Monica Britton - Academia.edu (original) (raw)

Papers by Monica Britton

Genome announcements, 2015

Papillomaviruses, of the family Papillomaviridae, are epitheliotropic, nonenveloped, circular, do... more Papillomaviruses, of the family Papillomaviridae, are epitheliotropic, nonenveloped, circular, double-stranded DNA viruses that contribute to benign and malignant tumors in humans and animals. We report here the whole-genome sequence of canine papillomavirus type 12, found at a pigmented plaque located on the skin of a mixed-breed bloodhound.

The primary goal of this proposal is to develop novel regeneration technologies needed to enginee... more The primary goal of this proposal is to develop novel regeneration technologies needed to engineer walnut rootstocks for pest and disease resistance. The productivity of the walnut industry of California is dependent the availability of superior rootstocks to combat soil disease and pest problems. Individual selections displaying resistance to either Phytophthora crown or root rots or to root lesion nematode,

Agrobacterium: From Biology to Biotechnology, 2008

The common soil bacteria Agrobacterium tumefaciens and Agrobacterium rhizogenes are unique geneti... more The common soil bacteria Agrobacterium tumefaciens and Agrobacterium rhizogenes are unique genetic pathogens capable of fundamentally redirecting plant metabolism in order to generate macroscopic tissue masses (crown galls and hairy roots, respectively) which support the growth of large populations of Agrobacteria. Central to pathogenesis is the horizontal transfer of a suite of oncogenes from the tumor-inducing (Ti) plasmids of A. tumefaciens and the root-inducing (Ri) plasmids of A. rhizogenes into the plant cell genome. These oncogenes alter the synthesis, perception and/or transport of phytohormones in planta, leading to the development of the crown gall and hairy root structures from single genetically transformed plant cells. Crown galls and hairy roots become effective sinks that divert plant resources to produce opine compounds that can only be metabolized by the infecting strain of Agrobacterium. The basic genetic and biochemical mechanisms underlying A. tumefaciens tumorigenesis were initially described over 20 years ago, with the characterization of the ipt, iaaM and iaaH oncogenes. However, the simplistic San Marcos,

PLoS ONE, 2012

Huanglongbing (HLB) or ''citrus greening'' is the most destructive citrus disease worldwide. In t... more Huanglongbing (HLB) or ''citrus greening'' is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.

Journal of Integrative Plant Biology, 2011

walnutresearch.ucdavis.edu

The Walnut Improvement Program is designed to provide the California walnut industry with superio... more The Walnut Improvement Program is designed to provide the California walnut industry with superior varieties, to fill specific needs, while improving our understanding of walnut genetics and building a base for future breeding. In 2004 we released three new ...

walnutresearch.ucdavis.edu

Plant parasitic nematodes can devastate walnut orchards and are able to remain dormant deep in th... more Plant parasitic nematodes can devastate walnut orchards and are able to remain dormant deep in the soil for several years, beyond where traditional pesticides can penetrate. The only effective pesticides are often very toxic to beneficial organisms and are detrimental to the environment; several of the most effective are in the process of being phased-out. To develop novel methods of diagnosis and control, it is necessary to characterize pathogens and their interactions with host and non-host plants by performing genomic and functional genetic analyses. This project focuses on the interaction between walnut roots and Pratylenchus vulnus, an important nematode parasite. The primary goal is to develop a knowledge base of the genes involved in the interaction between the nematode and the walnut root on which it feeds. Genomics tools, including DNA sequencing and microarrays, are being utilized to create a database available to the research community. The information is being analyzed to identify walnut genes whose expression is changed by nematode infection. This study will establish relationships between nematode infection of walnut roots and the expression of specific genes in the nematode and the walnut host and will allow diagnostic tests to be developed to identify the presence and population of specific parasites within the plant's rhizosphere. In addition, functional genomic techniques are being used to suppress the expression of specific nematode genes to identify those that may be able to be targeted by novel pesticides.

BMC Genomics, 2013

Background: Dengue is the most prevalent arboviral disease world-wide and its primary vector is t... more Background: Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only effective strategy to prevent dengue transmission. Aedes aegypti geographic populations exhibit great variability in insecticide resistance and susceptibility to dengue infection. The characterization of single nucleotide polymorphisms (SNPs) as molecular markers to study quantitatively this variation is needed greatly because this species has a low abundance of microsatellite markers and limited known restriction fragments length polymorphisms (RFLPs) and single-strand conformation polymorphism (SSCP) markers. Results: We used RNA-seq to characterize SNPs in three Ae. aegypti strains, including the Liverpool (LVP) strain, from which the current genome annotation is derived. We identified 131,764 unique genome locations with at least one alternative nucleotide to what is reported in the reference annotation. These comprised changes in both open-reading frames (ORFs) and untranslated regions (UTRs) of transcripts. An in depth-look at sequence variation in immunity genes revealed that those associated with autophagy, MD2-like receptors and Peptidoglycan Recognition Proteins had more sequence variation in their 3'UTRs than mutations associated with non-synonymous changes. This supports the conclusion that these genes had maintained their functional specificity while being adapted to different regulatory domains. In contrast, a number of peroxidases, serpins and Clip-domain serine proteases exhibited conservation of putative UTR regulatory sequences while displaying diversification of the ORFs. Transcriptome evidence also was found for~2500 novel transcriptional units (NTUs) not annotated in the reference genome.

BMC Genomics, 2012

Background: A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in... more Background: A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an alternative strategy must be used. We previously reported the development of a pipeline (AGSNP) for genome-wide SNP discovery in coding sequences and other single-copy DNA without a complete genome sequence in self-pollinating (autogamous) plants. Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.). Results: The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-copy sequences in it. To identify single-copy sequences, multiple genome equivalents of short SOLiD reads of another individual were mapped to shallow genome coverage of long Sanger or Roche 454 reads making up the reference sequence. The relative depth of SOLiD reads was used to filter out repeated sequences from single-copy sequences in the reference sequence. The second step was a search for SNPs between SOLiD reads and the reference sequence. Polymorphism within the mapped SOLiD reads would have precluded SNP discovery; hence both individuals had to be homozygous. The AGSNP pipeline was updated here for using SOLiD or other type of short reads of a heterozygous individual for these two principal steps. A total of 32.6X walnut genome equivalents of SOLiD reads of vegetatively propagated walnut scion cultivar 'Chandler' were mapped to 48,661 'Chandler' bacterial artificial chromosome (BAC) end sequences (BESs) produced by Sanger sequencing during the construction of a walnut physical map. A total of 22,799 putative SNPs were initially identified. A total of 6,000 Infinium II type SNPs evenly distributed along the walnut physical map were selected for the construction of an Infinium BeadChip, which was used to genotype a walnut mapping population having 'Chandler' as one of the parents. Genotyping results were used to adjust the filtering parameters of the updated AGSNP pipeline. With the adjusted filtering criteria, 69.6% of SNPs discovered with the updated pipeline were real and could be mapped on the walnut genetic map. A total of 13,439 SNPs were discovered by BES re-sequencing. BESs harboring SNPs were in 677 FPC contigs covering 98% of the physical map of the walnut genome. Conclusion: The updated AGSNP pipeline is a versatile SNP discovery tool for a high-throughput, genome-wide SNP discovery in both autogamous and allogamous species. With this pipeline, a large set of SNPs were identified in a single walnut cultivar.

The goal of this project is to build a set of comprehensive genomic tools for walnut. These will ... more The goal of this project is to build a set of comprehensive genomic tools for walnut. These will facilitate a more precise evaluation of breeding populations and will accelerate development of improved walnut cultivars to address the needs of both California growers and the consumers of this important agricultural commodity. Development of these tools includes (1) construction of a physical

Genome announcements, 2015

Papillomaviruses, of the family Papillomaviridae, are epitheliotropic, nonenveloped, circular, do... more Papillomaviruses, of the family Papillomaviridae, are epitheliotropic, nonenveloped, circular, double-stranded DNA viruses that contribute to benign and malignant tumors in humans and animals. We report here the whole-genome sequence of canine papillomavirus type 12, found at a pigmented plaque located on the skin of a mixed-breed bloodhound.

The primary goal of this proposal is to develop novel regeneration technologies needed to enginee... more The primary goal of this proposal is to develop novel regeneration technologies needed to engineer walnut rootstocks for pest and disease resistance. The productivity of the walnut industry of California is dependent the availability of superior rootstocks to combat soil disease and pest problems. Individual selections displaying resistance to either Phytophthora crown or root rots or to root lesion nematode,

Agrobacterium: From Biology to Biotechnology, 2008

The common soil bacteria Agrobacterium tumefaciens and Agrobacterium rhizogenes are unique geneti... more The common soil bacteria Agrobacterium tumefaciens and Agrobacterium rhizogenes are unique genetic pathogens capable of fundamentally redirecting plant metabolism in order to generate macroscopic tissue masses (crown galls and hairy roots, respectively) which support the growth of large populations of Agrobacteria. Central to pathogenesis is the horizontal transfer of a suite of oncogenes from the tumor-inducing (Ti) plasmids of A. tumefaciens and the root-inducing (Ri) plasmids of A. rhizogenes into the plant cell genome. These oncogenes alter the synthesis, perception and/or transport of phytohormones in planta, leading to the development of the crown gall and hairy root structures from single genetically transformed plant cells. Crown galls and hairy roots become effective sinks that divert plant resources to produce opine compounds that can only be metabolized by the infecting strain of Agrobacterium. The basic genetic and biochemical mechanisms underlying A. tumefaciens tumorigenesis were initially described over 20 years ago, with the characterization of the ipt, iaaM and iaaH oncogenes. However, the simplistic San Marcos,

PLoS ONE, 2012

Huanglongbing (HLB) or ''citrus greening'' is the most destructive citrus disease worldwide. In t... more Huanglongbing (HLB) or ''citrus greening'' is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.

Journal of Integrative Plant Biology, 2011

walnutresearch.ucdavis.edu

The Walnut Improvement Program is designed to provide the California walnut industry with superio... more The Walnut Improvement Program is designed to provide the California walnut industry with superior varieties, to fill specific needs, while improving our understanding of walnut genetics and building a base for future breeding. In 2004 we released three new ...

walnutresearch.ucdavis.edu

Plant parasitic nematodes can devastate walnut orchards and are able to remain dormant deep in th... more Plant parasitic nematodes can devastate walnut orchards and are able to remain dormant deep in the soil for several years, beyond where traditional pesticides can penetrate. The only effective pesticides are often very toxic to beneficial organisms and are detrimental to the environment; several of the most effective are in the process of being phased-out. To develop novel methods of diagnosis and control, it is necessary to characterize pathogens and their interactions with host and non-host plants by performing genomic and functional genetic analyses. This project focuses on the interaction between walnut roots and Pratylenchus vulnus, an important nematode parasite. The primary goal is to develop a knowledge base of the genes involved in the interaction between the nematode and the walnut root on which it feeds. Genomics tools, including DNA sequencing and microarrays, are being utilized to create a database available to the research community. The information is being analyzed to identify walnut genes whose expression is changed by nematode infection. This study will establish relationships between nematode infection of walnut roots and the expression of specific genes in the nematode and the walnut host and will allow diagnostic tests to be developed to identify the presence and population of specific parasites within the plant's rhizosphere. In addition, functional genomic techniques are being used to suppress the expression of specific nematode genes to identify those that may be able to be targeted by novel pesticides.

BMC Genomics, 2013

Background: Dengue is the most prevalent arboviral disease world-wide and its primary vector is t... more Background: Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only effective strategy to prevent dengue transmission. Aedes aegypti geographic populations exhibit great variability in insecticide resistance and susceptibility to dengue infection. The characterization of single nucleotide polymorphisms (SNPs) as molecular markers to study quantitatively this variation is needed greatly because this species has a low abundance of microsatellite markers and limited known restriction fragments length polymorphisms (RFLPs) and single-strand conformation polymorphism (SSCP) markers. Results: We used RNA-seq to characterize SNPs in three Ae. aegypti strains, including the Liverpool (LVP) strain, from which the current genome annotation is derived. We identified 131,764 unique genome locations with at least one alternative nucleotide to what is reported in the reference annotation. These comprised changes in both open-reading frames (ORFs) and untranslated regions (UTRs) of transcripts. An in depth-look at sequence variation in immunity genes revealed that those associated with autophagy, MD2-like receptors and Peptidoglycan Recognition Proteins had more sequence variation in their 3'UTRs than mutations associated with non-synonymous changes. This supports the conclusion that these genes had maintained their functional specificity while being adapted to different regulatory domains. In contrast, a number of peroxidases, serpins and Clip-domain serine proteases exhibited conservation of putative UTR regulatory sequences while displaying diversification of the ORFs. Transcriptome evidence also was found for~2500 novel transcriptional units (NTUs) not annotated in the reference genome.

BMC Genomics, 2012

Background: A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in... more Background: A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an alternative strategy must be used. We previously reported the development of a pipeline (AGSNP) for genome-wide SNP discovery in coding sequences and other single-copy DNA without a complete genome sequence in self-pollinating (autogamous) plants. Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.). Results: The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-copy sequences in it. To identify single-copy sequences, multiple genome equivalents of short SOLiD reads of another individual were mapped to shallow genome coverage of long Sanger or Roche 454 reads making up the reference sequence. The relative depth of SOLiD reads was used to filter out repeated sequences from single-copy sequences in the reference sequence. The second step was a search for SNPs between SOLiD reads and the reference sequence. Polymorphism within the mapped SOLiD reads would have precluded SNP discovery; hence both individuals had to be homozygous. The AGSNP pipeline was updated here for using SOLiD or other type of short reads of a heterozygous individual for these two principal steps. A total of 32.6X walnut genome equivalents of SOLiD reads of vegetatively propagated walnut scion cultivar 'Chandler' were mapped to 48,661 'Chandler' bacterial artificial chromosome (BAC) end sequences (BESs) produced by Sanger sequencing during the construction of a walnut physical map. A total of 22,799 putative SNPs were initially identified. A total of 6,000 Infinium II type SNPs evenly distributed along the walnut physical map were selected for the construction of an Infinium BeadChip, which was used to genotype a walnut mapping population having 'Chandler' as one of the parents. Genotyping results were used to adjust the filtering parameters of the updated AGSNP pipeline. With the adjusted filtering criteria, 69.6% of SNPs discovered with the updated pipeline were real and could be mapped on the walnut genetic map. A total of 13,439 SNPs were discovered by BES re-sequencing. BESs harboring SNPs were in 677 FPC contigs covering 98% of the physical map of the walnut genome. Conclusion: The updated AGSNP pipeline is a versatile SNP discovery tool for a high-throughput, genome-wide SNP discovery in both autogamous and allogamous species. With this pipeline, a large set of SNPs were identified in a single walnut cultivar.

The goal of this project is to build a set of comprehensive genomic tools for walnut. These will ... more The goal of this project is to build a set of comprehensive genomic tools for walnut. These will facilitate a more precise evaluation of breeding populations and will accelerate development of improved walnut cultivars to address the needs of both California growers and the consumers of this important agricultural commodity. Development of these tools includes (1) construction of a physical