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Participating Societies

American Bryological and Lichenological Society (ABLS)
American Fern Society (AFS)
American Society of Plant Taxonomists (ASPT)
Botanical Society of America (BSA)
Canadian Botanical Association (CBA/ABC)
Conference Wide
International Association for Plant Taxonomy (IAPT)
Mycological Society of America (MSA)
Northeast Section
Society of Herbarium Curators (SHC)
Southeastern Section
Mycological Section (MSA)

Presentations for Program:: Comparative Genomics/Transcriptomics

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SessionDate/TimeLocationTitleTypeAuthorsKeywords

Monday, July 19th

Monday, July 19th, 5:00 pm to 6:30 pm · Virtual/Virtual
Session P1: Contributed Posters: Comparative Genomics/Transcriptomics Posters
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P1GT001July 19th 5:00 pmVirtual/VirtualSimulating Haploid-Diploid Evolution: the (real) SLiM3 shadie
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Poster: Comparative Genomics/TranscriptomicsSorojsrisom, Elissa Suphapun; Ambrose, Barbara; Eaton, Deren.gametophyte
evolutionary simulation
alternation of generations
modeling lifecycles
P1GT002July 19th 5:00 pmVirtual/VirtualUsing Iso-seq to improve reference genome annotations and identify putative polycistronic loci in Yucca aloifolia
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Poster: Comparative Genomics/TranscriptomicsField, Richard; Heyduk, Karolina; Leebens-Mack, Jim.Genetics
genomics
transcriptomics
P1GT003July 19th 5:00 pmVirtual/VirtualPatterns between the parents: whole-genome comparison of two diploids in the Tragopogon triangle
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Poster: Comparative Genomics/TranscriptomicsPham, Kasey; Liu, Xiaoxian; Boatwright, J. Lucas; Soltis, Douglas E.; Soltis, Pamela S.; Barbazuk, W. Brad.Tragopogon
allopolyploid
Genome Assembly
sciart
P1GT004July 19th 5:00 pmVirtual/VirtualPlants and Pollutants: Exploring salt and cadmium stress response in Sea Rocket
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Poster: Comparative Genomics/TranscriptomicsVanden Hoek, Kathryn; Thomas, Shawn; Mendoza-Cózatl, David; Pires, Chris.Hydroponics
High-Throughput Phenotyping
Brassicaceae
RNAseq
Comparative genomics
P1GT005July 19th 5:00 pmVirtual/VirtualTransposable elements (TE) dynamics in the model grass genus Brachypodium: abundance, distribution and evolution of TE families
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Poster: Comparative Genomics/TranscriptomicsSancho, Rubén; Scarlett, Virginia; Vogel, John; Des Marais, David; Catalan, Pilar.transposable elements
Brachypodium
P1GT006July 19th 5:00 pmVirtual/VirtualModeling the stepwise evolution of sex chromosomes in the genus Asparagus
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Poster: Comparative Genomics/TranscriptomicsBentz, Philip; Carey, Sarah; Harkess, Alex; Leebens-Mack, Jim.phylogenetics
sex chromosomes
Dioecy
evolutionary strata
asparagus
sex-determination
genomics
P1GT007July 19th 5:00 pmVirtual/Virtual
Canceled
Traversome: complicated organelle genome structure resolution and isomer frequencies estimation
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Poster: Comparative Genomics/TranscriptomicsJin, JianJun; Eaton, Deren.genome structure
graph alignment
mitochondrial genome
chloroplast genome
sub-walks binomial model
Bayesian inference
P1GT008July 19th 5:00 pmVirtual/VirtualFive gigs and then some: assembling a large reference genome in the Liliales (Calochortus venustus; Liliaceae)
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Poster: Comparative Genomics/TranscriptomicsLandis, Jacob; Hernandez, Adriana; Pinilla Vargas, Maria; Zhang, Jing; Karimi, Nisa; Chan, Pattricia; Eifler, Evan; Givnish, Thomas; Strickler, Susan; Specht, Chelsea.Calochortus
Genome Assembly
Liliaceae
Flye
P1GT009July 19th 5:00 pmVirtual/VirtualTranscriptional variation across geographically disparate accessions of the invasive species Johnsongrass (Sorghum halepense)
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Poster: Comparative Genomics/TranscriptomicsHofford, Nate; Motley, M'Kayla; McKain, Michael.Transcriptomes
invasive species
subgenome dominance
polyploidy
P1GT010July 19th 5:00 pmVirtual/VirtualAssessing genetic differences related to differential resistance in hemlocks (Tsuga sp.) through comparative transcriptomics
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Poster: Comparative Genomics/TranscriptomicsVuruputoor, Vidya; Wegrzyn, Jill.transcriptomics
genomics
Tsuga sp.  
conservation
P1GT011July 19th 5:00 pmVirtual/VirtualRevealing the problems of whole genome duplication in regards to the search for serpentine stress QTL
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Poster: Comparative Genomics/TranscriptomicsGarza, Elyssa; Daundasekara, Kasuni; Pepper, Alan.Brassicaceae
serpentine
abiotic and biotic stress
Gene duplication
Whole genome duplication
P1GT012July 19th 5:00 pmVirtual/VirtualPresence of 7 cellulose synthase (CesA) genes within mosses suggests early diversification
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Poster: Comparative Genomics/TranscriptomicsHartmann, Aly; Schwartz, Rachel.CesA
moss
P1GT013July 19th 5:00 pmVirtual/VirtualA highly contiguous Vossia cuspidata genome provides insights into the diploidization of maize
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Poster: Comparative Genomics/TranscriptomicsDeb, Sontosh; Carey, Sarah; Harkess, Alex; Lewis, Michelle; McKain, Michael.polyploidy
Homoeologous exchange
Subgenome
phylogenomics
P1GT014July 19th 5:00 pmVirtual/VirtualCharacterization of GmWRKYs involved in a 3-way Interaction of Soybean, Soybean-Aphid and Soybean-Cyst-Nematode
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Poster: Comparative Genomics/TranscriptomicsPradhan, Bijaya; Nelson, Dillon; Neupane, Surendra; Nepal, Madhav.WRKY genes  
Soybean-SA-SCN intercation  
abiotic and biotic stress
Plant stress regulation  

Tuesday, July 20th

Tuesday, July 20th, 10:00 am to 12:00 pm · /
Session CGT1: Contributed Papers: Comparative Genomics/Transcriptomics I
Presiding: Arjan Banerjee, University of Toronto
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CGT1001July 20th 10:00 am/Applying Machine Learning to Classify the Origins of Gene Duplications
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Oral PaperMcKibben, Michael; Barker, Michael S..Machine learning
Whole genome duplication
Genetics
Tools
Paleologs
genome evolution
polyploidy
CGT1002July 20th 10:15 am/The Coptis chinensis genome sheds light on eudicot genome duplications
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Oral PaperLi, Zheng; Li, Zheng; Liu, Yifei; Barker, Michael S..Whole genome duplication
polyploidy
genome evolution
eudicot
Ranunculaceae
Ranunculales
CGT1003July 20th 10:30 am/Plant sex chromosome "Cytogenetics-By-Sequencing"
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Oral PaperCarey, Sarah; Bentz, Philip; Marks, Rose; VanBuren, Robert; Mercati, Francesco; Sunseri, Francesco; Leebens-Mack, Jim; Harkess, Alex.Dioecy
sex chromosomes
methods
Angiosperms
CGT1004July 20th 10:45 am/Assessing data quality among archived plastid genomes via novel software tools
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Oral PaperGruenstaeudl, Michael.plastid genome
Genome Assembly
sequence annotation
sequence coverage
quality control
software tool
CGT1005July 20th 11:00 am/Insights into ancient polyploidy and photosynthetic gene family evolution from newly sequenced Yucca genomes
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Oral PaperHeyduk, Karolina; Jenkins, Jerry; Shu, Shengqiang; Field, Richard; MacNeill, Bryan; McKain, Michael; Barry, Kerrie; Schmutz, Jeremy; Leebens-Mack, Jim.karyotype
chromosome
Photosynthesis
Genome Duplication
Yucca
CAM
CGT1006July 20th 11:15 am/Using de novo assemblies to identify genomic signatures of evolution between insect and hummingbird pollination in Costus (Costaceae)
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Oral PaperLandis, Jacob; Valderrama, Eugenio; Grunder, Nikolaus; Skinner, David; Pinilla Vargas, Maria; Almeida, Ana; Specht, Chelsea.Costus L.
nanopore
pollinator shifts
Genome Assembly
CGT1007July 20th 11:30 am/An unquiet sequence: mobility, evolution, and epigenetics of 5S rRNA genes in plants
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Oral PaperGarcia, Sonia; Vitales, Daniel; Pascual-Díaz, Joan Pere; Heitkam, Tony; Baader, Luisa; Maiwald, Sophie; Mann, Ludwig; Weber, Beatrice; Rodriguez, Roi; Kovarik, Ales.ribosomal DNA
repetitive DNA
molecular evolution
eccDNA
transposable elements
Asteraceae
cytogenetics
concerted evolution
CGT1008July 20th 11:45 am/Plastome evolution in Cuscuta subg. Grammica (Convolvulaceae)
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Oral PaperBanerjee, Arjan; Stefanovic, Sasa.Plastid
Plastome
Cuscuta
Convolvulaceae
Dodders
parasitic plants
Heterotrophy
Tuesday, July 20th, 12:30 pm to 2:30 pm · /
Session CGT2: Contributed Papers: Comparative Genomics/Transcriptomics II
Presiding: JianJun Jin, Columbia University
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CGT2001July 20th 12:30 pm/Disentangling the maze of maize anther development with single-cell RNA-seq
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Oral PaperMarchant, Daniel Blaine; Walbot, Virginia.maize
development
single-cell RNA-seq
anther
transcriptomics
CGT2002July 20th 12:45 pm/Gene co-expression reveals evolutionarily conserved and distinct photosynthetic networks in C4+CAM Portulaca
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Oral PaperGilman, Ian S.; Moreno-Villena, Jose; Zachary, Lewis; Goolsby, Eric; Edwards, Erika J..photosynthsis
CAM
C4
transcriptomics
co-expression network
Portulaca
genomics
CGT2003July 20th 1:00 pm/
Canceled
An annotated chromosome-scale Pedicularis genome assembly enables comparative transcriptomic investigations of floral diversity in the Hengduan Mountains
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Oral PaperJin, JianJun; Xu, YuXing; McKenzie, Patrick; Meek, Jared; Cohen, Rachel; Li, DeZhu; Yi, Tingshuang; Ree, Richard; Eaton, Deren.Pedicularis
Genome
Transcriptome
floral evolution
Orobanchaceae
Lamiales
CGT2004July 20th 1:15 pm/Differential Gene Expression of Smoke Induced Seed Germination of Shortgrass Prairie Native Species
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Oral PaperChen, Yanni; Johnson, Matthew.Smoke
differential gene expression
Seed Germination
Native Species
Karrikin Insensive 2 (KAI2)
CGT2005July 20th 1:30 pm/Progenitor-inclusive transcriptome profiling of polyploid Brassica napus reveals subgenome-dominant gene expression and alternative splicing in response to to Sclerotinia sclerotiorum
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Oral PaperAdams, Keith.polyploidy
gene expression
duplicated genes
Sclerotinia sclerotiorum
alternative splicing
abiotic and biotic stress
Brassica
Transcriptome
CGT2006July 20th 1:45 pm/Gene expression across fertilization and seed development in the minute water lily, Nymphaea thermarum (Nymphaeales): insights on epigenetic regulation during reproduction
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Oral PaperPovilus, Rebecca; Friedman, William.Nymphaeales
seed development
epigenetics
transcriptomics
CGT2007July 20th 2:00 pm/Characterization of WHY1 in Corallorhiza: evolution, expression, and selection across a trophic gradient
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Oral PaperMuti, Rachel; Barrett, Craig; Sinn, Brandon.Corallorhiza
WHY1
Whirly transcription factors
mycoheterotrophy
alternative splicing
nonsynonymous substitutions
differential gene expression
CGT2008July 20th 2:15 pm/A case of the blues, reds, and purples: flavonoid biosynthesis and evolution in Vaccinium L
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Oral PaperDrummond, Chloe Pak; Chamberlain, Ian; Renner, Tanya.Vaccinium  L.
bilberry
Flavonoids
Comparative genomics
transcriptomics
Tuesday, July 20th, 3:00 pm to 5:00 pm · /
Session CGT3: Contributed Papers: Comparative Genomics/Transcriptomics III
Presiding: Jim Leebens-Mack, University Of Georgia; C. Donovan Bailey, New Mexico State University
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CGT3001July 20th 3:00 pm/Comparative genomic approaches reveal differing stress response strategies in maples
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Oral PaperMcEvoy, Susan; Trouern-Trend, Alexander; Sezen, Uzay; Wegrzyn, Jill; Swenson, Nathan.maple
forest
tree
abiotic stress
calcium
genomics
soil
CGT3002July 20th 3:15 pm/Characterization of a mobile sex-determining region in Fragaria chiloensis with a haplotype-resolved genome assembly
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Oral PaperCauret, Caroline; Ashman, Tia-Lynn; Liston, Aaron.sex chromosomes
strawberry
Genome Assembly
CGT3003July 20th 3:30 pm/Chromosome-level genome assembly and annotation of invasive Japanese stiltgrass (Microstegium vimineum)
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Oral PaperRamachandran, Dhanushya; Corbett, Cameron; Huebner, Cynthia; Daly, Mark; Haimovitz, Jasmine; McKain, Michael; Swale, Thomas; Barrett, Craig.Japanese stiltgrass
genome  
Genome Assembly
Annotation
polyploidization
transposable elements
invasive species
Grasses
rapid adaptation
Comparative genomics
CGT3004July 20th 3:45 pm/A Reference Quality Genome Assembly and Investigation of Genome Duplication in the Mimosoid Legume Leucaena trichandra
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Oral PaperBailey, C. Donovan; Strickler, Susan; Ringelberg, Jens J.; Koenen, Erik J.M.; Liston, Aaron; Nagaswara-Rao, Madhugiri; Abair, Alexander; Hughes, Colin E.genomics
Comparative genomics
PacBio
Genome Duplication
CGT3005July 20th 4:00 pm/A chromosome-scale genome assembly of the fern Marsilea vestita
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Oral PaperRahmatpour, Nasim; Kuo, Li-Yaung; Kang, Jessica; Herman, Elaina; Zhou, Junhui; Wolniak, Stephen; Zipper, Richard; Delwiche, Charles; Mount, Stephan M; Li, Fay-Wei.Marsilea vestita
chromosome number
genome evolution
CGT3006July 20th 4:15 pm/Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)
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Oral PaperCai, Liming; Arnold, Brian; Xi, Zhenxiang; Khost, Danielle E.; Patel, Nikisha; Hartmann, Claire B.; Manickam, Sugumaran; Sasirat, Sawitree; Nikolov, Lachezar; Mathews, Sarah; Sackton, Timothy B.; Davis, Charles.horizontal gene transfer
gene loss
codon bias
transposable elements
intron loss
CGT3007July 20th 4:30 pm/Genome evolution in California redwoods
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Oral PaperScott, Alison Dawn; Zaman, Sumaira; Shrestha, Bikash; Vuruputoor, Vidya; Wegrzyn, Jill.redwood
conifer
Gymnosperm
polyploidy
CGT3008July 20th 4:45 pm/The Open Green Genomes Initiative: Comparative Investigation of Plant Genome Content and Structure Across the Land Plant Tree of Life
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Oral PaperLeebens-Mack, Jim.phylogenomics
Genome Assembly
genome evolution

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