2024
The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile
Bernardi G, Kavembe G, Bergman H, Bucciarelli G, Wood C. The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile. Journal Of Great Lakes Research 2024, 50: 102326. DOI: 10.1016/j.jglr.2024.102326.Peer-Reviewed Original ResearchGC-rich isochoresGC-rich regionBase compositionLake Magadi tilapiaGC-poorRepetitive elementsGC-rich genomic regionsGC-poor genomeRepetitive element analysisProtein coding genesGenomes of vertebratesMagadi tilapiaNile tilapiaGenome organizationGenome sequenceGC-richGenomic regionsCoding genesGenomeHot-waterNatural selectionAlcolapia grahamiFish speciesTilapiaCichlidsWhole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
Gatins R, Arias C, Sánchez C, Bernardi G, De León L. Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific. Gigabyte 2024, 2024: 1-18. PMID: 38550358, PMCID: PMC10973836, DOI: 10.46471/gigabyte.115.Peer-Reviewed Original ResearchBenchmarking Universal Single-Copy OrthologsTropical eastern PacificGenome assemblyPopulation expansionMarine fishUniversal Single-Copy OrthologsAnnotated genome assemblyGenome assembly sizeSingle-copy orthologsWhole-genome assemblyProtein-coding genesIsthmus of PanamaContig N50Illumina readsNuclear genomeGenomic resourcesDemographic historyRepetitive elementsMolecular resourcesHolacanthus passerLocal adaptationEastern PacificGenomeAngelfishMarine organismsA genotyping array for the globally invasive vector mosquito, Aedes albopictus
Cosme L, Corley M, Johnson T, Severson D, Yan G, Wang X, Beebe N, Maynard A, Bonizzoni M, Khorramnejad A, Martins A, Lima J, Munstermann L, Surendran S, Chen C, Maringer K, Wahid I, Mukherjee S, Xu J, Fontaine M, Estallo E, Stein M, Livdahl T, Scaraffia P, Carter B, Mogi M, Tuno N, Mains J, Medley K, Bowles D, Gill R, Eritja R, González-Obando R, Trang H, Boyer S, Abunyewa A, Hackett K, Wu T, Nguyễn J, Shen J, Zhao H, Crawford J, Armbruster P, Caccone A. A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors 2024, 17: 106. PMID: 38439081, PMCID: PMC10910840, DOI: 10.1186/s13071-024-06158-z.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingLow-coverage whole-genome sequencingSNP chipRepetitive elementsGenomic analysisNative rangePatterns of genomic variationWhole-genome sequencing dataSNP chip genotypesPopulation genomic analysesProtein-coding genesLevels of admixtureOrigin of invasionNon-coding regionsPercentage of repetitive elementsGenotyping of samplesChip genotypesGenetic clustersAncestry analysisGenomic variationGenotyping arraysGenotyping platformsMendelian genesGenetic variationGenotyping methods
2023
DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres
Malla A, Yu H, Farris D, Kadimi S, Lam T, Cox A, Smith Z, Lesch B. DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres. EMBO Reports 2023, 24: embr202256492. PMID: 37317657, PMCID: PMC10398668, DOI: 10.15252/embr.202256492.Peer-Reviewed Original ResearchConceptsMouse embryonic stem cellsBurst of transcriptionMajor satellite repeatsLong-term silencingRepetitive DNA elementsEmbryonic stem cellsSatellite transcriptionHeterochromatin stabilityHeterochromatin formationHeterochromatin structureChromatin stateSatellite repeatsGenome stabilityGenome integrityPericentromeric repeatsPericentromeric heterochromatinGenome featuresDNA elementsHistone H3Transcriptional activationHistone methyltransferaseRepetitive elementsDOT1L lossRepeat elementsTranscript production
2021
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Khetan S, Kales S, Kursawe R, Jillette A, Ulirsch JC, Reilly SK, Ucar D, Tewhey R, Stitzel ML. Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation. Nature Communications 2021, 12: 5242. PMID: 34475398, PMCID: PMC8413311, DOI: 10.1038/s41467-021-25514-6.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsTranscriptional activationEndoplasmic reticulum (ER) stress conditionsTranscriptional stress responseCis-regulatory effectsParallel reporter assaysT2D single nucleotide polymorphismsHigh linkage disequilibriumMultiple single nucleotide polymorphismsT2D genetic riskT2D-associated single nucleotide polymorphismsMIN6 β-cellsChromatin accessibilityCandidate single nucleotide polymorphismsT2D geneticsHuman genomeAssociation signalsRepetitive elementsFunctional characterizationNuclear elementsMolecular mechanismsReporter assaysStress responseAssociation studies
2008
Analysis of Insertional Sites of the SIRE1 Retroelement Family from Glycine Max Using GenBank BAC-end Sequences
Flasch DA, Rebman EK, Olfson EH, Nguyen KK, Geirut LE, Garland MC, Lindorfer CM, Laten HM. Analysis of Insertional Sites of the SIRE1 Retroelement Family from Glycine Max Using GenBank BAC-end Sequences. In Silico Biology Journal Of Biological Systems Modeling And Multi-Scale Simulation 2008, 8: 531-543. PMID: 19374136, DOI: 10.3233/isb-00374.Peer-Reviewed Original ResearchConceptsRetroelement familiesGenome Survey Sequence databasesProtein-coding genesLow copy number sequencesClear consensus sequenceTy1/copia familyBAC end sequencesClass II transposable elementsSoybean genomeCopia familiesGenomic assembliesPlant membersSatellite DNATransposable elementsRepetitive elementsConsensus sequenceGlycine maxSequence databasesCopy numberReverse transcriptase geneInsertional siteGenomeGenesSIRE1Transcriptase gene
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