genome assembly

The paper assembles high-quality genomes for twelve sheep breeds using long-read sequencing and phased haplotyping, enabling pangenome construction and structural variant analysis.

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

The paper presents an improved T. vivax genome assembly, revealing distinct VSG gene organization and expression mechanisms compared to T. brucei.

The paper presents a chromosome-level genome assembly for the chilli thrips Scirtothrips dorsalis, providing genomic resources for studying its biology and pest status.

The paper examines how demographic history affects genetic diversity and performance traits in insular and mainland lizard populations, finding elevated genetic load correlates with reduced bite force.

This study examines genomic divergence and diversity in three Hydrophis sea snake species, finding shared demographic patterns and linked selection, with chemosensory genes showing elevated diversity.

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

This study shows diploids in Candida glabrata adapt differently to fluconazole than haploids, acquiring distinct mutations and aneuploidies, leading to higher fitness and MICs in some cases.

YGEP provides a cloud platform for genomic evaluation and breeding in yaks, integrating pedigree reconstruction, genotype imputation, and genomic breeding value estimation with high accuracy.

The paper presents a haplotype-phased, chromosome-level genome assembly of the soybean rust pathogen Phakopsora pachyrhizi, improving upon previous fragmented assemblies.

This study assembles and annotates the genome of an invasive North American T. vulgare genotype using long-read sequencing, providing a reference for studying invasion biology and weed management.

The paper presents a chromosome-level genome assembly for the Eurasian great grey owl, improving resolution of sex chromosomes and microchromosomes compared to previous assemblies.

Two Portuguese rice-blast fungus isolates were assembled from PacBio HiFi reads into near-complete genomes; one isolate lacks Avr-Pii, Avr-Pia and Avr-Pik yet remains virulent on two rice cultivars.

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

This study uses genomic data to assess genetic diversity and adaptive potential in the Hermit Beetle, revealing severe genetic subdivision and recommending conservation strategies to protect its genomic integrity.

The paper generates genome assemblies for two Aegilops mutica accessions from different climates, identifying extensive structural variation and providing resources for wheat breeding and conservation.

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

The paper presents a chromosome-level genome assembly of the Olympia oyster, enabling insights into its biology and aiding conservation and restoration efforts.

The paper introduces sum-h2, a fast framework for evaluating genetic discovery from deep learning-derived phenotypes using heritability measures, and establishes a Genetic Discovery Arena for benchmarking.

PfPHAST is a streamlined amplicon sequencing panel for malaria genomic surveillance, offering better quality control and cost efficiency than MAD4HatTeR without sacrificing performance on shared targets.

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

This study characterizes microbial composition and functional potential during spontaneous ugba fermentation using genome-resolved metagenomics across three stages.

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.

This paper presents the first high-quality reference genome for Scalesia gordilloi, a critically endangered plant, using Oxford Nanopore sequencing to enable conservation and comparative genomics studies.

The paper presents gap-free telomere-to-telomere haplotype assemblies for a hybrid grouper, enabling genetic analysis and breeding applications.

The paper presents the first T2T genome assembly of Eucalyptus recurva, revealing genomic features and conservation insights.

PhAGE enables one-step integration of ~20 kb DNA fragments into E. coli genome, resolving the trade-off between simplicity and insert size in genome engineering.

This study identifies molecular convergence in Baltic Sea pipefish populations despite differing genomic structures and species relationships.