Journal: bioRxiv

Article Title: Pooled CRISPRi screening reveals fungal-specific vulnerabilities across environments and genetic backgrounds

doi: 10.64898/2025.12.19.695556

Figure Lengend Snippet: a) Single nucleotide polymorphisms (SNPs) detected by whole genome sequencing for the three strains when compared to the SC5314 reference genome. b) Overlap between sgRNAs with target binding regions affected by SNPs. The lower left histogram shows the total number of sgRNAs affected for each strain.

Article Snippet: WGS sequencing data was analyzed using a modified version of the Broad Institute Funpipe workflow with GATK v4.6.1.0 (van der ), Picard v3.1.0 ( Picard: A Set of Command Line Tools (in Java) for Manipulating High-Throughput Sequencing (HTS) Data and Formats such as SAM/BAM/CRAM and VCF , n.d.), bwa199 v0.7.18 , samtools v1.20 , bcftools v1.19 , bedtools v2.31.0 ( ).

Techniques: Sequencing, Binding Assay

Journal: bioRxiv

Article Title: Long-read sequencing of trios reveals increased germline and postzygotic mutation rates in repetitive DNA

doi: 10.1101/2025.07.18.665621

Figure Lengend Snippet: A. Distribution of distance between pairs of variants, including SNVs and indels, within 500 bp of each other. B. Mutation spectrum of individual de novo mutations (DNMs) and multinucleotide mutations (MnMs), including paired SNV calls within 500 bp of each other. C. An MnM represented in sequencing reads aligned to the T2T-CHM13 reference genome, and in assembled haplotypes from all members of the trio. D. All nine MnMs validated using assembled haplotypes.

Article Snippet: They have been examined for de novo variation before using Illumina whole exome and whole genome sequencing data , , , but were selected for LRS because no genetic (monogenic or polygenic) cause had been previously identified (Sui et al., companion manuscript).

Techniques: Mutagenesis, Sequencing

Journal: Scientific Data

Article Title: A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae)

doi: 10.1038/s41597-025-05613-5

Figure Lengend Snippet: Genome size estimation of Odontolabis cuvera using GenomeScope.

Article Snippet: The raw sequencing data and genome assembly of Odontolabis cuvera are publicly available through the National Center for Biotechnology Information (NCBI).

Techniques:

Journal: Scientific Data

Article Title: A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae)

doi: 10.1038/s41597-025-05613-5

Figure Lengend Snippet: Genome-wide chromosomal heatmap of Odontolabis cuvera , with individual chromosomes outlined in blue and contigs outlined in green.

Article Snippet: The raw sequencing data and genome assembly of Odontolabis cuvera are publicly available through the National Center for Biotechnology Information (NCBI).

Techniques: Genome Wide

Journal: Scientific Data

Article Title: A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae)

doi: 10.1038/s41597-025-05613-5

Figure Lengend Snippet: Genome characteristics of Odontolabis cuvera . The circular genome plot displays, from the outermost to the innermost ring: (1) chromosome length, (2) GC content, (3) gene density, and (4) the distribution of major transposable elements, including DNA transposons, SINEs, LINEs, LTR retrotransposons, and simple repeats.

Article Snippet: The raw sequencing data and genome assembly of Odontolabis cuvera are publicly available through the National Center for Biotechnology Information (NCBI).

Techniques: