PGCP: A comprehensive database of plant genomes for comparative phylogenomics
No abstract available.
Read PDFBrowse Papers
Search the literature by keyword, topic, or author. Filter to articles with full text available.
3689 results
The complete mitochondrial genome of <i>Glyptotendipes tokunagai</i> (Arthropoda; Insecta; Diptera; Chironomidae)
We present the complete mitochondrial genome sequence of <i>Glyptotendipes tokunagai</i> in this study. This circular genome encompasses 15,241 base pairs and exhibits a high AT content of 77%. It contains a total of 13 protein-coding …
Read PDFTaxaScope: a container-native, visualization-centric workstation for genome-based bacterial taxonomy
<h4>Introduction</h4>Genome-based bacterial taxonomy requires standardized and reproducible analytical workflows for species delineation and phylogenomic placement; however, the practical deployment of these workflows remains a significant barrier for experimental biologists and clinical scientists. Widely adopted tools …
Read PDFGenomic surveillance and phylo-evolutionary analysis of SARS-CoV-2 variants in Osun state, Nigeria during the second wave of COVID-19 pandemic
BACKGROUND: SARS-CoV-2 genome sequencing, genomic characterization, and global data sharing are recommended to facilitate countermeasures against COVID-19. This study involved whole genome sequencing and phylo-evolutionay analysis of SARS-CoV-2 variants circulating in Osun State, Nigeria between …
Read PDFPhylogenomic diversity of clinical <i>Saccharomyces cerevisiae</i> and the prevalence of probiotic-derived isolates in a tertiary care center in Hungary
<i>Saccharomyces cerevisiae</i> is traditionally considered a non-pathogenic microbe; however, recent evidence has established its role as an opportunistic fungal pathogen. The probiotic subtype, var. "<i>boulardii</i>," is widely administered for the prevention and treatment of gastrointestinal …
Read PDFExtended taxon sampling reveals conflicting mitochondrial phylogenomics in the holarctic Reticulitermes termites (Blattodea: Termitoidae)
Reticulitermes is a genus of subterranean termites that experienced a rapid radiation during the late Miocene, resulting in a widespread distribution across the Holarctic region. Despite decades of phylogenetic research that has delineated some well-supported …
Read PDFDraft genome sequences of <i>Alicyclobacillus</i> strains isolated from the Chinoike-Jigoku hot spring, Oita, Japan
The genus <i>Alicyclobacillus</i> is a thermoacidophilic bacterial genus found in diverse environments. Here, we report the draft genome sequence of <i>Alicyclobacillus</i> sp. strains CIJ1 and CIJ2 isolated from the Chinoike-Jigoku hot spring in Oita, Japan. …
Read PDFComparative genomics reveals synteny-guided remodeling of carbohydrate-foraging and intrinsic resistance in an ocular Chryseobacterium isolate, NG-CE01
BACKGROUND: Chryseobacterium spp. are environmentally widespread bacteria increasingly recognized as opportunistic pathogens in human and veterinary medicine, yet genome-scale determinants that may support persistence in host-associated microenvironments remain poorly defined. Isolates from anatomically specialized sites …
Read PDFComplete genome sequences of seven <i>Ralstonia solanacearum</i> phylotype IIB-4C/IIB-4E strains isolated from plantain trees in Ecuador
<i>Ralstonia solanacearum</i> has been causing an epidemic of Moko disease in Ecuador since early 2024. Here, we announce the publication of seven complete genome sequences from isolates belonging to the phylotype IIB sequevar IIB-4 and …
Read PDFHighlight: Leveraging Phylogenomics to Uncover the Loci of Repeated Evolution
No abstract available.
Read PDFDraft genome sequence of <i>Cronobacter dublinensis</i> S21, isolated from a child nutrition formula factory in Bangladesh
Here, we present the draft genome of <i>Cronobacter dublinensis</i> S21, isolated from a shoe rack at a child nutrition formula factory in Dhaka, Bangladesh. The genome is 4,564,625 bp with 4,085 predicted coding sequences and …
Read PDFScaling up Bayesian population phylogenomics through virtual dimension reduction
Population phylogenomics uses sampled genomes to jointly infer population genetic processes (ancestral and contemporary population sizes, historical gene flow) and a phylogenetic tree relating species or populations including species split times. This challenging problem has …
Read PDFIntegrated Phylogenomics and Expression Profiling of the Peptide Deformylase Gene Family in <i>Oryza sativa</i> Reveals Their Role in Development and Stress Tolerance
Peptide deformylase (PDF) belongs to a conserved enzyme family critical for N-terminal methionine excision (NME), an essential protein maturation process in prokaryotes and eukaryotic organelles (chloroplasts, mitochondria). To explore the potential functions of <i>OsPDFs</i> in …
Read PDFCharacterization of a conjugative IncFII/IncR plasmid harboring bla<sub>KPC-2</sub> in a clinical ST91 Citrobacter freundii isolate
BACKGROUND: Carbapenem-resistant Citrobacter freundii is increasingly reported and recognized as an opportunistic host of mobile carbapenemase-encoding elements in healthcare-associated settings. However, lineage-associated plasmid vehicles and their transfer-related features in this species remain incompletely characterized. OBJECTIVE: …
Read PDFPickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets
After collecting large datasets for phylogenomics studies, researchers must decide which genes or samples to include when reconstructing a species tree. Incomplete or unreliable datasets make the empiricist's decision more difficult. Researchers rely on ad …
Read PDF