short read genome sequencing  (Azenta)

Journal: Bioinformatics

Article Title: Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker

doi: 10.1093/bioinformatics/btag034

Figure Lengend Snippet: Performance evaluation of CNVSeeker and existing methods using different types of sequencing datasets from 1000 Genome Project (1KGP) and the Human Genome Structural Variation Consortium (HGSVC). CNVs were called by CNVSeeker and other methods on high-coverage WGS data (A), low-coverage WGS data (B), WES data (C), PB data (D), ONT data (E). The precision and recall percentage determined for each CNV type is indicated with the scales on the x -axis and y -axis, respectively. Each scatter point represents one sample, respectively. (F) CNV calls per sample generated by CNVSeeker and two integrated pipelines, MOPline and FusorSV. CNVs were called using the high-coverage WGS data of 25 samples from 1KGP. (H and I) Overlap of DELs (H) and DUPs (I) among the three pipelines. The numbers in the overlapping regions indicate the counts of shared CNVs. (G) Run time and maximum memory usage of each pipeline evaluated using high-coverage WGS data. All analyses were performed using 24 CPU cores.

Article Snippet: One key challenge is, different kinds of sequencing technologies such as short-read whole genome sequencing (WGS) and whole exome sequencing (WES), as well as long-read sequencing developed by Pacific Biosciences (PB) or Oxford Nanopore Technologies (ONT), require distinct algorithms for analysis.

Techniques: Sequencing, Generated

Journal: bioRxiv

Article Title: Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana

doi: 10.1101/2025.07.14.664700

Figure Lengend Snippet: Activation of TE families in A. thaliana seedlings . A. Heat treatments and timepoints for assessing ONSEN transcription levels with qRT-PCR. Sampling timepoints are indicated with green (control), black (heat stress), and orange (recovery) arrowheads. Recovery samples were taken after incubation for 48 hours at 22°C post the heat stress. B . ONSEN qRT-PCR expression profiles under 8-days heat regime (n=2). Leaf tissues from ∼100 seedlings were pooled for each replicate. C. ONSEN qRT-PCR expression profiles at regular intervals extending up to 48 hrs in wild-type (WT) and mutants (n=3). D. Relative expression levels of EVADE and AtCOPIA21 (n=3) in unstressed tissue of Arabidopsis lines. Mean ± SD plotted for qRT-PCR analysis in B-D. E, F. Inverse PCR profiles for detection of eccDNA for ONSEN (E) EVADE and AtCOPIA21 (F) . Unstressed (U), 48h heat-stressed (H) and 48h recovery post HS (R) samples were used for ONSEN. Unstressed plant material was used for EVADE and AtCOPIA21. Expected size for two and single LTR products have been indicated. eccDNA molecule (eccUni) universally observed in Arabidopsis tissues has been used as positive control. G. Number of de novo somatic insertions of different TE families identified in met1 and polIVpolV heat-stressed leaf tissues using whole genome re-sequencing. H. Genome-wide distribution of somatic ONSEN and EVADE insertions shown in G. Gene and reference TE densities are shown in 10 kbp windows. Centromere location has been shown by red blocks.

Article Snippet: To explore whether high levels of transcription and eccDNA can lead to transposition in somatic cells, we performed high coverage (>100x fold) Illumina short-read whole-genome sequencing on 48 hour heat-stressed leaf tissues pooled from ∼100 seedlings of met1 and polIVpolV, the two mutant backgrounds where most TE families show evidence of high activity ( , Additional file 1: Fig. S4 ).

Techniques: Activation Assay, Quantitative RT-PCR, Sampling, Control, Incubation, Expressing, Inverse PCR, Positive Control, Sequencing, Genome Wide