Rachel Brenchley

Rachel Brenchley
University of Salford · School of Environment and Life Sciences

BSc (Hons), MSc, PhD

About

46
Publications
2,541
Reads
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1,549
Citations
Additional affiliations
July 2009 - October 2014
University of Liverpool
Position
  • PostDoc Position
September 2005 - July 2009
The University of Manchester
Position
  • PhD Student

Publications

Publications (46)
Article
Full-text available
br/>Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene e...
Preprint
Full-text available
Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expres...
Data
Figure S1. Seedling screen of 201 progeny lines of a doubled haploid population. Figure S2. Physical positions and genetic marker positions of capture design contigs. Figure S3. Homozygosity scores calculated for the bulk segregant dataset along each POPSEQ‐based pseudo‐chromosome. Figure S4. Homozygosity scores calculated for the bulk segregant...
Data
Table S1. Summary of mapping statistics across the pseudo‐chromosome reference Table S2. Detailing gene regions within the peak interval 13 650 001–14 150 001 bp on the Genome Zipper‐based pseudo‐chromosome 7 Table S3. Detailing homozygous SNP alleles, in 23–43% of reads, in the bulk segregant dataset within the peak interval (13 650 001 and 14 1...
Article
Full-text available
Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L identifying a set of...
Article
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. T...
Conference Paper
Improved crop water-use efficiency (WUE) is critical for the long-term sustainability of agricultural production systems in the face of predicted future warmer and drier climates. Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that enhances WUE through an inverse day/night pattern of stomatal closure/opening and improves...
Article
Full-text available
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity...
Article
Full-text available
Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of sequence data required for whole genome studies. Even with the advent of next-generation sequencing tech...
Article
Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application...
Data
Full-text available
Figure S1. Synteny of PTPs in the three kinetoplastids. Comparison of the corresponding syntenic regions from the L. major, T. cruzi and T. brucei genomes around LmPTP1. Analyses were conducted via TBlastX using the Artemis comparison tool [132] with an E value of and default Gap settings. Outputs were manually annotated using GeneDB annotations.
Data
Full-text available
Figure S2 Phylogenetic tree of LMW-PTPs, mammalian Cdc25 with arsenate reductases type ArsC and ACR2. Sequences were inferred using the Neighbour-Joining method of PHYLIP. LMW-PTPs from Homo sapiens (HUMAN_P24666) and Saccharomyces cerevisiae (YEAST_P40347) are shown. ArsC reductases are included from Bacillus subtilis (BACSU_P45947) and Staphyloco...
Data
Table S1. A list of all kinetoplastid sequences described in this study. Sequences are listed in subgroups with the systematic GeneDB ID used in this analysis. Swiss-Prot IDs are also provided. As the T. cruzi proteome contains sequences from two closely related species, the 'duplications' have been listed where present. 'X' means there is no dupli...
Data
Table S2. PTP conserved motif analysis. Variations from consensus sequences are highlighted in red.
Data
Table S4. Atypical DSP motif analysis. Key functional residues are in bold in the column headings. All substitutions from the classic DSP motifs are highlighted in red.
Data
Table S5. Motif analysis for the PPP family of Ser/Thr phosphatases. Residues in red are substitutions from the conserved pattern: GDXHG – GDXVDRG – GNHE[82] (residues in bold coordinate metal ions at the catalytic site and the underlined His is the proton donor in catalysis).
Data
Table S3. Kinetoplastid-specific motifs in TriTryp classical Tyr-specific PTPs. Sequence motifs conserved in kinetoplastid PTPs but not in other eukaryotes. PcT1 and PcT2 are located at the N-terminal region before the phosphatase catalytic domain. T1–T4 are located in the phosphatase catalytic domain.
Data
Figure S3. Synteny of Cdc25-like Acr2 between L. major and T. brucei. Comparison of the corresponding syntenic regions from the L. major and T. brucei genomes around the ACR2 phosphatase (LmjF32.2740). Analyses were conducted via TBlastX using the Artemis comparison tool [132] with an E value of 1.00 and default Gap settings. Outputs were manually...
Article
Full-text available
The genomes of the three parasitic protozoa Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are the main subject of this study. These parasites are responsible for devastating human diseases known as Chagas disease, African sleeping sickness and cutaneous Leishmaniasis, respectively, that affect millions of people in the developing world...
Conference Paper
Next generation sequencing has paved the way for simultaneous mapping and identification of phenotype inducing mutations in living organisms. Such approaches are extremely useful in well-characterized genomes such as Arabidopsis but can be more difficult to adapt to crop species where genome resources are often poor and the genome sizes are large....

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Projects

Project (1)
Project
The over-arching goal is to define at the molecular level all of the genes and associated proteins required for Kalanchoë to achieve the water use efficient (WUE) adaptation of photosynthetic carbon dioxide fixation known as Crassulacean acid metabolism (CAM). To achieve this, we are decoding genomes and transcriptomes of a diverse range of Kalanchoë species to discover candidate genes required for CAM to function efficiently and we are generating transgenic RNAi and over-expression lines targeting each candidate CAM and circadian control gene in order to understand the importance of each gene to the efficient operation of the highly water-use efficient photosynthetic adaptation. Long-term, our research aims to provide the molecular genetic parts-list or blueprint for CAM that will allow further improvement of existing CAM crops such as Agave and Opuntia and also the engineering of novel crop varieties that are able to leverage the WUE CAM adaptation of photosynthesis during times of drought stress.