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Comparative Genomics/Transcriptomics

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IDTitleSection/TopicAuthorsKeywords
701Characterization of ancient whole-genome duplications from genomic and transcriptomic data: a machine learning approachComparative Genomics/TranscriptomicsSutherland, Brittany; Tiley, George; Barker, Michael.
519Characterization of Genes involved in Producing Anti-Cancer Compounds in the Euphorbia schimperiTranscriptomeComparative Genomics/TranscriptomicsAlqahtani, Aldanah; Jansen, Robert.
558Characterization of three chloroplast genomes of Birthwort family (Aristolochiaceae) and insights into diverse genome structure and rearrangement in AsarumComparative Genomics/TranscriptomicsGil, Hee-Young; Ha, Young-Ho; Choi, Kyung; Kim, Dong-Kap.Aristolochiaceae
Asarum
Aristolochia
IR expansion
repetitive DNA sequences
721Co-option and carnivory in the CaryophyllalesComparative Genomics/TranscriptomicsDrummond , Chloe Pak; Bocklund, Kylie; Lan, Tianying; Tan, Qiao Wen; Fukushima, Kenji; Rajaraman, Sitaram; Salojärvi, Jarkko; Albert, Victor; Renner, Tanya.carnivory
comparative genomics
Transcriptomics
Caryophyllales
654Comparative genomics of ecologically diverse Andropogoneae speciesComparative Genomics/TranscriptomicsDeb, Sontosh; Romay, Cinta; Rees, Evan; Song, Baoxing; LePak, Nick; Pasquet, Remy; Buckler, Edward; McKain, Michael; McKain, Michael.Vossia
Maize
genomics
polyploidy
Synteny
690Comparative phylogenomic and structural analyses of complete plastomes of the most basal lineage Proto-AraceaeComparative Genomics/TranscriptomicsKim, Seon-Hee; Maki, Masayuki; Lepschi, Brendan ; Kim, Seung-Chul.Comparative phylogenomics
Araceae
Proto-Araceae
Gymnostachydoideae
Orontioideae
Intercontinental disjunct distribution
plastome
458Comparative Transcriptomics of Repeated Reticulate Evolution in the Genus Cuscuta (Convolvulaceae)Comparative Genomics/TranscriptomicsFrangione, Erika; Stefanović, Saša.Transcriptome
hybrid
Polyploid
Next Generation Sequencing
Cuscuta
816Conserved alternative splicing across rapidly evolving taxaComparative Genomics/TranscriptomicsCatlin, Nathan; Wing, Rod A.; Barbazuk, W. Brad.Alternative splicing
Oryza
rice
splice
splicing
704Differential Gene Expression as a Tool for Assessing Homology among Extrafloral Nectaries in Passiflora L. (Passifloraceae)Comparative Genomics/TranscriptomicsMaynord, Silas; Krosnick, Shawn.Homology
Extrafloral Nectaries
Passiflora
Transcriptomics
278Diverse Sex Chromosomes in the SalicaceaeComparative Genomics/TranscriptomicsOlson, Matt; Sanderson, Brian; Hu, Nan; Guo, Minghao; Feng, Guanqiao; DiFazio, Stephen.Sex Chromosomes
Salicaceae
Dioecy
1011Elucidating evolution of specialized metabolism in the mint family (Lamiaceae)Comparative Genomics/TranscriptomicsGodden, Grant; Soltis, Pamela; Soltis, Douglas; Consortium, Mint Evolutionary Genomics.Lamiaceae
specialized metabolism
genomes
transcriptomes
Gene duplication
polyploidy
monoterpenes
iridoids
sesquiterpenes
426Evaluating the genetic basis of morphological variation in the floral nectar spurs of AquilegiaComparative Genomics/TranscriptomicsLiu, Jasen; Ballerini, Evangeline S.; Hodges, Scott.genetics
floral evolution
floral traits
development
aquilegia
1054Evolutionary dynamics of long intergenic noncoding RNA: temporal shifts of diversification and conservation across the AngiospermsComparative Genomics/TranscriptomicsAdams, Keith.genomics
non-coding RNAs
Genome Evolution
Molecular Evolution
Whole genome duplication
polyploidy
Gene Expression
161Evolution of Resistance Genes in Wheat (Triticum aestivum L.) and its RelativesComparative Genomics/TranscriptomicsPurintun, Jordan; Andersen, Ethan; Neupane, Surendra; Nepal, Madhav.Plant immunity
Disease resistance 
NBS-LRRs
Coiled coiled (CC)
CNL, TNL and RNL
499Exploring the evolutionary history of the CUP-SHAPED COTYLEDON (CUC) gene family in the honeysuckles (Lonicera, Caprifoliaceae) and relativesComparative Genomics/TranscriptomicsLee, Aaron; Rahman-Vyas, Hiba; Walker, Joseph; Donoghue, Michael; Smith, Stephen; Howarth, Dianella; Clement, Wendy.gene phylogeny
Asterids
genomics
Dipsacales
transcriptomes
Genome skimming
Gene duplication
357Fluctuation in size and content of mitochondrial genomes across four subfamilies of FabaceaeComparative Genomics/TranscriptomicsChoi, In-Su; Schwarz, Erika; Ruhlman, Tracey; Jansen, Robert.Legumes
evolution
mt DNA
IGT
HGT
677Genomic consequences of UV sex chromosomesComparative Genomics/TranscriptomicsCarey, Sarah; McDaniel, Stuart.moss
Sex Chromosomes
Ceratodon purpureus
343Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus DecalobaComparative Genomics/TranscriptomicsShrestha, Bikash; Weng, Mao-Lun; Theriot, Edward; Gilbert, Lawerence; Ruhlman, Tracey; Krosnick, Shawn; Jansen, Robert.Passifloraceae
IR expansion/contraction
plastid-encoded RNA polymerase
inversion
substitution rate analyses
162Identification and Characterization of Mitogen-Activated Protein Kinase Kinase Kinase (MKKK) Genes in Sunflower (Helianthus annuus L.)  Comparative Genomics/TranscriptomicsNeupane, Surendra; Schweitzer, Sara; Kaluwahandi, Shakila; Nepal, Madhav.Abiotic Stress
Cellular signaling
Protein kinase
MAPKKK cascade
Sunflower MAPKKKs
201Identification of Conserved Regulatory Modules in Dry and Fleshy Fruit DevelopmentComparative Genomics/TranscriptomicsRajewski, Alex; Maheepala, Dinusha; Henry, Ashley; Elkins, Kevan; Litt, Amy.Solanaceae
Tobacco
Tomato
Transcriptome
Transcription factor
evolution
Fruit Development
980In search of the regulatory basis of crassulacean acid metabolism (CAM): a comparative genomics approach in three species of Yucca LComparative Genomics/TranscriptomicsField , Richard D; Heyduk, Karolina; Leebens-Mack, Jim.genomics
photosynthesis
Gene Expression
Chromatin Structure
967Isolation and Characterization of some African Yam Bean (Sphenostylis sternocarpa Hochst ex. A. Rich Harms) fungal endophytes Comparative Genomics/TranscriptomicsKehinde, Iyabode; Oyekanmi, Joshua.fungal endophyte
African Yam Bean
Internal Transcribed Spacer
404Lost and Found: Return of the inverted repeat in the legume clade defined by its absenceComparative Genomics/TranscriptomicsRuhlman , Tracey A; Choi, In-Su; Jansen, Robert.plastome
recombination
inverted repeat
417Misconceptions about Plastome Organization and EvolutionComparative Genomics/TranscriptomicsJansen, Robert; Jansen, Robert; Ruhlman, Tracey; Goncalves, Deise.plastome
recombination
transcription
phylogenomics
283Multiple Independent Whole Genome Duplication Events in the BrassicalesComparative Genomics/TranscriptomicsMabry, Makenzie; Brose, Julia M. ; Blischak, Paul; Dismukes, Wade; Bottoms, Christopher ; Edger, Patrick; Washburn, Jacob; An, Hong; McKain, Michael; McKain, Michael; Barker, Michael; Al-Shehbaz, Ihsan; Schranz, M. Eric; Pires, Joseph.Brassicales
Genome Evolution
Transcriptomics
phylogeny
polyploidy
361Multiple structural types of plastid genomes within a single individualComparative Genomics/TranscriptomicsLee, Chaehee; Ruhlman, Tracey; Jansen, Robert.plastome
multiple genomic configuration
Cyperaceae
repetitive DNA sequences
PacBio SMRT sequencing
488New transcriptomic resources and orthologous nuclear markers for the species-rich flowering plant family AcanthaceaeComparative Genomics/TranscriptomicsDe Morais , Erica Barroso; Schoenenberger, Juerg; Conti, Elena; Antonelli, Alexandre; Szoevenyi, Peter.Acanthaceae
Lamiales
targeted markers
transcriptomes
phylogeny
147Patterns of subgenome evolution after allopolyploidization in a clade of Chilean MimulusComparative Genomics/TranscriptomicsSchlutius, Caroline; Puzey, Joshua.genomics
Mimulus
subgenome dominance
polyploidy
639Plastome evolution across the phylogenetic backbone of the parasitic plant genus Cuscuta (Convolvulaceae)Comparative Genomics/TranscriptomicsBanerjee, Arjan; Stefanović, Saša.Parasitic Plants
Heterotrophy
plastid
plastome
Cuscuta
Convolvulaceae
Dodders
629Plastome sequencing of the last two lineages of parasitic plants: Lennoaceae and KrameriaceaeComparative Genomics/TranscriptomicsSchneider, Adam; Braukmann, Thomas; Banerjee, Arjan; Stefanović, Saša.Lennoaceae
plastome
Krameriaceae
parasitic plant
parasitic reduction syndrmoe
Boraginales
935Species level variation in Conserved Non-coding SequencesComparative Genomics/TranscriptomicsYocca, Alan; Lu, Zefu; Schmitz, Bob; Edger, Patrick.comparative genomics
evolution
Epigenetics
CNS
Genome Evolution
Pangenomics
530Statistically modeling preferentially gene retention after the paleopolyploidy events in the tribe BrassiceaeComparative Genomics/TranscriptomicsHao, Yue ; Colle, Marivi; Edger, Patrick; Pires, Joseph; Conant, Gavin.polyploidy
biased fractionation
Brassica
829Structural organization of chloroplast genomes of five species of riverweeds (Podostemaceae) and comparative analysis in MalpighialesComparative Genomics/TranscriptomicsBedoya, Ana Maria; Ruhfel, Brad; Philbrick, C.T.; Madrinan, Santiago; Bove, Claudia; Mesterházy, Attila; Olmstead, Richard.chloroplast genome
Podostemaceae
Malpighiales
522Survey of Viridiplantae for homospermidine synthase-like genes: multiple parallel origins at multiple phylogenetic depthsComparative Genomics/TranscriptomicsLivshultz, Tatyana; Smith, Chelsea R.; Teisher, Jordan.special metabolism
alkaloids
Gene duplication
paralogy
orthology
parallel evolution
gene trees
671The first genome sequence for Penstemon (Plantaginaceae)Comparative Genomics/TranscriptomicsWolfe, Andi; Blischak, Paul.Whole Genome Sequencing
genome
Penstemon
Penstemon petiolatus genome
Plantaginanceae
771The genetic basis of hybrid novelty in monkeyflowers (Mimulus)Comparative Genomics/TranscriptomicsSchlutius, Caroline; Zheng, Xingyu; Matthews, Melia; Cooley, Arielle; Puzey, Joshua.hybrid novelty
Mimulus
petal lobe anthocyanin
GWAS
111The genetic basis of serpentine adaptation in Aquilegia eximia. Comparative Genomics/TranscriptomicsBlack, Danielle.evolution
serpentine
population differentiation
681The genome of the desiccation tolerant moss Syntrichia caninervisand its response to abiotic stressComparative Genomics/TranscriptomicsSilva, AndersoN; Fisher, Kirsten; Bei, Gao; Stark, Lloyd; Mishler, Brent; Zhang, Daoyuan; Oliver, Melvin.syntrichia caninervis
genome
Desiccation
Transcriptomics
160Transcriptome sequencing for development and assessment of genic SSR marker in Ipomoea speciesComparative Genomics/TranscriptomicsUnamba, Chibuikem I.N.; Singh, Gagandeep; Singh, Pradeep; Seth, Romit; Agbagwa, Ikechukwu O; Sharma, Ram K.Transcriptome
SSR marker 
Ipomoea
Next Generation Sequencing
Sequencing
811Using comparative genomics to uncover the secrets of the serpentine jewelflower: Caulanthus amplexicaulisComparative Genomics/TranscriptomicsGarza, Elyssa; Hawkins, Angela; Pepper, Alan.genome
serpentine
Caulanthus
Sequencing

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