Index Catalog // ScholarsArchive@OSU

The genome of Eucalyptus grandis

Creator:: Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Liston, Aaron, Spatafora, Joseph W., Dharmawardhana, Palitha, Raja, Rajani, Strauss, Steven H., Jaiswal, Pankaj, and et al.
Abstract:: Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
Resource Type:: Article

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia

Creator:: Muñoz-Rodríguez, Pablo, Carruthers, Tom, Wood, John R.I., Williams, Bethany R.M., Weitemier, Kevin, Kronmiller, Brent, Ellis, David, Anglin, Noelle L., Longway, Lucas, Harris, Stephen A., Rausher, Mark D., Kelly, Steven, Liston, Aaron, and Scotland, Robert W.
Abstract:: The sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our...
Resource Type:: Article
Full Text:: 97331, United States of America. 3 Center for Genome Research and Biocomputing, Oregon State

Geographic patterns of genetic variation in three genomes of North American diploid strawberries with special reference to Fragaria vesca subsp. bracteata

Creator:: Stanley, Lauren, Forrester, Nicole J., Govindarajulu, Rajanikanth, Liston, Aaron, and Ashman, Tia-Lynn
Abstract:: Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two...
Resource Type:: Article
Full Text:: evolutionary research in diploid Fragaria. 36 37 Key words: chloroplast, hybridization, genetic structure

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Creator:: Cronn, Richard, Liston, Aaron, Parks, Matthew, Gernandt, David S., Shen, Rongkun, and Mockler, Todd
Abstract:: Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence...
Resource Type:: Article
Full Text:: , 3Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA and

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Creator:: Njuguna, Wambui, Liston, Aaron, Cronn, Richard, Ashman, Tia-Lynn, and Bassil, Nahla
Abstract:: The cultivated strawberry is one of the youngest domesticated plants, developed in France in the 1700s from chance hybridization between two western hemisphere octoploid species. However, little is known about the evolution of the species that gave rise to this important fruit crop. Phylogenetic analysis of chloroplast genome sequences of...
Resource Type:: Article
Full Text:: and age of Fragaria based on whole chloroplast genome sequencing Molecular Phylogenetics and

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics

Creator:: Weitemier, Kevin, Straub, Shannon C. K., Cronn, Richard C., Fishbein, Mark, Schmickl, Roswitha, McDonnell, Angela, and Liston, Aaron
Abstract:: PREMISE OF THE STUDY: Hyb-Seq, the combination of target enrichment and genome skimming allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. METHODS AND RESULTS: Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were utilized to design enrichment probes for 3385...
Resource Type:: Article
Full Text:: -Like Alignment Tool. Genome Research 12: 656-664. KNAUS, B. 2012. Short read toolbox. Website http

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

Creator:: Straub, Shannon C. K., Cronn, Richard C., Edwards, Christopher, Fishbein, Mark, and Liston, Aaron
Abstract:: Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
Resource Type:: Article

Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

Creator:: Tennessen, Jacob A., Govindarajulu, Rajanikanth, Liston, Aaron, and Ashman, Tia-Lynn
Abstract:: Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild...
Resource Type:: Article
Full Text:: Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Creator:: Schmickl, Roswitha, Liston, Aaron, Zeisek, Vojtěch, Oberlander, Kenneth, Weitemier, Kevin, Straub, Shannon C. K., Cronn, Richard C., Dreyer, Léanne L., and Suda, Jan
Abstract:: Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
Resource Type:: Article
Full Text:: University Center for Genome Research and Biocomputing / CGRB) for Illumina sequencing support, Sanjuro

ViningKellyForestryGenomeEucalyptusGrandis.pdf

Creator:: Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Liston, Aaron, Spatafora, Joseph W., Dharmawardhana, Palitha, Raja, Rajani, Strauss, Steven H., Jaiswal, Pankaj, and et al.
Abstract:: Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
Full Text:: , 2082-Cordley Hall, Corvallis, Oregon 97331, USA. 18Center for Genome Research and Biocomputing, Oregon

ScholarsArchive@OSU

The genome of Eucalyptus grandis

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia

Geographic patterns of genetic variation in three genomes of North American diploid strawberries with special reference to Fragaria vesca subsp. bracteata

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

ViningKellyForestryGenomeEucalyptusGrandis.pdf

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