant enrichment of several energy metabolic pathways and gene ontology terms. Behavioural assays show significant increases in locomotor activity, weight reduction and successful mating after mounting all direct/indirect measures of increased activity. These results suggest that feeding on lures leads to complex physiological changes, which result in more competitive males. These results do not negate the pheromone effect, but do strongly suggest that the phytochemical-induced sexual selection is governed by both female preference and male competitive mechanisms.
Publisher: Wiley
Date: 11-06-2016
DOI: 10.1111/PBI.12578
Publisher: Springer Science and Business Media LLC
Date: 12-02-2013
DOI: 10.1038/NCOMMS2450
Abstract: The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency.
Publisher: Springer Science and Business Media LLC
Date: 18-10-2013
Publisher: Wiley
Date: 28-09-2023
DOI: 10.1002/ECE3.10575
Publisher: Springer Science and Business Media LLC
Date: 19-06-2010
DOI: 10.1007/S00122-010-1383-9
Abstract: The β-, γ- and δ-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic ersity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally erse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic α-kafirins. Significant ersity was found for each locus, with the cysteine-rich β-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce β-kafirin. An analysis of flour viscosity reveals that these β-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less ersity at the protein level within the cysteine-rich γ-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the δ-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the δ-kafirin locus displayed comparatively low genetic variation. This study has identified genetic ersity in all single copy seed storage protein genes, including a null mutant for β-kafirin in Sorghum.
Publisher: Wiley
Date: 10-10-2012
Publisher: Wiley
Date: 24-08-2009
Publisher: MDPI AG
Date: 12-03-2023
Abstract: Phylum Cnidaria represents a unique group among venomous taxa, with its delivery system organised as in idual organelles, known as nematocysts, heterogeneously distributed across morphological structures rather than packaged as a specialised organ. Acontia are packed with large nematocysts that are expelled from sea anemones during aggressive encounters with predatory species and are found in a limited number of species in the superfamily Metridioidea. Little is known about this specialised structure other than the commonly accepted hypothesis of its role in defence and a rudimentary understanding of its toxin content and activity. This study utilised previously published transcriptomic data and new proteomic analyses to expand this knowledge by identifying the venom profile of acontia in Calliactis polypus. Using mass spectrometry, we found limited toxin ersity in the proteome of acontia, with an abundance of a sodium channel toxin type I, and a novel toxin with two ShK-like domains. Additionally, genomic evidence suggests that the proposed novel toxin is ubiquitous across sea anemone lineages. Overall, the venom profile of acontia in Calliactis polypus and the novel toxin identified here provide the basis for future research to define the function of acontial toxins in sea anemones.
Publisher: IEEE
Date: 04-2014
Start Date: 2015
End Date: 04-2019
Amount: $392,700.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2022
End Date: 05-2025
Amount: $475,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2016
End Date: 12-2022
Amount: $3,732,019.00
Funder: Australian Research Council
View Funded Activity