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Comparative Genomics/Transcriptomics

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IDTitleSection/TopicAuthorsKeywords
898A case of the blues, reds, and purples: flavonoid biosynthesis and evolution in Vaccinium L
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Comparative Genomics/TranscriptomicsDrummond, Chloe Pak; Chamberlain, Ian; Renner, Tanya.Vaccinium  L.
bilberry
Flavonoids
Comparative genomics
transcriptomics
864A chromosome-scale genome assembly of the fern Marsilea vestita
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Comparative Genomics/TranscriptomicsRahmatpour, 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
994A highly contiguous Vossia cuspidata genome provides insights into the diploidization of maize
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Comparative Genomics/TranscriptomicsDeb, Sontosh; Carey, Sarah; Harkess, Alex; Lewis, Michelle; McKain, Michael.polyploidy
Homoeologous exchange
Subgenome
phylogenomics
749
Canceled
An annotated chromosome-scale Pedicularis genome assembly enables comparative transcriptomic investigations of floral diversity in the Hengduan Mountains
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Comparative Genomics/TranscriptomicsJin, JianJun; Xu, YuXing; McKenzie, Patrick; Meek, Jared; Cohen, Rachel; Li, DeZhu; Yi, Tingshuang; Ree, Richard; Eaton, Deren.Pedicularis
Genome
Transcriptome
floral evolution
Orobanchaceae
Lamiales
174An unquiet sequence: mobility, evolution, and epigenetics of 5S rRNA genes in plants
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Comparative Genomics/TranscriptomicsGarcia, 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
282Applying Machine Learning to Classify the Origins of Gene Duplications
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Comparative Genomics/TranscriptomicsMcKibben, Michael; Barker, Michael S..Machine learning
Whole genome duplication
Genetics
Tools
Paleologs
genome evolution
polyploidy
516A Reference Quality Genome Assembly and Investigation of Genome Duplication in the Mimosoid Legume Leucaena trichandra
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Comparative Genomics/TranscriptomicsBailey, 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
348Assessing data quality among archived plastid genomes via novel software tools
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Comparative Genomics/TranscriptomicsGruenstaeudl, Michael.plastid genome
Genome Assembly
sequence annotation
sequence coverage
quality control
software tool
925Assessing genetic differences related to differential resistance in hemlocks (Tsuga sp.) through comparative transcriptomics
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Comparative Genomics/TranscriptomicsVuruputoor, Vidya; Wegrzyn, Jill.transcriptomics
genomics
Tsuga sp.  
conservation
862Characterization of a mobile sex-determining region in Fragaria chiloensis with a haplotype-resolved genome assembly
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Comparative Genomics/TranscriptomicsCauret, Caroline; Ashman, Tia-Lynn; Liston, Aaron.sex chromosomes
strawberry
Genome Assembly
998Characterization of GmWRKYs involved in a 3-way Interaction of Soybean, Soybean-Aphid and Soybean-Cyst-Nematode
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Comparative Genomics/TranscriptomicsPradhan, Bijaya; Nelson, Dillon; Neupane, Surendra; Nepal, Madhav.WRKY genes  
Soybean-SA-SCN intercation  
abiotic and biotic stress
Plant stress regulation  
525Characterization of WHY1 in Corallorhiza: evolution, expression, and selection across a trophic gradient
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Comparative Genomics/TranscriptomicsMuti, Rachel; Barrett, Craig; Sinn, Brandon.Corallorhiza
WHY1
Whirly transcription factors
mycoheterotrophy
alternative splicing
nonsynonymous substitutions
differential gene expression
780Chromosome-level genome assembly and annotation of invasive Japanese stiltgrass (Microstegium vimineum)
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Comparative Genomics/TranscriptomicsRamachandran, 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
327Comparative genomic approaches reveal differing stress response strategies in maples
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Comparative Genomics/TranscriptomicsMcEvoy, Susan; Trouern-Trend, Alexander; Sezen, Uzay; Wegrzyn, Jill; Swenson, Nathan.maple
forest
tree
abiotic stress
calcium
genomics
soil
164Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)
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Comparative Genomics/TranscriptomicsCai, 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
600Differential Gene Expression of Smoke Induced Seed Germination of Shortgrass Prairie Native Species
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Comparative Genomics/TranscriptomicsChen, Yanni; Johnson, Matthew.Smoke
differential gene expression
Seed Germination
Native Species
Karrikin Insensive 2 (KAI2)
482Disentangling the maze of maize anther development with single-cell RNA-seq
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Comparative Genomics/TranscriptomicsMarchant, Daniel Blaine; Walbot, Virginia.maize
development
single-cell RNA-seq
anther
transcriptomics
737Five gigs and then some: assembling a large reference genome in the Liliales (Calochortus venustus; Liliaceae)
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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
233Gene co-expression reveals evolutionarily conserved and distinct photosynthetic networks in C4+CAM Portulaca
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Comparative Genomics/TranscriptomicsGilman, Ian S.; Moreno-Villena, Jose; Zachary, Lewis; Goolsby, Eric; Edwards, Erika J..photosynthsis
CAM
C4
transcriptomics
co-expression network
Portulaca
genomics
874Gene expression across fertilization and seed development in the minute water lily, Nymphaea thermarum (Nymphaeales): insights on epigenetic regulation during reproduction
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Comparative Genomics/TranscriptomicsPovilus, Rebecca; Friedman, William.Nymphaeales
seed development
epigenetics
transcriptomics
733Genome evolution in California redwoods
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Comparative Genomics/TranscriptomicsScott, Alison Dawn; Zaman, Sumaira; Shrestha, Bikash; Vuruputoor, Vidya; Wegrzyn, Jill.redwood
conifer
Gymnosperm
polyploidy
838Insights into ancient polyploidy and photosynthetic gene family evolution from newly sequenced Yucca genomes
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Comparative Genomics/TranscriptomicsHeyduk, 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
657Modeling the stepwise evolution of sex chromosomes in the genus Asparagus
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Comparative Genomics/TranscriptomicsBentz, Philip; Carey, Sarah; Harkess, Alex; Leebens-Mack, Jim.phylogenetics
sex chromosomes
Dioecy
evolutionary strata
asparagus
sex-determination
genomics
530Patterns between the parents: whole-genome comparison of two diploids in the Tragopogon triangle
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Comparative Genomics/TranscriptomicsPham, Kasey; Liu, Xiaoxian; Boatwright, J. Lucas; Soltis, Douglas E.; Soltis, Pamela S.; Barbazuk, W. Brad.Tragopogon
allopolyploid
Genome Assembly
sciart
416Plants and Pollutants: Exploring salt and cadmium stress response in Sea Rocket
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Comparative Genomics/TranscriptomicsVanden Hoek, Kathryn; Thomas, Shawn; Mendoza-Cózatl, David; Pires, Chris.Hydroponics
High-Throughput Phenotyping
Brassicaceae
RNAseq
Comparative genomics
704Plant sex chromosome "Cytogenetics-By-Sequencing"
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Comparative Genomics/TranscriptomicsCarey, Sarah; Bentz, Philip; Marks, Rose; VanBuren, Robert; Mercati, Francesco; Sunseri, Francesco; Leebens-Mack, Jim; Harkess, Alex.Dioecy
sex chromosomes
methods
Angiosperms
249Plastome evolution in Cuscuta subg. Grammica (Convolvulaceae)
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Comparative Genomics/TranscriptomicsBanerjee, Arjan; Stefanovic, Sasa.Plastid
Plastome
Cuscuta
Convolvulaceae
Dodders
parasitic plants
Heterotrophy
956Presence of 7 cellulose synthase (CesA) genes within mosses suggests early diversification
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Comparative Genomics/TranscriptomicsHartmann, Aly; Schwartz, Rachel.CesA
moss
1065Progenitor-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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Comparative Genomics/TranscriptomicsAdams, Keith.polyploidy
gene expression
duplicated genes
Sclerotinia sclerotiorum
alternative splicing
abiotic and biotic stress
Brassica
Transcriptome
952Revealing the problems of whole genome duplication in regards to the search for serpentine stress QTL
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Comparative Genomics/TranscriptomicsGarza, Elyssa; Daundasekara, Kasuni; Pepper, Alan.Brassicaceae
serpentine
abiotic and biotic stress
Gene duplication
Whole genome duplication
463Simulating Haploid-Diploid Evolution: the (real) SLiM3 shadie
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Comparative Genomics/TranscriptomicsSorojsrisom, Elissa Suphapun; Ambrose, Barbara; Eaton, Deren.gametophyte
evolutionary simulation
alternation of generations
modeling lifecycles
332The Coptis chinensis genome sheds light on eudicot genome duplications
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Comparative Genomics/TranscriptomicsLi, Zheng; Li, Zheng; Liu, Yifei; Barker, Michael S..Whole genome duplication
polyploidy
genome evolution
eudicot
Ranunculaceae
Ranunculales
731The Open Green Genomes Initiative: Comparative Investigation of Plant Genome Content and Structure Across the Land Plant Tree of Life
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Comparative Genomics/TranscriptomicsLeebens-Mack, Jim.phylogenomics
Genome Assembly
genome evolution
894Transcriptional variation across geographically disparate accessions of the invasive species Johnsongrass (Sorghum halepense)
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Comparative Genomics/TranscriptomicsHofford, Nate; Motley, M'Kayla; McKain, Michael.Transcriptomes
invasive species
subgenome dominance
polyploidy
342Transposable elements (TE) dynamics in the model grass genus Brachypodium: abundance, distribution and evolution of TE families
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Comparative Genomics/TranscriptomicsSancho, Rubén; Scarlett, Virginia; Vogel, John; Des Marais, David; Catalan, Pilar.transposable elements
Brachypodium
766
Canceled
Traversome: complicated organelle genome structure resolution and isomer frequencies estimation
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Comparative Genomics/TranscriptomicsJin, JianJun; Eaton, Deren.genome structure
graph alignment
mitochondrial genome
chloroplast genome
sub-walks binomial model
Bayesian inference
739Using de novo assemblies to identify genomic signatures of evolution between insect and hummingbird pollination in Costus (Costaceae)
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Comparative Genomics/TranscriptomicsLandis, Jacob; Valderrama, Eugenio; Grunder, Nikolaus; Skinner, David; Pinilla Vargas, Maria; Almeida, Ana; Specht, Chelsea.Costus L.
nanopore
pollinator shifts
Genome Assembly
573Using Iso-seq to improve reference genome annotations and identify putative polycistronic loci in Yucca aloifolia
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Comparative Genomics/TranscriptomicsField, Richard; Heyduk, Karolina; Leebens-Mack, Jim.Genetics
genomics
transcriptomics

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