| ID | Title | Section/Topic | Authors | Keywords |
|---|
| 681 | A drought GxE experiment reveals patterns of differential expression and drought tolerance genes in Artemisia tridentata (big sagebrush; Asteraceae) | Comparative Genomics/Transcriptomics | Melton, Anthony; Navock, Kara; Ellestad, Paige; Martinez, Peggy; Morales, Walker; Milliken, Erin; Serpe, Marcelo; Novak, Stephen; Buerki, Sven. | sagebrush
gene expression
drought |
| 596 | Ancient yet Dynamic: The Evolution of a Fern Genome | Comparative Genomics/Transcriptomics | Marchant, Daniel Blaine; Soltis, Douglas; Soltis, Pamela; Leebens-Mack, Jim; Chen, Zhonghua. | fern
polyploidy
Horizontal Gene Transfer
genomics
Plant Evolution |
| 338 | An estimate of gene content and chromosomal organization in the last common ancestor of extant angiosperms | Comparative Genomics/Transcriptomics | Leebens-Mack, Jim. | Amborella trichopoda
comparative genomics
Karyotype Evolution
Angiosperms |
| 179 | Balancing read length and sequencing depth: optimizing Nanopore long-read sequencing for monocots with an emphasis on Liliales | Comparative Genomics/Transcriptomics | De La Cerda, Gisel; Landis, Jacob; Hernandez, Adriana; Tribble, Carrie; Eifler, Evan; Li, Fay-Wei; Zhang, Jing; Karimi, Nisa; Chan, Patricia; Givnish, Thomas; Strickler, Susan; Specht, Chelsea. | Nanopore
genome sequencing
Calochortus
monocot |
| 760 | Chromosome-scale reference genome and RAD based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits | Comparative Genomics/Transcriptomics | Reatini, Bryan; Cang, Alice; Jiang, Qiuyu; Dlugosch, Katrina. | Yellow starthistle
genome assembly
genetic map
QTL mapping |
| 1266 | Comparative genomics offers new insights into the evolution of the heterostyly supergen | Comparative Genomics/Transcriptomics | Conti, Elena; Potente, Giacomo; Narjes, Yousefi; Keller, Barbara. | Supergene
convergent evolution
Primulaceae
reproductive biology
Heterostyly
Floral dimorphism
floral evolution
Gene duplication
Suppression of recombination |
| 319 | Comparative transcriptomics provides insights into the genetic mechanisms regulating functional floral traits across Calochortus (Liliaceae) | Comparative Genomics/Transcriptomics | Hernandez, Adriana; Landis, Jacob; Tribble, Carrie; Eifler, Evan; Givnish, Thomas; Strickler, Susan; Specht, Chelsea. | RNA-Seq
Floral traits
trichomes
comparative transcriptomics
gene expression |
| 857 | Determining the genomic architecture of Thalictrum sexual dimorphism | Comparative Genomics/Transcriptomics | Sain, Melody; Baum, David. | Dioecy
sex determination
genomics
Evolution
homeotic
eudicot
Sexual system
k-mer
short read data |
| 721 | EASEL (Efficient, Accurate, Scalable Eukaryotic modeLs), a tool for improvement of eukaryotic genome annotation | Comparative Genomics/Transcriptomics | Webster, Cynthia; Shrestha, Bikash; Zaman, Sumaira; Vuruputoor, Vidya; Bennett, Jeremy; Monyak, Daniel; Richter, Peter; Bhattarai, Akriti; Fetter, Karl; Wegrzyn, Jill. | |
| 530 | Effect of light intensity on thinleaf huckleberry (Vaccinium membranaceum Douglas ex Torr.) flavonoid biosynthesis | Comparative Genomics/Transcriptomics | Yin, Shuhan; Drummond, Chloe; Renner, Tanya. | Huckleberry
Light
Flavonoid Biosynthesis
metabolomics
Transcriptomics |
| 801 | Energy allocation and senescence in the transition between annual and perennial populations of Draba albertina | Comparative Genomics/Transcriptomics | Sipperly, Nicolette; Carlson, David; Tacatta, Jorgen; Davalos, Liliana; Bomblies, Kirsten. | life history
Disposable soma
gene expression |
| 891 | Evolutionary dynamics of orchid mitogenomes | Comparative Genomics/Transcriptomics | Valencia-D., Janice; Neubig, Kurt. | mitogenome
Evolution
Orchidaceae
Genome rearrangement
Horizontal Gene Transfer |
| 886 | Evolution of flooding tolerance in maize relatives | Comparative Genomics/Transcriptomics | Deb, Sontosh; Adhikari, Bishnu; Hofford, Nathaniel; MacNeill, Bryan; Motley, M'Kayla; McKain, Michael. | climate change
flooding
gene expression
Root anatomy
Aerenchyma
Wild relatives
polyploidy |
| 673 | Exploring the structural variation and genome inheritance patterns using three generation red oak pedigree | Comparative Genomics/Transcriptomics | Kapoor, Beant; Jenkins, Jerry; Schmutz, Jeremy; Zhebentyayeva, Tetyana; Kulheim, Carsten; Lasky, Jesse; Leites, Laura; Schlarbaum, Scott; Carlson, John E.; Staton, Margaret; Coggeshall, Mark; Romero-Severson, Jeanne; Islam-Faridi, Nurul. | Northern red oak
Reference genome
Structural variation
Haplotype blocks
Recombination breakpoints |
| 850 | Flavonoid expression in Vaccinium membranaceum Douglas ex Torr. leaves across gradients of latitude and elevation | Comparative Genomics/Transcriptomics | Drummond, Chloe; Yin, Shuhan; Renner, Tanya. | Flavonoid Biosynthesis
Huckleberry
Transcriptomics
Latitude
Elevation
Landscape Transcriptomics |
| 240 | Generating transcriptome data to reveal genetic mechanisms of floral traits in multiple species of Calochortus (Liliaceae) | Comparative Genomics/Transcriptomics | Landis, Jacob; Hernandez, Adriana; Tribble, Carrie; Eifler, Evan; Givnish, Thomas; Strickler, Susan; Specht, Chelsea. | Calochortus
Nanopore
transcriptome
functional traits
comparative transcriptomics |
| 1052 | Grow and then Show: understanding inducible phenotypes in solanum lycopersicum through transcriptomic analysis | Comparative Genomics/Transcriptomics | Quinchiguango Archuleta, Inti. | |
| 807 | Hijacking a metagenomic strategy for rapid comparative subgenomics for polyploids and their progenitors | Comparative Genomics/Transcriptomics | Reynolds, Gillian; Mumey, Brendan; Strnadova-Neeley, Veronika; Lachowiec, Jennifer. | genomics
polyploidy
bioinformatics |
| 627 | Identification of Ni tolerance and low Ca tolerance QTL in Caulanthus amplexicaulis | Comparative Genomics/Transcriptomics | Garza, Elyssa; Daundasekara, Kasuni; Pepper, Alan. | Abiotic stress
metal
Nickel
genome
Brassicaceae
low calcium
Serpentine |
| 707 | Identifying and Classifying Potential Disease Resistance Genes in White Pines | Comparative Genomics/Transcriptomics | Bhattarai, Akriti; Wegrzyn, Jill. | Transcriptomics
disease resistance |
| 291 | Impacts of allopolyploidy on gene expression in Nicotiana section Repandae | Comparative Genomics/Transcriptomics | Ostovar, Talieh; Landis, Jacob; McCarthy, Elizabeth; Stajich, Jason; Waters, Elizabeth; Litt, Amy. | Nicotiana
allopolyploidy
comparative transcriptomics
hybrids |
| 509 | Inference of developmental trajectories from single-cell sequencing data | Comparative Genomics/Transcriptomics | Shushkov, Philip. | Transcriptomics
cell type
developmental trajectory
xylem
Phloem |
| 244 | Multi-omic investigation of stress responses in Sea beet (Beta vulgaris ssp. maritima, Amaranthaceae) and preliminary metabolomics data in Ice Plant (Mesembryanthemum crystallinum, Aizoaceae) | Comparative Genomics/Transcriptomics | Radford, Zachary; Crum, Alexandra; Fredericksen, Brett; Schaut, Madelyn; Maeda, Hiroshi; Yang, Ya. | Co-expression network
Chenopodiaceae
Caryophyllales
time course
hyperspectral imaging
metabolite profiling
HPLC
transcriptome
quantum yield
stress experiments
high light
methyl jasmonate
salt stress
halophyte
betalain |
| 200 | Omic strategies for identification of Amaranth species | Comparative Genomics/Transcriptomics | Hubert, Julia; Kyte, Sarah; Charron, Andréanne; Colville, Adam; Klein, Daniel; Brière, Stephan C.; Gagnon, Marie-Claude; Galindo Gonzalez, Leonardo Miguel. | amaranths
Amaranthus palmeri
genome skimming
chloroplast sequencing
Comparative -omics
protein biotyping
DNA barcoding |
| 398 | Patterns of plastid genome evolution across parasitic and mycoheterotrophic plants | Comparative Genomics/Transcriptomics | Stone, Philippa; Lam, Vivienne; Darby, Hayley; Graham, Sean. | Chloroplast genome
mycoheterotrophs
Parasitic |
| 91 | Phylogenetically localizing and dating the mesohexaploidy of the tribe Brassiceae | Comparative Genomics/Transcriptomics | Thomas, Shawn; Abrahams, Richard; Harkess, Alex; Washburn, Jacob; Pires, Joseph; Arias, Tatiana. | Transcriptomics
phylogenomics
whole genome duplication
polyploidy
Brassicaceae |
| 90 | Plagiarism in the Poaceae: the role of lateral gene transfer in grass evolution | Comparative Genomics/Transcriptomics | Dunning, Luke; Raimondeau, Pauline; Bianconi, Matheus; Pereira, Lara; Parisod, Christian; Christin, Pascal-Antoine. | phylogenomics
Poaceae
lateral gene transfer |
| 883 | Plastid phylogenomics and molecular evolution of fully mycoheterotrophic Thismiaceae | Comparative Genomics/Transcriptomics | Garrett, Natalie (Lis); Viruel, Juan; Klimpert, Nathaniel; Soto Gomez, Marybel; Lam, Vivienne; Merckx, Vincent; Graham, Sean. | Plastid genome degradation
Purifying selection
Mycoheterotrophy
Heme biosynthesis
Genome rearrangement
Gene loss |
| 875 | Plastome Structural Evolution in Neo-Astragalus (Astragalus L., Fabaceae) | Comparative Genomics/Transcriptomics | Charboneau, Joseph; Cronn, Richard; Liston, Aaron; Wojciechowski, Martin; Sanderson, Michael. | Chloroplast genome
Leguminosae
inverted repeat-lacking clade
inversion mechanisms |
| 336 | Progress on the Open Green Genomes Project, a DOE Joint Genome Institute Community Science Program Initiative | Comparative Genomics/Transcriptomics | Leebens-Mack, Jim. | comparative genomics
Vascular Plants
Embryophytes |
| 963 | The conservation of sexual systems and sex-determining regions in the dioecious species of Myricaceae | Comparative Genomics/Transcriptomics | Akozbek, Laramie; Carey, Sarah; Hale, Haley; Leslie, Goertzen; Harkess, Alex. | Dioecy
Myricaceae
k-mer
Sex chromosome
sex-determining region |
| 879 | The divergent genetic networks underlying the convergent evolution of seed shattering in rice | Comparative Genomics/Transcriptomics | Li, Xiang; Caicedo, Ana. | convergent evolution
seed dispersal
Rice
transcriptomes |
| 665 | Canceled The draft genome of Schiedea membranacea: a foundation for understanding evolution in the genus | Comparative Genomics/Transcriptomics | McDonnell, Angela; Loke, Elena; Moore, Michael; Sakai, Ann; Weller, Stephen; Wagner, Warren; Skogen, Krissa; Weisenberger, Lauren; Wickett, Norman. | |
| 492 | Canceled The drivers and consequences of sex chromosome turnover in strawberries | Comparative Genomics/Transcriptomics | Cauret, Caroline; Sternberger, Anne; Liston, Aaron; Ashman, Tia-Lynn. | Strawberries
Sex chromosome
transcriptome |
| 162 | The Penstemon kunthii draft genome: integrating a genetic map with assembled sequence | Comparative Genomics/Transcriptomics | Schlenk, Noelle; Wessinger, Carolyn; Hileman, Lena. | Penstemon
genome assembly
genetic map |
| 58 | Tracking a Cryptic Invader of the Vancouver Wetland with Genetics and Morphology< | Comparative Genomics/Transcriptomics | Buckholtz, Gracy. | Typha
Estuary
Microsatellite
Invasive
Cattail
Vancouver |
| 897 | Transcriptomic analysis of asymptomatic variety pepper (Capsicum annuum) against the tomato brown rugose fruit virus (ToBRFV) | Comparative Genomics/Transcriptomics | Hernandez-Gonzalez, Alam. | RNA-Seq
Transcriptomics
bell pepper
bioinformatic |
| 845 | Transcriptomics of seasonal leaf senescence in a deciduous conifer (Larix laricina) | Comparative Genomics/Transcriptomics | Amee, Maurice; Cobo, Irene; Scott, Alison; Maher, Olivia; Wegrzyn, Jill. | comparative transcriptomics
seasonal senescence
RNA-Seq
conifer
differential gene expression |
| 180 | Utilizing the long and the short: comparison of different genome assembly programs for a 5.5 GB Liliales genome | Comparative Genomics/Transcriptomics | Landis, Jacob; De La Cerda, Gisel; Hernandez, Adriana; Zhang, Jing; Powell, Adrian; Givnish, Thomas; Specht, Chelsea; Strickler, Susan. | Calochortus
monocot
genome assembly
Nanopore |
