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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)
Society of Herbarium Curators (SHC)
Southeastern Section
Mycological Section (MSA)

Presentations for Program:: Comparative Genomics/Transcriptomics

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SessionDate/TimeLocationTitleTypeAuthorsKeywords

Monday, July 23rd

Monday, July 23rd, 5:30 pm to 7:00 pm · Grand Ballroom - Exhibit Hall/Mayo Civic Center
Session P: Contributed Posters: Comparative Genomics and Transcriptomics
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PGT001July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterDetecting Differential Gene Expression Linked to Foraging Behavior in Cuscuta harperi
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Poster: Comparative Genomics/TranscriptomicsWebster, Rebecca.Next generation sequencing
Illumina
Dodder
Cuscuta
Holoparasite
VOC Recognition
Foraging Behavior
PGT002July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterGenome-wide Identification of Mitogen Activated Protein Kinase (MAP Kinase) Cascade Genes in Sunflower
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Poster: Comparative Genomics/TranscriptomicsSchweitzer, Sarah; Neupane, Surendra; Andersen, Ethan; Zhou, Ruanbao; Fenell, Anne; Nepal, Madhav.MAP Kinase Gene Family
Abiotic Stress 
Signal Transduction Pathway
MAPK
MAPKK
MAPKKK
Zik
Raf
MEKK
PGT003July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterGenome-wide Identification of Disease Resistance Genes in Sunflower (Helianthus annuus L.)
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Poster: Comparative Genomics/TranscriptomicsNeupane, Surendra; Nepal, Madhav.NBS-genes
Sunflower
TNLs
CNLs
RNLs
Phylogeny of R-genes
PGT004July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterEvolutionary Conservation of PBS1 Homologs in Family Poaceae
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Poster: Comparative Genomics/TranscriptomicsAndersen, Ethan; Ali, Shaukat; Byamukama, Emmanuel; Yen, Yang; Neupane, Surendra; Nepal, Madhav.Disease Resistance  
Plant Immunity
Grasses
Decoy
Evolutionary Conservation
PGT005July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterGenome-wide identification of resistant genes in domesticated and wild rice varieties (Oryza spp; Poaceae)
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Poster: Comparative Genomics/TranscriptomicsAllasi Canales , Nataly Olivia.NBS-LRR
Oryza
positive selection
R gene phylogeny
PGT006July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterIdentifying Gene Candidates of the Shikonin Biosynthesis Pathway in the Chinese Medicinal Plant Lithospermum erythrorhizon
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Poster: Comparative Genomics/TranscriptomicsAuber, Robert; Crook, Joseph; Widhalm, Joshua; Wisecaver, Jennifer.Specialized Metabolite
De novo Transcriptome
Differential Expression Analysis
PGT007July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterAssessing Contemporary Evolution in Helianthus annuus using RNA-Seq
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Poster: Comparative Genomics/TranscriptomicsSpear, Marissa M.; Etterson, Julie; Gross, Briana.RNA-Seq
Evolution
Resurrection
Helianthus
PGT008July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterMethylation repatterning in the endosperm and embryo of interploid Mimulus hybrids
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Poster: Comparative Genomics/TranscriptomicsLawrence , Amelia H; Kinser, Taliesin; Puzey, Joshua.Methylation
Endosperm
Hybridization
Polyploid
Interploid
Mimulus
PGT009July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterDifferential gene expression linked to a reversion from dioecy to gynodioecy in Carica papaya
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Poster: Comparative Genomics/TranscriptomicsChae, Taylor; Harkess, Alex; Moore, Rich.Quantitative Genetics
Evolution
Differential Expression Analysis
PGT010July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterComparative transcriptomics and Selection of Differentially Expressed Genes in Drought-Shocked Mentzelia (Loasaceae)
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Poster: Comparative Genomics/TranscriptomicsWiggins, Raegan; Devitt, Jessica; Schenk, John.Differential Expression Analysis
drought
Adaptive response
Mentzelia
Natural Selection
Transcriptome evolution
Expression variance and evolution model
Xerophytes
Loasaceae
PGT011July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterMachine learning approaches for the inference of WGDs from gene age distributions
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Poster: Comparative Genomics/TranscriptomicsTrostle, Alex; Goyal, Anshu; Galuska, Sally; Reardon, Chris; Tiley, George; Ellis, Jake; Li, Zheng; Sutherland, Brittany; Barker, Michael.Polyploidy
Genomics
Machine Learning
WGD
paleopolyploidy
gene duplication
PGT012July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterLTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons
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Poster: Comparative Genomics/TranscriptomicsOu, Shujun; Jiang, Ning.LTR retrotransposon
LTR_retriever
transposable element
genome annotation
Evolution
PGT013July 23rd 5:30 pmGrand Ballroom - Exhibit Hall/Mayo Civic CenterIntragenomic variation of ribosomal genes and evidence of concerted evolution in the opportunistic pathogen Candida
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Poster: Comparative Genomics/TranscriptomicsBuchheim, Mark; Alanagreh, Lo'ai.Candida
Chlamydomonas
Haematococcus
concerted evolution
parasexuality
intragenomic variation
ITS2

Tuesday, July 24th

Tuesday, July 24th, 8:00 am to 12:00 pm · 102/Mayo Civic Center
Session 21: Contributed Papers: Comparative Genomics and Transcriptomics I
Presiding: Jeremy Coate, Reed College
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21001July 24th 8:00 am102/Mayo Civic CenterComparative Transcriptomics and Genomic Patterns of Discordance in Capsiceae
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Oral PaperSpalink, Daniel; Stoffel, Kevin; Genevieve, Walden; Amanda, Hulse-Kemp; Theresa, Hill; Allen, Van Deynze; Bohs, Lynn Allison.Capsiceae
genealogical discordance
pungency
positive selection
21002July 24th 8:15 am102/Mayo Civic CenterCaught in action: Fine-scale plastome evolution in the parasitic plants of Cuscuta sect. Ceratophorae (Convolvulaceae)
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Oral PaperBanerjee, Arjan; Stefanovic, Sasa.Parasitic plant
Cuscuta
Convolvulaceae
plastome
Plastid
Heterotrophy
21003July 24th 8:30 am102/Mayo Civic CenterVariation in photosynthetic function and gene expression in parasitic dodder
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Oral PaperSchneider, Adam; Besik, Ariana; Ensminger, Ingo; Stefanovic, Sasa.Cuscuta
photosynthesis
pulse amplutide modified (PAM) fluorimetry
transcriptomics
21004July 24th 8:45 am102/Mayo Civic CenterElucidating Floral Nectary Development in Cleomaceae Using Histology and Transcriptomics
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Oral PaperCarey, Shane; Hall, Jocelyn.Cleomaceae
transcriptomics
histology
Nectary
21005July 24th 9:00 am102/Mayo Civic CenterGenes, Genomes, and Gamma
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Oral PaperChanderbali, Andre; Berger, Brent; Albert, Victor; Howarth, Dianella; Soltis, Douglas; Soltis, Pamela S..gamma
Pentapetalae
Buxales
Trochodendrales
paleohexaploidy
eudicots
21006July 24th 9:15 am102/Mayo Civic CenterTranscriptomics, phylogeny, and biochemistry elucidate evolution of chemical diversity and complexity in Lamiaceae
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Oral PaperBuell, C. Robin; Crisovan, Emily; Dudareva, Natalia; Garcia, Nicolas; Godden, Grant; Henry, Laura; Kamileen, Mohamed O.; Kates, Heather; Kilgore, Matthew B.; Lichman, Benjamin R.; Mavrodiev, Evgeny; Newton, Linsey; Rodriguez-Lopez, Carlos; O'Connor, Sarah E.; Soltis, Douglas; Soltis, Pamela S.; Vaillancourt, Brieanne; Wiegert-Rininger, Krystle; Zhao, Dongyan.Lamiaceae
transcriptomes
Genomics
Specialized metabolism
monoterpenes
sesquiterpenes
iridoids
phylogeny
Biochemistry
21007July 24th 9:30 am102/Mayo Civic CenterAncient whole genome duplications as drivers of chemical diversification in Lamiaceae
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Oral PaperKinser, Taliesin; Godden, Grant; Soltis, Douglas; Soltis, Pamela S.; Consortium, Mint Evolutionary Genomics.chemical diversification
Polyploidy
Phylogenomics
ancient WGDs
transcriptomics
July 24th 9:45 am102/Mayo Civic CenterBreak
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21009July 24th 10:15 am102/Mayo Civic CenterGene co-expression network connectivity is an important determinant of selective constraint during flower diversification in the magic flowers (Achimenes)
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Oral PaperRoberts, Wade; Roalson, Eric.Achimenes
co-expression network
flower diversification
Gesneriaceae
pollination syndrome
selective constraint
transcriptomics
21010July 24th 10:30 am102/Mayo Civic CenterQuantifying transcriptome size variation and dosage responses immediately following ploidy change in Arabidopsis thaliana
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Oral PaperSong, Michael; Potter, Barney; Doyle, Jeff; Coate, Jeremy.Polyploidy
dosage
transcriptomes
whole genome duplication
Evolution
21011July 24th 10:45 am102/Mayo Civic CenterExploring genetic mechanisms of polyploidy-induced salinity tolerance in Arabidopsis thaliana
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Oral PaperKenny, Cecile; Doyle, Jeff; Coate, Jeremy.Polyploidy
salt stress
RNA-Seq
21012July 24th 11:00 am102/Mayo Civic CenterPreferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflict induced by hybridization
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Oral PaperPires, Joseph Chris; Emery, Marianne; Willis, Madeline; Hao, Yue; Barry, Kerrie; Schmutz, Jeremy; Lyons, Eric; Edger, Patrick; Conant, Gavin.Genomics
Polyploidy
Phylogenomics
Hybridization
evolutionary genomics
21013July 24th 11:15 am102/Mayo Civic CenterExploring serpentine tolerance in Caulanthus amplexicaulis through the integration of multiple genomic datasets
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Oral PaperGarza, Elyssa; Hawkins, Angela; Pepper, Alan.genome
Brassicaceae
Serpentine
Caulanthus
Adaptation
21014July 24th 11:30 am102/Mayo Civic CenterDifferential drought response and transcriptome size plasticity between aiploid and autotetraploid Tolmiea
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Oral PaperVisger, Clayton; Soltis, Pamela S.; Soltis, Douglas.Polyploidy
transcriptomics
autopolyploidy
Tolmiea
21015July 24th 11:45 am102/Mayo Civic CenterIdentifying sequence heteroplasmy across entire organellar genomes of Daucus carota using whole genome sequence data
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Oral PaperRamsey, Adam; Phan, Vinthuy; Pham, Diem-Trang; Melton, Caroline; Daigle, Bernie; Mandel, Jennifer.carrot
mitochondria
chloroplast
SNP
bioinformatic pipeline
NGS
Tuesday, July 24th, 1:00 pm to 5:45 pm · 102/Mayo Civic Center
Session 25: Contributed Papers: Comparative Genomics and Transcriptomics II
Presiding: Hannah Marx, University of Arizona
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25001July 24th 1:00 pm102/Mayo Civic CenterAssessing genome assembly quality using the LTR Assembly Index (LAI)
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Oral PaperOu, Shujun; Chen, Jinfeng; Jiang, Ning.genome
assembly continunity
LTR retrotransposon
LTR Assembly Index
25002July 24th 1:15 pm102/Mayo Civic CenterIncorporating a fern genome into land plant evolutionary genomics
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Oral PaperMarchant, Daniel Blaine; Sessa, Emily; Wolf, Paul; Soltis, Pamela S.; Soltis, Douglas.ferns
Polyploidy
genome evolution
transposable elements
transcriptomics
25003July 24th 1:30 pm102/Mayo Civic CenterAncient polyploidy is associated with higher genetic diversity in vascular plants
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Oral PaperBarker, Michael; Jorgensen, Stacy; Qi, Xinshuai.Polyploidy
Genetic diversity
WGD
paleopolyploidy
25004July 24th 1:45 pm102/Mayo Civic CenterGene Expression Plasticity and the Persistence of Plant Species across Environmental Variation
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Oral PaperMarx, Hannah; Maitner, Brian; Wisely, Eldridge; Jorgensen, Stacy; Dlugosch, Katrina; Barker, Michael.Differential Expression Analysis
Harvard Forest
Plasticity
NEON
RNAseq
25005July 24th 2:00 pm102/Mayo Civic CenterFrom deep phylogeny to species complexes: The evolution of genomic repetitive elements in ferns
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Oral PaperGrusz, Amanda; Fehrenbach, Patrick; Sigel, Erin.apomixis
Hybridization
Polyploidy
transposable elements
25006July 24th 2:15 pm102/Mayo Civic CenterAncient sex chromosome systems in plants
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Oral PaperCarey, Sarah; Johnson, Matthew; Payton, Adam; Conrad, Roth; Landis, Jacob; Olsson, Sanna; Huttunen, Sanna; Burleigh, Gordon; McDaniel, Stuart.Sex chromosomes
Bryophytes
25007July 24th 2:30 pm102/Mayo Civic CenterTesting a "two gene" model for sex chromosome evolution in asparagus
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Oral PaperHarkess, Alex; Leebens-Mack, Jim; Meyers, Blake; Huang, Kun; Batish, Mona.Sex chromosomes
dioecy
25008July 24th 2:45 pm102/Mayo Civic CenterThe genomic composition and domestication of Asian rice revealed by 3,400 rice genomes
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Oral PaperOu, Shujun; Jiang, Ning.Oryza
domestication
Rice
selective sweep
population structure
25009July 24th 3:00 pm102/Mayo Civic Center
Canceled
Plastome Evolution in Apocynaceae
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Oral PaperStraub, Shannon; Boutte, Julien; Walter, Lauren; Lunderman, Elizabeth; Bailey, Donovan; Livshultz, Tatyana; Simoes, André; Fishbein, Mark.Apocynaceae
plastome
intracellular gene transfer
pseudogene
July 24th 3:15 pm102/Mayo Civic CenterBreak
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25011July 24th 3:45 pm102/Mayo Civic CenterGene Family Expansion in the Sonoran Desert Clade of Asclepias
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Oral PaperBoutte, Julien; Fishbein, Mark; Coriton, Olivier; Rousseau-Gueutin, Mathieu; Straub, Shannon.gene duplication
FISH
Copy Number Estimation
25012July 24th 4:00 pm102/Mayo Civic CenterVariation in evolutionary rates across genomes in orchids
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Oral PaperValencia, Janice ; Neubig, Kurt; Whitten, William.
25013July 24th 4:15 pm102/Mayo Civic CenterTranscription Factor Family Evolution in Fully Mycoheterotrophic Orchids
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Oral PaperSinn, Brandon; Ranjbaran, Ali; Barrett, Craig.Orchid
fungi
transcriptomics
transcription factors
gene family evolution
25014July 24th 4:30 pm102/Mayo Civic CenterComparative genomics of a species radiation: sequencing the apple tribe
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Oral PaperDaCosta, Jeffrey; Yant, Levi; Potter, Daniel; Mathews, Sarah.Maleae
Rosaceae
Comparative Genomics
whole genome duplication
25015July 24th 4:45 pm102/Mayo Civic CenterTransposon diversity and abundance variation as a consequence of climatic variables in Andropogoneae (Poaceae)
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Oral PaperMcKain, Michael; Pienaar, Jason; Zudock, Kristina; AuBuchon, Taylor; Saeidi, Saman; Pasquet, Remy; Layton, Daniel; Welker, Cassiano; Art-han, Watchara; Traiperm, Paweena; McAllister, Chrissy; Kellogg, Elizabeth.Andropogoneae
Poaceae
genome evolution
transposable elements
bioclim
25016July 24th 5:00 pm102/Mayo Civic CenterThe interplay of alternative splicing and gene duplication in Oryza
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Oral PaperCatlin, Nathan; Wing, Rod A.; Soltis, Douglas; Soltis, Pamela S.; Barbazuk, W. Brad.Alternative splicing
gene duplication
Oryza
transcriptomics
25017July 24th 5:15 pm102/Mayo Civic CenterCharacterizing persistent bacterial co-habitants and their genetic contribution to an araphid pennate diatom
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Oral PaperParks, Matthew; Wickett, Norman; Alverson, Andrew.Diatoms
phycosphere
bacteria
horizontal gene transfer

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