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Presentations for Program:: Comparative Genomics/Transcriptomics

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Monday, July 25th

Monday, July 25th, 8:15 am to 9:45 am · Birch/Hilton
Session CGT1: Contributed Papers: Comparative Genomics/Transcriptomics I
Presiding: Maurice Amee, University of Connecticut
CGT1001July 25th 8:15 amBirch/HiltonImpacts of allopolyploidy on gene expression in Nicotiana section RepandaeOral PaperOstovar, Talieh; Landis, Jacob; McCarthy, Elizabeth; Stajich, Jason; Waters, Elizabeth; Litt, Amy.Nicotiana
comparative transcriptomics
CGT1002July 25th 8:30 amBirch/HiltonComparative transcriptomics provides insights into the genetic mechanisms regulating functional floral traits across Calochortus (Liliaceae)Oral PaperHernandez, Adriana; Landis, Jacob; Tribble, Carrie; Eifler, Evan; Givnish, Thomas; Strickler, Susan; Specht, Chelsea.RNA-Seq
Floral traits
comparative transcriptomics
gene expression
CGT1003July 25th 8:45 amBirch/HiltonTranscriptomics of seasonal leaf senescence in a deciduous conifer (Larix laricina)Oral PaperAmee, Maurice; Cobo, Irene; Scott, Alison; Maher, Olivia; Wegrzyn, Jill.comparative transcriptomics
seasonal senescence
differential gene expression
CGT1004July 25th 9:00 amBirch/HiltonGrow and then Show: understanding inducible phenotypes in solanum lycopersicum through transcriptomic analysisOral PaperQuinchiguango Archuleta, Inti.
CGT1005July 25th 9:15 amBirch/HiltonMulti-omic investigation of stress responses in Sea beet (Beta vulgaris ssp. maritima, Amaranthaceae) and preliminary metabolomics data in Ice Plant (Mesembryanthemum crystallinum, Aizoaceae)Oral PaperRadford, Zachary; Crum, Alexandra; Fredericksen, Brett; Schaut, Madelyn; Maeda, Hiroshi; Yang, Ya.Co-expression network
time course
hyperspectral imaging
metabolite profiling
quantum yield
stress experiments
high light
methyl jasmonate
salt stress
CGT1006July 25th 9:30 amBirch/HiltonA drought GxE experiment reveals patterns of differential expression and drought tolerance genes in Artemisia tridentata (big sagebrush; Asteraceae)Oral PaperMelton, Anthony; Navock, Kara; Ellestad, Paige; Martinez, Peggy; Morales, Walker; Milliken, Erin; Serpe, Marcelo; Novak, Stephen; Buerki, Sven.sagebrush
gene expression
Monday, July 25th, 10:15 am to 12:00 pm · Birch/Hilton
Session CGT2: Contributed Papers: Comparative Genomics/Transcriptomics II
Presiding: Margaret Staton, University Of Tennessee, Knoxville; Beant Kapoor, University of Tennessee, Knoxville; Gillian Reynolds, Montana State University
CGT2001July 25th 10:15 amBirch/HiltonAncient yet Dynamic: The Evolution of a Fern GenomeOral PaperMarchant, Daniel Blaine; Soltis, Douglas; Soltis, Pamela; Leebens-Mack, Jim; Chen, Zhonghua.fern
Horizontal Gene Transfer
Plant Evolution
CGT2002July 25th 10:30 amBirch/HiltonExploring the structural variation and genome inheritance patterns using three generation red oak pedigreeOral PaperKapoor, 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
CGT2003July 25th 10:45 amBirch/HiltonTracking a Cryptic Invader of the Vancouver Wetland with Genetics and Morphology<Oral PaperBuckholtz, Gracy.Typha
CGT2004July 25th 11:00 amBirch/HiltonHijacking a metagenomic strategy for rapid comparative subgenomics for polyploids and their progenitorsOral PaperReynolds, Gillian; Mumey, Brendan; Strnadova-Neeley, Veronika; Lachowiec, Jennifer.genomics
Monday, July 25th, 1:30 pm to 3:15 pm · Birch/Hilton
Session CGT3: Contributed Papers: Comparative Genomics/Transcriptomics III
Presiding: Susan Strickler, Boyce Thompson Institute For Plant Research
CGT3001July 25th 1:30 pmBirch/HiltonBalancing read length and sequencing depth: optimizing Nanopore long-read sequencing for monocots with an emphasis on LilialesOral PaperDe 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
CGT3002July 25th 1:45 pmBirch/HiltonUtilizing the long and the short: comparison of different genome assembly programs for a 5.5 GB Liliales genomeOral PaperLandis, Jacob; De La Cerda, Gisel; Hernandez, Adriana; Zhang, Jing; Powell, Adrian; Givnish, Thomas; Specht, Chelsea; Strickler, Susan.Calochortus
genome assembly
CGT3003July 25th 2:00 pmBirch/HiltonEASEL (Efficient, Accurate, Scalable Eukaryotic modeLs), a tool for improvement of eukaryotic genome annotationOral PaperWebster, Cynthia; Shrestha, Bikash; Zaman, Sumaira; Vuruputoor, Vidya; Bennett, Jeremy; Monyak, Daniel; Richter, Peter; Bhattarai, Akriti; Fetter, Karl; Wegrzyn, Jill.
CGT3004July 25th 2:15 pmBirch/HiltonDetermining the genomic architecture of Thalictrum sexual dimorphismOral PaperSain, Melody; Baum, David.Dioecy
sex determination
Sexual system
short read data
CGT3005July 25th 2:30 pmBirch/HiltonOmic strategies for identification of Amaranth speciesOral PaperHubert, 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
CGT3006July 25th 2:45 pmBirch/HiltonEvolutionary dynamics of orchid mitogenomesOral PaperValencia-D., Janice; Neubig, Kurt.mitogenome
Genome rearrangement
Horizontal Gene Transfer
CGT3007July 25th 3:00 pmBirch/HiltonTranscriptomic analysis of asymptomatic variety pepper (Capsicum annuum) against the tomato brown rugose fruit virus (ToBRFV)Oral PaperHernandez-Gonzalez, Alam.RNA-Seq
bell pepper
Monday, July 25th, 3:45 pm to 5:30 pm · Birch/Hilton
Session CGT4: Contributed Papers: Comparative Genomics/Transcriptomics IV
Presiding: Jim Leebens-Mack, University Of Georgia
CGT4001July 25th 3:45 pmBirch/HiltonPlagiarism in the Poaceae: the role of lateral gene transfer in grass evolutionOral PaperDunning, Luke; Raimondeau, Pauline; Bianconi, Matheus; Pereira, Lara; Parisod, Christian; Christin, Pascal-Antoine.phylogenomics
lateral gene transfer
CGT4002July 25th 4:00 pmBirch/HiltonPhylogenetically localizing and dating the mesohexaploidy of the tribe BrassiceaeOral PaperThomas, Shawn; Abrahams, Richard; Harkess, Alex; Washburn, Jacob; Pires, Joseph; Arias, Tatiana.Transcriptomics
whole genome duplication
CGT4003July 25th 4:15 pmBirch/HiltonPatterns of plastid genome evolution across parasitic and mycoheterotrophic plantsOral PaperStone, Philippa; Lam, Vivienne; Darby, Hayley; Graham, Sean.Chloroplast genome
CGT4004July 25th 4:30 pmBirch/HiltonPlastome Structural Evolution in Neo-Astragalus (Astragalus L., Fabaceae)Oral PaperCharboneau, Joseph; Cronn, Richard; Liston, Aaron; Wojciechowski, Martin; Sanderson, Michael.Chloroplast genome
inverted repeat-lacking clade
inversion mechanisms
CGT4005July 25th 4:45 pmBirch/HiltonPlastid phylogenomics and molecular evolution of fully mycoheterotrophic ThismiaceaeOral PaperGarrett, Natalie (Lis); Viruel, Juan; Klimpert, Nathaniel; Soto Gomez, Marybel; Lam, Vivienne; Merckx, Vincent; Graham, Sean.Plastid genome degradation
Purifying selection
Heme biosynthesis
Genome rearrangement
Gene loss
CGT4006July 25th 5:00 pmBirch/HiltonAn estimate of gene content and chromosomal organization in the last common ancestor of extant angiospermsOral PaperLeebens-Mack, Jim.Amborella trichopoda
comparative genomics
Karyotype Evolution
CGT4007July 25th 5:15 pmBirch/HiltonChromosome-scale reference genome and RAD based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traitsOral PaperReatini, Bryan; Cang, Alice; Jiang, Qiuyu; Dlugosch, Katrina.Yellow starthistle
genome assembly
genetic map
QTL mapping
Monday, July 25th, 5:30 pm to 7:00 pm · Idlughet (Eklutna) Exhibit Hall/Dena'ina Center
Session P: Contributed Posters: Comparative Genomics/Transcriptomics Posters
PGT001July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterThe Penstemon kunthii draft genome: integrating a genetic map with assembled sequencePoster: Comparative Genomics/TranscriptomicsSchlenk, Noelle; Wessinger, Carolyn; Hileman, Lena.Penstemon
genome assembly
genetic map
PGT002July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterThe conservation of sexual systems and sex-determining regions in the dioecious species of MyricaceaePoster: Comparative Genomics/TranscriptomicsAkozbek, Laramie; Carey, Sarah; Hale, Haley; Leslie, Goertzen; Harkess, Alex.Dioecy
Sex chromosome
sex-determining region
PGT003July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterEffect of light intensity on thinleaf huckleberry (Vaccinium membranaceum Douglas ex Torr.) flavonoid biosynthesisPoster: Comparative Genomics/TranscriptomicsYin, Shuhan; Drummond, Chloe; Renner, Tanya.Huckleberry
Flavonoid Biosynthesis
PGT004July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterIdentifying and Classifying Potential Disease Resistance Genes in White PinesPoster: Comparative Genomics/TranscriptomicsBhattarai, Akriti; Wegrzyn, Jill.Transcriptomics
disease resistance
PGT005July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterProgress on the Open Green Genomes Project, a DOE Joint Genome Institute Community Science Program InitiativePoster: Comparative Genomics/TranscriptomicsLeebens-Mack, Jim.comparative genomics
Vascular Plants
PGT006July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterGenerating transcriptome data to reveal genetic mechanisms of floral traits in multiple species of Calochortus (Liliaceae)Poster: Comparative Genomics/TranscriptomicsLandis, Jacob; Hernandez, Adriana; Tribble, Carrie; Eifler, Evan; Givnish, Thomas; Strickler, Susan; Specht, Chelsea.Calochortus
functional traits
comparative transcriptomics
PGT007July 25th 5:30 pmIdlughet (Eklutna) Exhibit Hall/Dena'ina CenterEvolution of flooding tolerance in maize relativesPoster: Comparative Genomics/TranscriptomicsDeb, Sontosh; Adhikari, Bishnu; Hofford, Nathaniel; MacNeill, Bryan; Motley, M'Kayla; McKain, Michael.climate change
gene expression
Root anatomy
Wild relatives

Tuesday, July 26th

Tuesday, July 26th, 8:00 am to 9:45 am · Katmai/Hilton
Session CGT5: Contributed Papers: Comparative Genomics/Transcriptomics V
Presiding: Xiang Li,
CGT5001July 26th 8:00 amKatmai/HiltonIdentification of Ni tolerance and low Ca tolerance QTL in Caulanthus amplexicaulisOral PaperGarza, Elyssa; Daundasekara, Kasuni; Pepper, Alan.Abiotic stress
low calcium
CGT5002July 26th 8:15 amKatmai/HiltonInference of developmental trajectories from single-cell sequencing dataOral PaperShushkov, Philip.Transcriptomics
cell type
developmental trajectory
CGT5003July 26th 8:30 amKatmai/HiltonEnergy allocation and senescence in the transition between annual and perennial populations of Draba albertinaOral PaperSipperly, Nicolette; Carlson, David; Tacatta, Jorgen; Davalos, Liliana; Bomblies, history
Disposable soma
gene expression
CGT5004July 26th 8:45 amKatmai/HiltonThe divergent genetic networks underlying the convergent evolution of seed shattering in riceOral PaperLi, Xiang; Caicedo, Ana.convergent evolution
seed dispersal
CGT5005July 26th 9:00 amKatmai/HiltonComparative genomics offers new insights into the evolution of the heterostyly supergenOral PaperConti, Elena; Potente, Giacomo; Narjes, Yousefi; Keller, Barbara.Supergene
convergent evolution
reproductive biology
Floral dimorphism
floral evolution
Gene duplication
Suppression of recombination
CGT5006July 26th 9:15 amKatmai/HiltonFlavonoid expression in Vaccinium membranaceum Douglas ex Torr. leaves across gradients of latitude and elevationOral PaperDrummond, Chloe; Yin, Shuhan; Renner, Tanya.Flavonoid Biosynthesis
Landscape Transcriptomics
CGT5007July 26th 9:30 amKatmai/Hilton
The drivers and consequences of sex chromosome turnover in strawberries
Oral PaperCauret, Caroline; Sternberger, Anne; Liston, Aaron; Ashman, Tia-Lynn.Strawberries
Sex chromosome

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