2025
Experiences from dual genome next-generation sequencing panel testing for mitochondrial disorders: a comprehensive molecular diagnosis
Gorman E, Dai H, Feng Y, Craigen W, Chen D, Xia F, Meng L, Liu P, Rigobello R, Neogi A, Eng C, Wang Y. Experiences from dual genome next-generation sequencing panel testing for mitochondrial disorders: a comprehensive molecular diagnosis. Frontiers In Genetics 2025, 16: 1488956. PMID: 40110048, PMCID: PMC11920145, DOI: 10.3389/fgene.2025.1488956.Peer-Reviewed Original ResearchNext-generation sequencingMitochondrial genomeComprehensive molecular diagnosisMitochondrial disordersMitochondrial diseaseMolecular diagnosisNext-generation sequencing panel testingMolecular diagnosis of mitochondrial disordersDiagnosis of mitochondrial disordersDisease-causing genesPanel testingMtDNA genomeNuclear genomeNuclear genesMtDNA heteroplasmyDiagnosing mitochondrial disordersMitochondrial heteroplasmyHeteroplasmy levelsGenomeP/LP variantsGenetic heterogeneityMtDNAHeteroplasmyGenomic testingPhenotypic variability
2024
Whole 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 organismsGiants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores
Ahuja N, Cao X, Schultz D, Picciani N, Lord A, Shao S, Jia K, Burdick D, Haddock S, Li Y, Dunn C. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biology And Evolution 2024, 16: evae048. PMID: 38502059, PMCID: PMC10980510, DOI: 10.1093/gbe/evae048.Peer-Reviewed Original ResearchConceptsK-mer spectraMitochondrial genomeGenomic diversityK-mersNuclear genomeEstimate nuclear genome sizesMitochondrial gene orderNuclear genome sizeGenome assembly projectsRearranged mitochondrial genomesK-mer countingGenome skimmingGene orderGenome sizeRead coverageSequencing depthPhylogenetic samplingIllumina sequencingCnidarian speciesGenomeAssembly projectsSiphonophoresZooplankton communityAbundant predatorsSpecies
2023
Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality
Hong Y, Battle S, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake N, Lek M, Rotter J, Rich S, Kooperberg C, Reiner A, Auer P, Heard-Costa N, Liu C, Lai M, Murabito J, Levy D, Grove M, Alonso A, Gibbs R, Dugan-Perez S, Gondek L, Guallar E, Arking D. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nature Communications 2023, 14: 6113. PMID: 37777527, PMCID: PMC10542802, DOI: 10.1038/s41467-023-41785-7.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsOwn circular genomeState of heteroplasmyAging-related diseasesNuclear genomeMitochondrial genomeCircular genomeMtDNA single nucleotide variantsMitochondrial DNASomatic cellsMitochondrial mutationsMtDNA heteroplasmyGenomeNucleotide variantsHeteroplasmyDNA moleculesFunctional roleMitochondriaUK BiobankCertain cancersVariantsDNAMutationsCopiesCellsBabesia duncani multi-omics identifies virulence factors and drug targets
Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu X, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez L, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb O, Le Roch K, Mamoun C. Babesia duncani multi-omics identifies virulence factors and drug targets. Nature Microbiology 2023, 8: 845-859. PMID: 37055610, PMCID: PMC10159843, DOI: 10.1038/s41564-023-01360-8.Peer-Reviewed Original ResearchConceptsDrug targetsVirulence factorsCandidate virulence factorsRNA-seq dataIntraerythrocytic life cycleAttractive drug targetB. duncaniNuclear genomeGenome annotationApicomplexan parasitesApicomplexan pathogensEpigenetic profilesEpigenetic analysisParasite metabolismMalaria-like diseaseHuman erythrocytesLife cycle stagesBabesia speciesGenomeMetabolic requirementsCycle stagesLife cycleBiologySmall moleculesPotent inhibitor
2020
Analysis of Cell and Nucleus Genome by Next-Generation Sequencing
Oh J, Abyzov A. Analysis of Cell and Nucleus Genome by Next-Generation Sequencing. 2020, 35-65. DOI: 10.1007/978-3-030-62532-0_3.Peer-Reviewed Original ResearchSingle-cell genomesBulk of cellsNext-generation sequencing technologiesMosaic variantsNuclear genomeNucleus genomeGenomic mosaicismAnalysis of cellsGenome analysisNext-generation sequencingCell genomeSequencing technologiesGenomeGenomic variantsSingle cellsCellsVariantsMosaicismDiscoverySequencingValuable insightsEnvironmental exposures
2019
Mitochondrial DNA stress signalling protects the nuclear genome
Wu Z, Oeck S, West AP, Mangalhara KC, Sainz AG, Newman LE, Zhang XO, Wu L, Yan Q, Bosenberg M, Liu Y, Sulkowski PL, Tripple V, Kaech SM, Glazer PM, Shadel GS. Mitochondrial DNA stress signalling protects the nuclear genome. Nature Metabolism 2019, 1: 1209-1218. PMID: 32395698, PMCID: PMC7213273, DOI: 10.1038/s42255-019-0150-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorCell NucleusCytosolDNA DamageDNA-Binding ProteinsDNA, MitochondrialGenomeHigh Mobility Group ProteinsInterferon-Stimulated Gene Factor 3InterferonsMembrane ProteinsMiceMice, KnockoutMice, NudeNF-kappa BNucleotidyltransferasesProtein Serine-Threonine KinasesSignal TransductionConceptsMtDNA stressNuclear DNAGene expressionThousands of copiesMost cell typesRepair responseAcute antiviral responseNuclear genomeCircular mtDNAHigher-order structureInterferon gene expressionEssential proteinsMitochondrial DNACultured primary fibroblastsDNA stressUnphosphorylated formInterferon-stimulated gene expressionMouse melanoma cellsNDNA repairSignaling responseOxidative phosphorylationNDNA damageMtDNA damageMtDNAPrimary fibroblastsAbnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma
Xu J, Reznik E, Lee HJ, Gundem G, Jonsson P, Sarungbam J, Bialik A, Sanchez-Vega F, Creighton CJ, Hoekstra J, Zhang L, Sajjakulnukit P, Kremer D, Tolstyka Z, Casuscelli J, Stirdivant S, Tang J, Schultz N, Jeng P, Dong Y, Su W, Cheng EH, Russo P, Coleman JA, Papaemmanuil E, Chen YB, Reuter VE, Sander C, Kennedy SR, Hsieh JJ, Lyssiotis CA, Tickoo SK, Hakimi AA. Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma. ELife 2019, 8: e38986. PMID: 30924768, PMCID: PMC6459676, DOI: 10.7554/elife.38986.Peer-Reviewed Original ResearchConceptsClear cell papillary renal cell carcinomaMtDNA-encoded proteinsPapillary renal cell carcinomaMetabolic phenotypeRenal cell carcinomaNuclear genomeDistinct metabolic phenotypesMitochondrial DNACell carcinomaRespiratory metabolismGenomic sequencingMolecular phenotypesAbnormal oxidative metabolismSugar alcohol sorbitolPresence of glycogenStudy of cancerMajority of cancersOncogenic alterationsPhenotypeOxidative stressOxidative metabolismCytoplasmic clarityDriver lesionsImmunohistochemical stainingKidney tumors
2017
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast*
Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast*. Molecular & Cellular Proteomics 2017, 16: 512-523. PMID: 28122942, PMCID: PMC5383775, DOI: 10.1074/mcp.m116.063818.Peer-Reviewed Original ResearchConceptsN-terminusMitochondrial proteinsCleavage eventsMature mitochondrial proteinN-terminal presequenceNovel protein isoformsN-end ruleAmino acidsMultiple cleavage eventsMitochondrial processingNuclear genomeHuman U937 cellsMature proteinMitochondrial peptidasesYeast proteinsProtein isoformsSequence levelCanonical motifsIndividual proteinsPresequenceDistinct enzymesPolypeptide cleavageCleavage siteYeastProtein
2015
Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40*
Kuszak A, Jacobs D, Gurnev P, Shiota T, Louis J, Lithgow T, Bezrukov S, Rostovtseva T, Buchanan S. Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40*. Journal Of Biological Chemistry 2015, 290: 26204-26217. PMID: 26336107, PMCID: PMC4646270, DOI: 10.1074/jbc.m115.642173.Peer-Reviewed Original ResearchConceptsC-terminal domainPresequence peptideC-terminusMitochondrial outer membraneAmino acidsΒ-barrel domainYeast Candida glabrataOuter membrane complexSubstrate Binding AffinityTranslocase complexNuclear genomeTom40 proteinMitochondrial proteinsProtein transportTom40Substrate recognitionHelical domainOuter membraneMembrane complexCentral subunitN-terminusPlanar lipid membranesTransport functionTerminusChannel conformation
2014
Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex
Sistrom M, Evans B, Bjornson R, Gibson W, Balmer O, Mäser P, Aksoy S, Caccone A. Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex. Genome Biology And Evolution 2014, 6: 2811-2819. PMID: 25287146, PMCID: PMC4224348, DOI: 10.1093/gbe/evu222.Peer-Reviewed Original ResearchConceptsT. brucei complexGenomic variationLife historyVariable life historiesAverage linkage disequilibriumTrypanosoma brucei complexGenome-wide studiesMeiotic reciprocal recombinationWhole genome sequencesMultiple genetic backgroundsHuman pathogenicityNumber of subspeciesHuman-infective parasiteNuclear genomeComparative genomicsChromosome sizeEukaryotic parasitesGenomic regionsHuman African trypanosomiasisRegulatory genesTaxonomic designationsDiverse hostsSingle nucleotide polymorphismsGenetic variationReciprocal recombination
2012
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti†
Cornillot E, Hadj-Kaddour K, Dassouli A, Noel B, Ranwez V, Vacherie B, Augagneur Y, Brès V, Duclos A, Randazzo S, Carcy B, Debierre-Grockiego F, Delbecq S, Moubri-Ménage K, Shams-Eldin H, Usmani-Brown S, Bringaud F, Wincker P, Vivarès CP, Schwarz RT, Schetters TP, Krause PJ, Gorenflot A, Berry V, Barbe V, Mamoun C. Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti†. Nucleic Acids Research 2012, 40: 9102-9114. PMID: 22833609, PMCID: PMC3467087, DOI: 10.1093/nar/gks700.Peer-Reviewed Original ResearchConceptsGenome-wide phylogenetic analysisLateral transfer eventsSmallest nuclear genomesGenome-scale reconstructionB. microtiMinimal metabolic requirementsApicomplexan genomesMitochondrial genomeNuclear genomeProtozoan parasitismMultigene familyApicomplexan parasitesPhylum ApicomplexaPhylogenetic analysisNew cladeGenomeGenomic sequencingCopy numberTransfer eventsApicomplexaMetabolic requirementsBabesia microtiSequencingSpeciesProtozoa
2008
The Trichoplax genome and the nature of placozoans
Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS. The Trichoplax genome and the nature of placozoans. Nature 2008, 454: 955-960. PMID: 18719581, DOI: 10.1038/nature07191.Peer-Reviewed Original ResearchConceptsSimplest free-living animalsPlacozoan Trichoplax adhaerensWhole-genome phylogenetic analysisLife history stagesDiverse cell typesFree-living animalsMetazoan formsNuclear genomeCompact genomeTrichoplax adhaerensGene structureGene contentHistory stagesPhylogenetic analysisCellular complexityTranscription factorsPathway genesGenomeDevelopmental processesPlacozoansCell typesEumetazoansSyntenyBilateriansTrichoplax
1997
Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes
Moriyama E, Powell J. Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes. Journal Of Molecular Evolution 1997, 45: 378-391. PMID: 9321417, DOI: 10.1007/pl00006243.Peer-Reviewed Original ResearchConceptsSynonymous substitution ratesHigher synonymous substitution ratesNuclear genesMitochondrial genesSubstitution ratesDivergence time estimatesBase composition biasNuclear genomeSynonymous ratesHeterogeneity of ratesRelated speciesCodon usageBase compositionComposition biasMutation rateGenesDrosophilaMtDNATime estimatesTurnover rateTransversionsGenomeSpeciesDivergenceSubstitution number
1990
EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP
Goddard K, Caccone A, Powell J. EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP. Evolution 1990, 44: 1656-1670. PMID: 28564311, DOI: 10.1111/j.1558-5646.1990.tb03854.x.Peer-Reviewed Original ResearchDrosophila obscura groupObscura groupOld World speciesWorld speciesDNA divergenceSingle-copy DNA divergencePartial reproductive isolationGroups of DrosophilaDNA-DNA hybridizationNew World speciesObscura subgroupMelanogaster subgroupAffinis subgroupNuclear genomeReproductive isolationChromosomal divergenceEvolutionary implicationsMonophyletic groupClassical systematicsRELATED TAXAMitochondrial DNASpeciesHybrid formationOld WorldGenomeExtreme rates and heterogeneity in insect DNA evolution
Caccone A, Powell J. Extreme rates and heterogeneity in insect DNA evolution. Journal Of Molecular Evolution 1990, 30: 273-280. PMID: 2109089, DOI: 10.1007/bf02099997.Peer-Reviewed Original ResearchConceptsSingle-copy DNA divergenceDNA-DNA hybridization studiesSingle-copy DNAInsect genomesGenome evolutionDNA divergenceNuclear genomeDNA evolutionEvolutionary changeChromosomal similaritiesInterspecific hybridsMost vertebratesMorphological similarityGenomeIntronsHybridization studiesInsectsMammalsBirdsDNAExtreme variationVertebratesTaxaExonsSimilarity
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