genome assembly

This study develops genetic tools for Piscinibacter sakaiensis to enable functional genomics and engineering for PET degradation.

The paper analyzes the global genomic diversity of C. neoformans over three decades, identifying key genetic features, lineage divergence, and resistance mechanisms.

pGGTOX enables efficient, marker-free genome editing across Enterobacteriaceae using homologous recombination, with applications in gene deletion, plasmid modification, and CRISPR delivery.

The paper analyzes plasmid transmission dynamics in Rhizobium leguminosarum, finding variation in plasmid types and their association with partner quality decline due to nitrogen fertilization.

The paper presents a chromosome-level genome assembly of Trebouxia sp. 'A48' and identifies features related to its lichen symbiosis and evolutionary adaptations.

This study presents chromosome-level genome assemblies for Nicotiana attenuata and Nicotiana obtusifolia using long-read sequencing and Hi-C data, achieving high BUSCO completeness.

The paper identifies a human supergene region containing BRCA1, CCDC200, and U2 snRNAs, showing linkage disequilibrium and balancing selection across populations.

The paper develops a hybrid sequencing strategy combining short-read and long-read methods to enhance genotype-phenotype analysis at single-cell resolution.

This paper develops a site-directed transposase system for precise genomic insertion of gene-sized DNA without double-strand breaks, achieving on-target insertion with minimal off-target effects.

This paper evaluates metadata completeness in SARS-CoV-2 genomic records and shows how enriched metadata improves genomic epidemiology analyses.

This study generates genomic and epigenomic maps of mouse centromeres and pericentromeres using long-read sequencing and epigenetic analyses, revealing satellite DNA composition and chromatin state differences.

This paper develops an efficient PEG-mediated protoplast transformation system for Ophiocordyceps xuefengensis, enabling stable genetic manipulation and functional gene expression.

The paper presents a chromosome-level genome assembly for wild alpine reindeer and improves the assembly for Svalbard reindeer, providing gene annotations and comparisons with prior assemblies.

This paper introduces plaque-2-sequence, a low-cost, high-throughput method for sequencing phage genomes directly from plaques, enabling rapid and scalable genomic analysis of phages.

LRGE estimates genome size from long read overlaps, outperforming k-mer-based methods and being more efficient than assembly-based approaches.

Tile-X improves long read assembly by precomputing read ordering, enhancing scalability and efficiency without sacrificing quality.

The paper presents the first telomere-to-telomere assemblies for two Paracoccidioides species, revealing chromosomal rearrangements and mitochondrial introgression.

The paper presents the first genome assembly of Potamopyrgus antipodarum, revealing a recent whole-genome duplication and its potential role in asexuality transitions.

The paper characterizes six chimeric plasmids from Salmonella Heidelberg, revealing multidrug resistance and increased pathogenicity through genetic and functional analysis.

This study presents a de novo genome assembly for Rauvolfia serpentina and analyzes paleodemographic histories of Apocynaceae species, revealing a population bottleneck during the Mid-Pleistocene.

This paper presents high-quality genome assemblies for Indrella ampulla, a land snail, and reports demographic history and genomic insights into its evolution and color polymorphism.

The paper presents a draft genome of the vampire squid, revealing ancestral chromosomal features and evolutionary changes in octopod karyotypes.

This study characterizes the phenotypic and genomic diversity of Candida dubliniensis isolates from HIV-positive individuals, revealing significant variability in drug resistance and other clinically relevant traits.

The paper presents a near telomere-to-telomere genome assembly of the Chilean jack mackerel using PacBio and Hi-C data, achieving high completeness and enabling comparative genomics analyses.

The paper presents a de novo whole genome assembly of the green shore crab using long-read sequencing and provides a DNA extraction protocol for brachyuran crabs.

The paper reports the draft genome of a predatory bacterium isolated from northern peatland soil and describes its genomic features.

This paper introduces SpAD, a high-throughput label-free imaging platform for live-cell drug and genetic screens, enabling rapid, unbiased profiling of cellular responses.

This study analyzes rice centromeres to understand their genetic diversity and evolution, finding that structural variations and retrotransposon insertions drive centromere innovation.

This paper uses composite interval mapping and genomic prediction to identify QTL and improve prediction accuracy for nut quality traits in American and interspecific hybrid hazelnuts.

This study provides a comprehensive pan-genomic analysis of mungbean, revealing its demographic history, genomic variation, and genotype-phenotype-environment relationships across diverse environments.