genome assembly

DipGNNome introduces a deep learning framework for diploid genome assembly using graph neural networks and beam-search, achieving results comparable to state-of-the-art methods.

This study evaluates room temperature preservation methods for mosquitoes to generate high-quality reference genomes, finding that squished samples in ethanol or Allprotect work best for Hi-C data.

The paper presents a chromosome-level reference genome for Chrosomus eos and analyzes its syntenic relationship with the zebrafish genome.

The paper isolates and characterizes two Myxococcus faecalis strains from mangroves in Brazil, showing genomic similarity to strains from soil and human feces.

This study uses RAD-seq to analyze genomic diversity and population structure in bay pipefish, finding high diversity and panmixia across two locations in Coos Bay.

This study evaluates three weight optimisation approaches for genomic prediction ensembles in maize, finding that weighted models improve prediction performance when weights differ from equal weights, but no single method clearly outperforms others.

The paper presents a chromosome-level, haplotype-resolved genome assembly for the barn owl, resolving microchromosomes and enabling structural variation studies.

This paper improves simulation accuracy for digital breeding by integrating GWAS-derived genetic architecture into trait simulations, achieving high concordance with empirical data.

Third nuclear genome for arthropod pinworms (Thelastomatoidea): a PacBio long-read Cranifera cranifera assembly (242 Mb, N50 43 kb, 90.5-94% BUSCO) plus a 24644-base mitogenome and male redescription.

The paper examines genetic diversity and structure within the Olotillo maize race in Mexico, finding that genetic clusters align with geographic origin rather than race identity, and highlights inbreeding and directional selection across scales.

Pipeasm automates large chromosome-scale genome assembly using HiFi, ONT, and HiC data, enabling diploid genome assembly with a Snakemake pipeline.

This study analyzes genome-wide data from Early Bronze Age individuals in Lower Austria to explore social structure and genetic relationships, revealing patrilocal society and long-distance genetic connections.

This study analyzes genomic data from 200 medieval individuals to reveal the genetic structure and origins of the Rus population, identifying Slavic-related and Fenno-Ugrian components with shared ancestry from ancient Baltic populations.

This paper uses trio-binning to assemble the Cannabis genome, revealing structural variation and defining paralog cohorts with high resolution.

The paper presents a chromosome-level genome assembly for Ostrinia scapulalis, improving upon previous fragmented assemblies and enabling better comparative genomic studies.

This study shows artificial light at night causes molecular stress and genetic changes in bats, affecting their behavior and population connectivity.

The paper presents complete telomere-to-telomere cowpea genomes, revealing centromere evolution and subspecies divergence in Phaseoleae.

This study shows that CPR-4, a homologue of human cathepsin B, induces DNA damage and mutagenesis in C. elegans under crowding stress, leading to increased mutation rates and competitive growth advantages.

RefLA improves genome assembly speed and quality by using a reference genome to guide long-read assembly, outperforming both de novo and fast assemblers.

This study produces high-quality genome assemblies for two Neotropical bumblebee species using long-read sequencing.

This paper maps genetic linkage in cowpea using SNP and morphological markers, identifying Mendelian and non-Mendelian inheritance patterns and creating a genetic map for breeding improvement.

This study presents a high-quality genome assembly of Anolis distichus, revealing insights into neo-sex chromosome evolution and differential evolutionary pressures.

The paper presents a chromosome-level genome assembly for the rare lava gull using Oxford Nanopore sequencing, providing a resource for phylogeography and population genetics studies.

This paper introduces PERFECT PCR, a method that improves DNA data storage density and accuracy, achieving 94% of theoretical maximum storage density with significantly lower error rates.

The paper analyzes ancient genomes from Roca Vecchia to determine genetic contributions from Minoans and local populations during the Bronze Age.

This paper presents a near-complete lamprey genome assembly, revealing gene family expansions and regulatory elements linked to vertebrate innovations.

The paper analyzes over 2,000 Caenorhabditis briggsae wild strains to uncover genetic diversity, population structure, and evolutionary mechanisms shaping phenotypic variation.

The paper presents the first telomere-to-telomere, chromosome-level reference genome for the common five-lined skink, providing a highly complete and annotated genome sequence.

This study develops a method using developmental regulators to improve soybean transformation and CRISPR-mediated genome editing efficiency.

CiFi improves Hi-C analysis by combining 3C with PacBio HiFi sequencing, enabling better coverage in repetitive regions and low-input samples.