Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of genome assemblies of Neospora caninum and Toxoplasma gondii using third-generation sequencing data reveals misassembly and karyotype differences. ( A ) Comparative analysis of the T. gondii type II ( Tg ME49) genome assembly and the N. caninum Liverpool ( Nc Liv) strain genome assembly, obtained based on Sanger technology sequencing data. ( B ) Comparative alignment of the Nc Liv genome assemblies using Sanger and third-generation (long-read) technology. ( C ) Comparative alignment of the T. gondii type II ( Tg ME49) genome assemblies based on Sanger technology sequencing data or third-generation (long-read) technology of T. gondii type I ( Tg RH). ( D ) Comparative alignment of the T. gondii type I ( Tg RH) and the Nc Liv genome assemblies based on third-generation (long-read) sequencing technology. ( E ) Chromosomal layout of N. caninum . Karyotype, chromosome length, telomeres, putative centromeres, and large repeats are shown.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Regions of synteny breaks between N. caninum and T. gondii are populated by three conserved domains. ( A ) Sequence identity of domains identified at regions where chromosomal rearrangements have occurred. ( B ) Graphical representation of Chromosome VIII of Nc Liv. Comparative alignment to the T. gondii chromosomes. Percentages of sequence identity are shown. Regions examined for the presence of motifs are indicated (light green). The position of the putative centromere is indicated in orange. Note that large repetitive regions were not identified in this chromosome. 5′ (light purple) and 3′ (dark purple) telomeres are indicated. The identity and number of domains found per region, in Chromosome VII, are indicated.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of mitochondrial genome structures and annotations of Neospora and Toxoplasma reveals gene fragmentation and reshuffling between species and strains. ( A ) The repetitive nature of the gene structure in a 32-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( B ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( C ) Comparative alignment between two Nc Liv mitochondrial contigs of 16 and 32 kb, respectively. ( D ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a Nc Uru1 mitochondrial contig of 38 kb. ( E ) Comparative alignment between two Nc Uru1 mitochondrial contigs of 16 and 38 kb, respectively. ( F ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Uru1 is graphically represented in a YASS plot. ( G ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a T. gondii mitochondrial contigs of 39 kb.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques:

Journal: BMC Cancer

Article Title: The landscape of coding RNA editing events in pediatric cancer

doi: 10.1186/s12885-021-08956-5

Figure Lengend Snippet: The StrongArm RNA-Seq mapping and RNA editing detection pipelines. A Schematic workflow of StrongArm RNA-seq mapping pipeline. The pipeline starts with competitive mapping of 5 different combinations of mapper and database, followed by further local refinement. B RNA editing identification pipeline. RNA-Seq BAM files are aligned with StrongArm as shown in (A), and germline and somatic DNA variants are also called from the same patient using WGS or WES of matched tumor and germline DNA. The pipeline searches for RNA-specific (RNA editing) variants in coding (CDS) regions by comparing RNA-Seq reads to DNA-Seq. A series of false editing filters is then employed to remove RNA editing artifacts, followed by manual review of the BAM alignment. The RNA editing candidates are then used to evaluate the editing levels cross the whole cohort

Article Snippet: Fig. 1 The StrongArm RNA-Seq mapping and RNA editing detection pipelines.

Techniques: RNA Sequencing, DNA Sequencing