Peter McAtee
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View article: A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues
A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues Open
The ability to quantify the colour of fruit is extremely important for a number of applied fields including plant breeding, postharvest assessment, and consumer quality assessment. Fruit and other plant organs display highly complex colour…
View article: A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues
A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues Open
BackgroundThe ability to quantify the colour of fruit is extremely important for a number of applied fields including plant breeding, postharvest assessment, and consumer quality assessment. Fruit and other plant organs display highly comp…
View article: Additional file 4 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Additional file 4 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors Open
Additional file 4: Additional data 4. Table of TPM for the RNA-seq data.
View article: Additional file 3 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Additional file 3 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors Open
Additional file 3: Additional data 3. Details of the RNA-seq data used in this study.
View article: Additional file 1 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Additional file 1 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors Open
Additional file 1: Additional data 1. Table of transcription factors, with corresponding colour module assignments and connectivity.
View article: Additional file 6 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Additional file 6 of A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors Open
Additional file 6: Additional data 6. Numbers of transcription factor classes within each colour module.
View article: An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors
An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors Open
BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual…
View article: Genetic Analysis of Walnut (<i>Juglans regia</i> L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform
Genetic Analysis of Walnut (<i>Juglans regia</i> L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform Open
Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnu…
View article: Sensory-Directed Genetic and Biochemical Characterization of Volatile Terpene Production in Kiwifruit
Sensory-Directed Genetic and Biochemical Characterization of Volatile Terpene Production in Kiwifruit Open
Terpene volatiles are found in many important fruit crops, but their relationship to flavor is poorly understood. Here, we demonstrate using sensory descriptive and discriminant analysis that 1,8-cineole contributes a key floral/eucalyptus…
View article: Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes
Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes Open
The ETYHLENE RESPONSE FACTOR/APETALA2 (ERF/AP2) transcription factors have been shown to control a wide range of developmental and environmental responses in plants. These include hormonal responses to ethylene and Abscisic Acid (ABA) as w…
View article: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit
Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit Open
The results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the i…
View article: Re-programming of<i>Pseudomonas syringae</i>pv.<i>actinidiae</i>gene expression during early stages of infection of kiwifruit
Re-programming of<i>Pseudomonas syringae</i>pv.<i>actinidiae</i>gene expression during early stages of infection of kiwifruit Open
Background Pseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae ( Psa ) initiated a worldwide pandemic in 2008 on cultivars of Actin…
View article: Additional file 12: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 12: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Markers used in this study. List of names of extracted FASTA sequences for SNP markers used to construct the genome (TXT 841Â kb)
View article: Additional file 11: of Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit
Additional file 11: of Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit Open
A spreadsheet containing all the primers used for reverse transcription and reverse transcription quantitative PCR. The data includes the gene chosen, locus ID number, primer sequences, product size and PCR efficiency. (XLSX 13 kb)
View article: Additional file 7: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 7: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Details of sequenced cDNAâ s generated. Fasta formatted sequences of 812 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 1204Â kb)
View article: Additional file 2: of Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit
Additional file 2: of Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit Open
Reads per Kilobase per Million (RPKM) for all Psa genes (sheet 1) and k-means analysis for those genes with >â 50 RPKM for at least one time point (sheet 2). (XLSX 2078 kb)
View article: Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10Â kb)
View article: Additional file 5: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 5: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
‘Hongyang’ Gene models that align to Red5 genome.List of Actinidia chinensis ‘Hongyang’ genes that align to the Red5 whole genome sequence. Additional file 5A: models from original ‘Hongyang’ annotation [14]. Additional file 5B: models fro…
View article: Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Revised â Hongyangâ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114Â kb)
View article: Additional file 2: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 2: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
BAC alignment to chromosome 25.Table summarising alignments of contigs from 22 BAC clones to chromosome 25 of the Red5 assembly (XLSX 15Â kb)
View article: Additional file 13: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 13: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Comparison of Actinidia ESTâ s to manually annotated gene models.Summary of the raw results for the best BLAT gene set match protein of the sequenced cDNAs and manually annotated predicted peptides. (XLSX 102Â kb)
View article: Additional file 9: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 9: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Selected gene models used for phylogeny.Table of EXPANSIN genes and ACS genes identified in this study (XLSX 19Â kb)
View article: Additional file 8: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 8: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
Sequenced cDNAâ s used to verify the gene models.Fasta formatted predicted protein sequences of 550 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models …
View article: Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants
Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants Open
BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb)
View article: Apple dwarfing rootstocks exhibit an imbalance in carbohydrate allocation and reduced cell growth and metabolism
Apple dwarfing rootstocks exhibit an imbalance in carbohydrate allocation and reduced cell growth and metabolism Open
Apple dwarfing rootstocks cause earlier shoot termination and reduced root and shoot mass. To identify physiological factors responsible for rootstock-induced growth restriction, we compared vascular-enriched gene expression between two dw…