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Generation and characterization of a knockout mouse of an enhancer of EBF3
Genomic studies of neurodevelopmental disorders (NDDs) have identified several relevant genomic variants. EBF3 is a gene with an excess of protein-coding de novo variants and underlies Hypotonia, Ataxia, and Delayed Development Syndrome. We previously identified …
Read PDFProteomic profiling revealed unique disease biology associated with 1q abnormalities in multiple myeloma
Gain or amplification of chromosome 1q (+1q) is a common genomic alteration occurring in the plasma cells in nearly 40% of multiple myeloma patients. Although it is associated with inferior outcomes and is more common …
Read PDFSurvival and genomic stability of <i>Yersinia enterocolitica</i> in environmental <i>Acanthamoeba</i> spp
<h4>Introduction</h4>Free-living amoebae (FLA) are widespread protozoa that can host bacterial pathogens, promoting their persistence in the environment. <i>Yersinia enterocolitica</i>, a foodborne zoonotic pathogen, has been detected within amoebae, but its intracellular dynamics remain unclear.<h4>Methods</h4>In this …
Read PDF<i>Plasmodium</i> LCCL domain-containing modular proteins have their origins in the ancestral alveolate
<i>Plasmodium</i> species encode a unique set of six modular proteins named LCCL lectin domain adhesive-like proteins (LAPs) that operate as a complex and that are essential for malaria parasite transmission from mosquito to vertebrate. LAPs …
Read PDFTeaching computational genomics and bioinformatics on a high performance computing cluster-a primer
The burgeoning field of genomics as applied to personalized medicine, epidemiology, conservation, agriculture, forensics, drug development, and other fields comes with large computational and bioinformatics costs, which are often inaccessible to student trainees in classroom …
Read PDFRobust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships
Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach concatenates hundreds or thousands of genomic segments, providing a straightforward, computationally efficient, and effective means of …
Read PDF<i>Rhizobium acaciae</i> sp. nov., a new nitrogen-fixing symbiovar isolated from root nodules of <i>Acacia saligna</i> in Tunisia
Three bacterial strains, 1AS11<sup>T</sup>, 1AS12 and 1AS13, members of the new symbiovar salignae and isolated from root nodules of <i>Acacia saligna</i> grown in Tunisia, were characterized using a polyphasic approach. All three strains were assigned …
Read PDFPhylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among …
Read PDFGenome-Wide Identification and Expression Analysis of the <i>DMP</i> and <i>MTL</i> Genes in Sweetpotato (<i>Ipomoea batatas</i> L.)
Sweetpotato (<i>Ipomoea batatas</i> L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature …
Read PDFThe emergence and spread of a novel sequence type of Corynebacterium diphtheriae in Vietnam
Diphtheria remains a public health concern in Vietnam. This study used whole-genome sequencing to characterize the genetic diversity, virulence, and antimicrobial resistance profiles of 21 Corynebacterium diphtheriae isolates collected from 2013 to 2024. Phylogenetic relationships …
Read PDFDNA barcodes are ineffective for species identification of <i>Acropora</i> corals from the aquarium trade
Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations …
Read PDFComparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini
Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host-specific fungus Colletotrichum lupini greatly impacts lupin …
Read PDFComparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium
'Boju' and 'Huaiju' are cultivars of the Chrysanthemum (Chrysanthemum morifolium Ramat.) in the family Asteraceae, valued for their medicinal, tea, and ornamental properties, and valued by individuals. However, the yield and quality of medicinal chrysanthemums …
Read PDFClavibacter michiganensis Reframed: The Story of How the Genomics Era Made a New Face for an Old Enemy
<h4>Objective</h4>Bacterial wilt and canker of tomato caused by the gram-positive corynebacterial species Clavibacter michiganensis is an economically important disease threatening the tomato industry in both open-air and greenhouse productions around the world. The disease occurs …
Read PDFHistorical biogeography and evolutionary diversification of <i>Lilium</i> (Liliaceae): New insights from plastome phylogenomics
Here, we infer the historical biogeography and evolutionary diversification of the genus <i>Lilium</i>. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus <i>Lilium</i> (14 plastomes were newly sequenced) …
Read PDFPangenomic insights into <i>Dehalobacter</i> evolution and acquisition of functional genes for bioremediation
<i>Dehalobacter</i> is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a <i>Dehalobacter</i> population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using …
Read PDFPlastid Phylogenomics Provide Evidence to Accept Two New Members of <i>Ligusticopsis</i> (Apiaceae, Angiosperms)
<i>Peucedanum nanum</i> and <i>P. violaceum</i> are recognized as members of the genus <i>Peucedanum</i> because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar …
Read PDFOrnithinibacillus liuyingii sp. nov.: a novel multidrug-resistant and potentially pathogenic bacterium isolated from Apodemus chevrieri lung tissue
Ornithinibacillus liuyingii sp. nov. was proposed, with type strain 27F3T (= GDMCC 1.5626T = JCM 38003T) isolated from the lung of Apodemus chevrieri collected on the Guizhou Plateau, China. Phylogenetic distinctiveness from its closest relative, …
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