Cronn Lab:Research

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(Conservation Mitogenomics)
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(Conservation Mitogenomics)
 
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The basis of climatic adaptation in '''Douglas-fir''' (''[http://en.wikipedia.org/wiki/Pseudotsuga_menziesii Pseudotsuga menziesii]'') - possibly the most ecologically and economically important forest species in coastal western North America - is poorly understood, and this limits our ability to predict population changes to climate and offer science-based prescriptions for management. The Transcriptome Observatory merges a large-scale translocation study with expressed gene (transcriptome) sequencing to define seasonal leaf transcriptomes and identify expressed genes showing significant differences between geographic region. Our goal is to identify genes that contribute to climatic sensing and adaptation in this conifer.
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The basis of climatic adaptation in '''Douglas-fir''' (''[http://en.wikipedia.org/wiki/Pseudotsuga_menziesii Pseudotsuga menziesii]'') - possibly the most ecologically and economically important conifer in western North America - is poorly understood. This limits our ability to predict population changes to climate and offer science-based prescriptions for management. The Transcriptome Observatory merges a large-scale translocation study with expressed gene (transcriptome) sequencing to define seasonal leaf transcriptomes, and differences in gene expression that define trees from different geographic region. Our goal is to identify genes that contribute to climatic sensing and adaptation in Douglas-fir.
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==Conservation Mitogenomics==
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==Conifer Evolutionary Genomics==
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We contribute to the ''[http://www.huh.harvard.edu/research/mathews-lab/atolHtmlSite/ '''Gymnosperm Tree of Life''']'', a collaboration between scientists at 15 universities, state and federal institutions who seek to document the complete evolutionary record of gymnosperms.  Our group works with ''[http://www.science.oregonstate.edu/bpp/faculty/liston/ '''Aaron Liston''']'' and ''[http://faculty.umaine-biology.net/index.php?action=1&facno=4 '''Chris Campbell''']'' to define chloroplast genomic diversity in members of the pine family (''[http://en.wikipedia.org/wiki/Pinaceae '''Pinaceae''']'').
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Mitochondrial genome sequences are the most commonly-used molecule for characterizing animal biodiversity. Our group has adapted Multiplexed Sequencing-by-Synthesis (see '''Cronn et al., 2008''' (''[http://nar.oxfordjournals.org/cgi/content/abstract/36/19/e122]'') for high-throughput genetic analysis of complete animal mitochondrial genomes. This work is being conducted with Michael Schwartz at the '''USFS Wildlife Genetics Laboratory''' (''[http://www.rmrs.nau.edu/wildlife/genetics/]''), with primary focus on '''Fisher''' (''[http://en.wikipedia.org/wiki/Martes_pennanti  Martes pennanti]'') and other regionally rare carnivores.
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==Conifer Transcriptome Analysis==
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The basis of climatic adaptation in conifers is poorly understood, and this limits our ability to predict population changes to climate and offer science-based prescriptions for management. We have initiated transcriptome analyses to define seasonal variation in gene expression for a number of important conifers.  The '''Douglas-fir''' (''[http://en.wikipedia.org/wiki/Pseudotsuga_menziesii Pseudotsuga menziesii]'') Transcriptome Observatory merges a large-scale translocation study with expressed gene sequencing to define seasonal leaf transcriptomes and differences in gene expression that relate to climatic variation. Similarly, the (''[http://www.fs.fed.us/pnw/olympia/silv/wfts/ Western Forest Transcriptome Survey]'') is a collaboration to identify climate-responsive genes from diverse forest species.
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==Conservation Mitogenomics==
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==Development of DNA tools to aid genetic conservation and restoration in Port-Orford-cedar==
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Mitochondrial DNA sequences are among the most commonly-used molecules for assessing animal biodiversity. Our group has adapted ''[http://nar.oxfordjournals.org/cgi/content/abstract/36/19/e122 '''Multiplexed Sequencing-by-Synthesis''' ]'' to enable high-throughput genetic analysis of complete animal mitochondrial genomes. This work is being conducted with the ''[http://www.rmrs.nau.edu/wildlife/genetics/ '''USFS Wildlife Genetics Laboratory''' ]'', with primary focus on '''Fisher''' ''[http://en.wikipedia.org/wiki/Martes_pennanti (Martes pennanti)]'' and other regionally rare carnivores, as well as '''West-Slope Cutthroat Trout''' ''[http://en.wikipedia.org/wiki/Westslope_cutthroat_trout (Oncorhynchus clarkii lewisi)]'' .
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'''Port-Orford-cedar''' (''[http://en.wikipedia.org/wiki/Chamaecyparis_lawsoniana Chamaecyparis lawsoniana]'') is a conifer native to coastal Oregon and northern California which is of horticultural importance.  This project is in the process of developing molecular markers for this taxon to determine whether genetic variation in resistant Port-Orford-cedar breeding populations is similar in kind and amount to trees in unmanaged natural populations.  This marker system will then also be used to identify geographic regions harboring Port-Orford-cedar that possess novel genetic variation and consider expanding resistance testing of those populations or expanded seed collections for ex situ genetic conservation as well as characterize the baseline genetic data for Port-Orford-cedar to be used for future management consideration relating to climate change and genetic conservation efforts.
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==Antelope Bitterbrush Landscape Genetics==
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==Development of DNA tools to aid genetic conservation and restoration in false cypresses==
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'''Antelope bitterbrush''' (''[http://en.wikipedia.org/wiki/Purshia_tridentata Purshia tridentata]'') is an important forage and cover shrub in the inter-mountain region of western North America.
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In western North America, ''[http://en.wikipedia.org/wiki/Chamaecyparis_lawsoniana '''Port Orford-cedar''']'' and ''[http://en.wikipedia.org/wiki/Callitropsis_nootkatensis '''Yellow-cedar''']'' both show evidence of decline due to biotic and abiotic stresses. These species have exceptional ecological and economic value, and conservation of genetic resources is a focus of USFS activities. We are developing microsatellite markers for these species using Multiplexed Sequencing-by-Synthesis. Our experience shows this to be an efficient, inexpensive, and rapid way to identify tens of thousands of microsatellite-containing sequences. Microsatellites are being used to define spatial genetic structure and characterize valuable resistant breeding materials in these species.
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==Development of Microsatellites using Sequencing-By-Synthesis Technology==
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==Restoration Landscape Genetics==
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Development of '''microsatellites''' (simple-sequence repeats) has historically been a time consuming and expensive task.  We developed an approach to isolate and sequence microsatellites by combining traditional hybridization/enrichment with multiplexed massively parallel sequencing-by-synthesis technology. The approach is rapid and inexpensive, and the resulting library of microreads contains tens of thousands of microsatellite-containing sequences.
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We are working to understand how key restoration species respond to climate, with the goal of defining seed transfer guidelines. Efforts to date include ''[http://en.wikipedia.org/wiki/Purshia_tridentata '''Antelope bitterbrush''' ]'', ''[http://en.wikipedia.org/wiki/Artemisia_tridentata '''Big Sagebrush''' ]'', and a number of grass species.

Current revision

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Contents

Douglas-fir Transcriptome Observatory

The basis of climatic adaptation in Douglas-fir (Pseudotsuga menziesii) - possibly the most ecologically and economically important conifer in western North America - is poorly understood. This limits our ability to predict population changes to climate and offer science-based prescriptions for management. The Transcriptome Observatory merges a large-scale translocation study with expressed gene (transcriptome) sequencing to define seasonal leaf transcriptomes, and differences in gene expression that define trees from different geographic region. Our goal is to identify genes that contribute to climatic sensing and adaptation in Douglas-fir.

Conifer Evolutionary Genomics

We contribute to the Gymnosperm Tree of Life, a collaboration between scientists at 15 universities, state and federal institutions who seek to document the complete evolutionary record of gymnosperms. Our group works with Aaron Liston and Chris Campbell to define chloroplast genomic diversity in members of the pine family (Pinaceae).

Conifer Transcriptome Analysis

The basis of climatic adaptation in conifers is poorly understood, and this limits our ability to predict population changes to climate and offer science-based prescriptions for management. We have initiated transcriptome analyses to define seasonal variation in gene expression for a number of important conifers. The Douglas-fir (Pseudotsuga menziesii) Transcriptome Observatory merges a large-scale translocation study with expressed gene sequencing to define seasonal leaf transcriptomes and differences in gene expression that relate to climatic variation. Similarly, the (Western Forest Transcriptome Survey) is a collaboration to identify climate-responsive genes from diverse forest species.

Conservation Mitogenomics

Mitochondrial DNA sequences are among the most commonly-used molecules for assessing animal biodiversity. Our group has adapted Multiplexed Sequencing-by-Synthesis to enable high-throughput genetic analysis of complete animal mitochondrial genomes. This work is being conducted with the USFS Wildlife Genetics Laboratory , with primary focus on Fisher (Martes pennanti) and other regionally rare carnivores, as well as West-Slope Cutthroat Trout (Oncorhynchus clarkii lewisi) .

Development of DNA tools to aid genetic conservation and restoration in false cypresses

In western North America, Port Orford-cedar and Yellow-cedar both show evidence of decline due to biotic and abiotic stresses. These species have exceptional ecological and economic value, and conservation of genetic resources is a focus of USFS activities. We are developing microsatellite markers for these species using Multiplexed Sequencing-by-Synthesis. Our experience shows this to be an efficient, inexpensive, and rapid way to identify tens of thousands of microsatellite-containing sequences. Microsatellites are being used to define spatial genetic structure and characterize valuable resistant breeding materials in these species.

Restoration Landscape Genetics

We are working to understand how key restoration species respond to climate, with the goal of defining seed transfer guidelines. Efforts to date include Antelope bitterbrush , Big Sagebrush , and a number of grass species.

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