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Comparative Genomics/Transcriptomics

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IDTitleSection/TopicAuthorsKeywords
886Ancient polyploidy is associated with higher genetic diversity in vascular plantsComparative Genomics/TranscriptomicsBarker, Michael; Jorgensen, Stacy; Qi, Xinshuai.Polyploidy
Genetic diversity
WGD
paleopolyploidy
411Ancient sex chromosome systems in plantsComparative Genomics/TranscriptomicsCarey, Sarah; Johnson, Matthew; Payton, Adam; Conrad, Roth; Landis, Jacob; Olsson, Sanna; Huttunen, Sanna; Burleigh, Gordon; McDaniel, Stuart.Sex chromosomes
Bryophytes
557Ancient whole genome duplications as drivers of chemical diversification in LamiaceaeComparative Genomics/TranscriptomicsKinser, Taliesin; Godden, Grant; Soltis, Douglas; SOLTIS, PAMELA S.; Consortium, Mint Evolutionary Genomics.chemical diversification
Polyploidy
Phylogenomics
ancient WGDs
transcriptomics
222Assessing Contemporary Evolution in Helianthus annuus using RNA-SeqComparative Genomics/TranscriptomicsSpear, Marissa M.; Etterson, Julie; Gross, Briana.RNA-Seq
Evolution
Resurrection
Helianthus
649Assessing genome assembly quality using the LTR Assembly Index (LAI)Comparative Genomics/TranscriptomicsOu, Shujun; Chen, Jinfeng; Jiang, Ning.genome
assembly continunity
LTR retrotransposon
LTR Assembly Index
385Caught in action: Fine-scale plastome evolution in the parasitic plants of Cuscuta sect. Ceratophorae (Convolvulaceae)Comparative Genomics/TranscriptomicsBanerjee, Arjan; Stefanovic, Sasa.Parasitic plant
Cuscuta
Convolvulaceae
plastome
Plastid
Heterotrophy
884Characterizing persistent bacterial co-habitants and their genetic contribution to an araphid pennate diatomComparative Genomics/TranscriptomicsParks, Matthew; Wickett, Norman; Alverson, Andrew.Diatoms
phycosphere
bacteria
horizontal gene transfer
688Comparative genomics of a species radiation: sequencing the apple tribeComparative Genomics/TranscriptomicsDaCosta, Jeffrey; Yant, Levi; Potter, Daniel; Mathews, Sarah.Maleae
Rosaceae
Comparative Genomics
whole genome duplication
531Comparative Transcriptomics and Genomic Patterns of Discordance in CapsiceaeComparative Genomics/TranscriptomicsSpalink, Daniel; Stoffel, Kevin; Genevieve, Walden; Amanda, Hulse-Kemp; Theresa, Hill; Allen, Van Deynze; BOHS , LYNN ALLISON.Capsiceae
genealogical discordance
pungency
positive selection
571Comparative transcriptomics and Selection of Differentially Expressed Genes in Drought-Shocked Mentzelia (Loasaceae)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
70Detecting Differential Gene Expression Linked to Foraging Behavior in Cuscuta harperiComparative Genomics/TranscriptomicsWebster, Rebecca.Next generation sequencing
Illumina
Dodder
Cuscuta
Holoparasite
VOC Recognition
Foraging Behavior
378Differential drought response and transcriptome size plasticity between aiploid and autotetraploid TolmieaComparative Genomics/TranscriptomicsVisger, Clayton; SOLTIS, PAMELA S.; Soltis, Douglas.Polyploidy
transcriptomics
autopolyploidy
Tolmiea
431Differential gene expression linked to a reversion from dioecy to gynodioecy in Carica papaya Comparative Genomics/TranscriptomicsChae, Taylor; Harkess, Alex; Moore, Rich.Quantitative Genetics
Evolution
Differential Expression Analysis
647Dynamic of LTR Retrotransposons in Plant Genome EvolutionComparative Genomics/TranscriptomicsOu, Shujun; Jiang, Ning.LTR retrotransposon
genome size
Copia
genome evolution
803Elucidating Floral Nectary Development in Cleomaceae Using Histology and TranscriptomicsComparative Genomics/TranscriptomicsCarey, Shane; Hall, Jocelyn.Cleomaceae
transcriptomics
histology
Nectary
107Evolutionary Conservation of PBS1 Homologs in Family PoaceaeComparative Genomics/TranscriptomicsAndersen, Ethan; Ali, Shaukat; Byamukama, Emmanuel; Yen, Yang; Neupane, Surendra; Nepal, Madhav.Disease Resistance  
Plant Immunity
Grasses
Decoy
Evolutionary Conservation
494Exploring genetic mechanisms of polyploidy-induced salinity tolerance in Arabidopsis thalianaComparative Genomics/TranscriptomicsKenny, Cecile; Doyle, Jeff; Coate, Jeremy.Polyploidy
salt stress
RNA-Seq
686Exploring serpentine tolerance in Caulanthus amplexicaulis through the integration of multiple genomic datasetsComparative Genomics/TranscriptomicsGarza, Elyssa; Hawkins, Angela; Pepper, Alan.genome
Brassicaceae
Serpentine
Caulanthus
Adaptation
899From deep phylogeny to species complexes: The evolution of genomic repetitive elements in fernsComparative Genomics/TranscriptomicsGrusz, Amanda; Fehrenbach, Patrick; Sigel, Erin.apomixis
Hybridization
Polyploidy
transposable elements
600Gene co-expression network connectivity is an important determinant of selective constraint during flower diversification in the magic flowers (Achimenes)Comparative Genomics/TranscriptomicsRoberts, Wade; Roalson, Eric.Achimenes
co-expression network
flower diversification
Gesneriaceae
pollination syndrome
selective constraint
transcriptomics
407Gene Expression Plasticity and the Persistence of Plant Species across Environmental VariationComparative Genomics/TranscriptomicsMarx, Hannah; Maitner, Brian; Wisely, Eldridge; Jorgensen, Stacy; Dlugosch, Katrina; Barker, Michael.Differential Expression Analysis
Harvard Forest
Plasticity
NEON
RNAseq
614Gene Family Expansion in the Sonoran Desert Clade of AsclepiasComparative Genomics/TranscriptomicsBoutte, Julien; FISHBEIN, MARK; Coriton, Olivier; Rousseau-Gueutin, Mathieu; Straub, Shannon.gene duplication
FISH
Copy Number Estimation
752Genes, Genomes, and GammaComparative Genomics/TranscriptomicsChanderbali, Andre; Berger, Brent; Albert, Victor; Howarth, Dianella; Soltis, Douglas; SOLTIS, PAMELA S..gamma
Pentapetalae
Buxales
Trochodendrales
paleohexaploidy
eudicots
105Genome-wide Identification of Mitogen Activated Protein Kinase (MAP Kinase) Cascade Genes in SunflowerComparative 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
106Genome-wide Identification of Disease Resistance Genes in Sunflower (Helianthus annuus L.)Comparative Genomics/TranscriptomicsNeupane, Surendra; Nepal, Madhav.NBS-genes
Sunflower
TNLs
CNLs
RNLs
Phylogeny of R-genes
114Genome-wide identification of resistant genes in domesticated and wild rice varieties (Oryza spp; Poaceae)Comparative Genomics/TranscriptomicsAllasi Canales , Nataly Olivia.NBS-LRR
Oryza
positive selection
R gene phylogeny
142Identifying Gene Candidates of the Shikonin Biosynthesis Pathway in the Chinese Medicinal Plant Lithospermum erythrorhizonComparative Genomics/TranscriptomicsAuber, Robert; Crook, Joseph; Widhalm, Joshua; Wisecaver, Jennifer.Specialized Metabolite
De novo Transcriptome
Differential Expression Analysis
112Identifying sequence heteroplasmy across entire organellar genomes of Daucus carota using whole genome sequence dataComparative Genomics/TranscriptomicsRamsey, Adam; Phan, Vinthuy; Pham, Diem-Trang; Melton, Caroline; Daigle, Bernie; Mandel, Jennifer.carrot
mitochondria
chloroplast
SNP
bioinformatic pipeline
NGS
801Incorporating a fern genome into land plant evolutionary genomicsComparative Genomics/TranscriptomicsMarchant, Daniel Blaine; Sessa, Emily; Wolf, Paul; SOLTIS, PAMELA S.; Soltis, Douglas.ferns
Polyploidy
genome evolution
transposable elements
transcriptomics
943Intragenomic variation of ribosomal genes and evidence of concerted evolution in the opportunistic pathogen CandidaComparative Genomics/TranscriptomicsBuchheim, Mark; Alanagreh, Lo'ai.Candida
Chlamydomonas
Haematococcus
concerted evolution
parasexuality
intragenomic variation
ITS2
652LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposonsComparative Genomics/TranscriptomicsOu, Shujun; Jiang, Ning.LTR retrotransposon
LTR_retriever
transposable element
genome annotation
Evolution
598Machine learning approaches for the inference of WGDs from gene age distributionsComparative 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
282Methylation repatterning in the endosperm and embryo of interploid Mimulus hybridsComparative Genomics/TranscriptomicsLawrence , Amelia H; Kinser, Taliesin; Puzey, Joshua.Methylation
Endosperm
Hybridization
Polyploid
Interploid
Mimulus
792Plastome Evolution in ApocynaceaeComparative Genomics/TranscriptomicsStraub, Shannon; Boutte, Julien; Walter, Lauren; Lunderman, Elizabeth; Bailey, Donovan; Livshultz, Tatyana; Simoes, André; FISHBEIN, MARK.Apocynaceae
plastome
intracellular gene transfer
pseudogene
342Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflict induced by hybridizationComparative Genomics/TranscriptomicsPIRES , JOSEPH CHRIS; Emery, Marianne; Willis, Madeline; Hao, Yue; Barry, Kerrie; Schmutz, Jeremy; Lyons, Eric; Edger, Patrick; Conant, Gavin.Genomics
Polyploidy
Phylogenomics
Hybridization
evolutionary genomics
210Quantifying transcriptome size variation and dosage responses immediately following ploidy change in Arabidopsis thalianaComparative Genomics/TranscriptomicsSong, Michael; Potter, Barney; Doyle, Jeff; Coate, Jeremy.Polyploidy
dosage
transcriptomes
whole genome duplication
Evolution
769Testing a "two gene" model for sex chromosome evolution in asparagusComparative Genomics/TranscriptomicsHarkess, Alex; Leebens-Mack, Jim; Meyers, Blake; Huang, Kun; Batish, Mona.Sex chromosomes
dioecy
657The genomic composition and domestication of Asian rice revealed by 3,400 rice genomesComparative Genomics/TranscriptomicsOu, Shujun; Jiang, Ning.Oryza
domestication
Rice
selective sweep
population structure
941The interplay of alternative splicing and gene duplication in OryzaComparative Genomics/TranscriptomicsCatlin, Nathan; Wing, Rod A.; Soltis, Douglas; SOLTIS, PAMELA S.; Barbazuk, W. Brad.Alternative splicing
gene duplication
Oryza
transcriptomics
604Transcription Factor Family Evolution in Fully Mycoheterotrophic OrchidsComparative Genomics/TranscriptomicsSinn, Brandon; Ranjbaran, Ali; Barrett, Craig.Orchid
fungi
transcriptomics
transcription factors
gene family evolution
954Transcriptomics, phylogeny, and biochemistry elucidate evolution of chemical diversity and complexity in LamiaceaeComparative Genomics/TranscriptomicsBuell, 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
942Transposon diversity and abundance variation as a consequence of climatic variables in Andropogoneae (Poaceae)Comparative Genomics/TranscriptomicsMcKain, 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
908Variation in evolutionary rates across genomes in orchidsComparative Genomics/TranscriptomicsValencia, Janice ; Neubig, Kurt; Whitten, William.
87Variation in photosynthetic function and gene expression in parasitic dodderComparative Genomics/TranscriptomicsSchneider, Adam; Besik, Ariana; Ensminger, Ingo; Stefanovic, Sasa.Cuscuta
photosynthesis
pulse amplutide modified (PAM) fluorimetry
transcriptomics

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