A5041015145- Plant Physiology and Cultivation Studies
- Plant-Microbe Interactions and Immunity
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Transgenic Plants and Applications
- RNA and protein synthesis mechanisms
- Phytochemicals and Antioxidant Activities
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Plant Gene Expression Analysis
- Reproductive biology and impacts on aquatic species
- Plant Pathogens and Fungal Diseases
- Plant biochemistry and biosynthesis
- Aquaculture disease management and microbiota
- Zebrafish Biomedical Research Applications
- Plant Stress Responses and Tolerance
- Plant Pathogenic Bacteria Studies
- Genetic diversity and population structure
- Insect-Plant Interactions and Control
- Plant Reproductive Biology
- Machine Learning in Bioinformatics
- Aquaculture Nutrition and Growth
- Algorithms and Data Compression
- Plant Disease Resistance and Genetics
- Physiological and biochemical adaptations
- Vitamin C and Antioxidants Research
Plant & Food Research
2012-2024
Queensland University of Technology
2018
Mt Albert Primary School
2012-2014
Fondazione Edmund Mach
2012
Hawke's Bay Regional Council
2012
University of Auckland
2012
Wellcome Sanger Institute
2004-2009
The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This achieved by a combination of initial manual annotation HAVANA team, experimental validation refinement based on these results.The gene features are divided into eight different categories which only first two (known novel coding sequence) confidently predicted be genes. 5' rapid amplification cDNA ends (RACE) RT-PCR were used experimentally verify annotation. Of 420 loci tested, 229...
Abstract Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) skin color (MYB1). However, the pattern expression allelic variation at these loci does not explain all anthocyanin-related phenotypes. One such example open-pollinated seedling cv Sangrado that green develops red cortex late maturity. We used methods...
We present a draft assembly of the genome European pear (Pyrus communis) 'Bartlett'. Our was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length 1.2 Mb) covers total 577.3 Mb, representing most expected 600 Mb Pyrus genome. A 829,823 putative single nucleotide polymorphisms (SNPs) were detected re-sequencing...
Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants animals. concentration tightly regulated plants, partly to respond stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control biosynthesis pathway. This regulation requires cis-acting upstream open reading frame (uORF) represses translation downstream GGP under high concentration. Disruption this...
Most published genome sequences are drafts, and most dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that not assigned to chromosomes, predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft has 164 Mb of unassigned pseudo-chromosomes, omissions have been identified in the models.A second an A. (genotype Red5) was fully sequenced. This new resulted a 554.0 assembly with all...
The Ensembl ( http://www.ensembl.org/ ) project provides a comprehensive and integrated source of annotation large genome sequences. Over the last year number genomes available from site has increased by 7 to 16, with addition six vertebrate chimpanzee, dog, cow, chicken, tetraodon frog insect honeybee. majority have been annotated automatically using gene build system, showing its flexibility reliably annotate wide variety genomes. With genomes, comparative analysis provided users greatly...
The woodland strawberry, Fragaria vesca is a model fruit for number of rosaceous crops. We have engineered altered concentrations anthocyanin in F. vesca, to determine the impact on plant growth and quality. Anthocyanin were significantly increased by over-expression or decreased knock-down R2R3 MYB activator, MYB10. In contrast, potential bHLH partner MYB10 (bHLH33) did not affect pathway when knocked down using RNAi constructs. Metabolic analysis fruits revealed that, all polyphenolics...
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is comprehensive and integrated source annotation genome sequences, available via interactive website, web services or flat files. As well as being one leading sources annotation, an open software engineering develop portable system able handle very genomes associated requirements. facilities range from sequence analysis data storage...
The Ensembl pipeline is an extension to the system which allows automated annotation of genomic sequence. software comprises two parts. First, there a set Perl modules (“Runnables” and “RunnableDBs”) are `wrappers' for variety commonly used analysis tools. These retrieve sequence data from relational database, run analysis, write results back database. They inherit common interface, simplifies writing new wrapper modules. On top this sits job submission (the “RuleManager”) efficient reliable...
PTI and ETI are the two major defence mechanisms in plants. is triggered by detection of pathogen effectors, or their activity, plant cell most time involves internal receptors known as resistance (R) genes. An increasing number R genes responsible for recognition specific effectors have been characterised over years; however, methods to identify often challenging cannot always be translated crop plants.We present a novel method that trigger hypersensitive response (HR) Nicotiana...
Abstract The assessment of the genetic structuring biodiversity is crucial for management and conservation. This particularly critical widely distributed highly mobile deep‐water teleosts, such as hoki ( Macruronus novaezelandiae ). species significant to Māori people supports largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge management. Here, we apply comprehensive genomic analysis shed light on demographic this by (1) assembling...
The kiwifruit cultivar Actinidia chinensis ‘Hort16A’ is resistant to the polyphagous armoured scale insect pest Hemiberlesia lataniae (Hemiptera: Diaspididae). A cDNA microarray consisting of 17,512 unigenes selected from over 132,000 expressed sequence tags (ESTs) was used measure transcriptomic profile A. canes in response a controlled infestation H. lataniae. After 2 days, 272 transcripts were differentially expressed. 7 5,284 (30%) grouped into 22 major functional categories using MapMan...
Abstract Background The genetic control of sex determination in teleost species is poorly understood. This partly because the diversity mechanisms that determine this large group vertebrates, including constitutive genes linked to chromosomes, polygenic mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly New Zealand silver trevally ( Pseudocaranx georgianus ) together with sex-specific whole sequencing data detect sexually divergent...
Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when priori sequence information unavailable. Sufficient coverage at each locus essential distinguish heterozygous from homozygous sites accurately. The number of GBS samples able be pooled in one lane limited present read depth required site per sample for accurate calling single-nucleotide polymorphisms. Loci bias was observed using slight...
Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able predict physiological responses in growth and other economic traits is crucial address challenges inherent the selection of grow-out locations. This will become an even more significant issue under various predicted future climate change scenarios. this study, we used teleost silver trevally (Pseudocaranx georgianus), a species...
Abstract Background The genetic control of sex determinism in teleost species is poorly understood. This partly because the diversity determining mechanisms this large group, including constitutive genes linked to chromosomes, polygenic mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly New Zealand silver trevally ( Pseudocaranx georgianus ) together with whole sequencing detect sexually divergent regions, identify candidate develop...
Abstract The zebrafish genome, which consists of 25 linkage groups and is ~1.4Gb in size, being sequenced, finished analysed its entirety at the Wellcome Trust Sanger Institute. manual annotation provided by Human Vertebrate Analysis Annotation (HAVANA) group released regular intervals onto Genome (Vega) database ("http://vega.sanger.ac.uk":http://vega.sanger.ac.uk) may be viewed as a DAS source Ensembl ("http://www.ensembl.org/Danio_rerio":http://www.ensembl.org/Danio_rerio). Our compiled...
Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen of kiwifruit. This causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families diploid A. chinensis seedlings grown the field show range susceptibilities to disease with up 100% some families succumbing Psa. But effect selection for resistance Psa on alleles that remain surviving has not been assessed. The objective this work was analyse, removal from allele frequency an...
Both commercial and experimental genotypes of kiwifruit (Actinidia spp.) exhibit large differences in response to insect pests. An understanding the vine's physiological feeding its genetic basis will be important assisting development varieties with acceptable levels pest resistance. This experiment describes transcriptome changes observed bark 2 7 days after commencement by armored scale pest, Hemiberlesia lataniae. Using a cDNA microarray consisting 17,512 unigenes, we measured analyzed...
The zebrafish genome, which consists of 25 linkage groups and is ~1.4Gb in size, being sequenced, finished analysed its entirety at the Wellcome Trust Sanger Institute. manual annotation provided by Human Vertebrate Analysis Annotation (HAVANA) group released regular intervals onto Genome (Vega) database ("http://vega.sanger.ac.uk":http://vega.sanger.ac.uk) may be viewed as a DAS source Ensembl ("http://www.ensembl.org/Danio_rerio":http://www.ensembl.org/Danio_rerio). Our compiled close...