Journal: GigaScience

Article Title: Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

doi: 10.1093/gigascience/giab017

Figure Lengend Snippet: The QUAST-LG report for the NG50, number of misassemblies, and number of contigs for the A. arabiensis original Canu assemblies and those processed by 3D-DNA and SALSA2

Article Snippet: To maximize the use of the data, tools, and workflows of this study, we present a pipeline for obtaining superior-quality genome assemblies for malaria mosquitoes based on Hi-C scaffolding of Oxford Nanopore sequencing contigs (Fig. ).

Techniques:

Journal: GigaScience

Article Title: Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

doi: 10.1093/gigascience/giab017

Figure Lengend Snippet: The pipeline for obtaining superior-quality genome assemblies for malaria mosquitoes based on Hi-C scaffolding of Oxford Nanopore sequencing contigs.

Article Snippet: To maximize the use of the data, tools, and workflows of this study, we present a pipeline for obtaining superior-quality genome assemblies for malaria mosquitoes based on Hi-C scaffolding of Oxford Nanopore sequencing contigs (Fig. ).

Techniques: Hi-C, Scaffolding, Nanopore Sequencing

Journal: BMC Genomics

Article Title: Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

doi: 10.1186/1471-2164-8-45

Figure Lengend Snippet: Schematic representation of HB3 var genes . Genes are organized as in figure 1 and grouped according to 5' flanking sequence (Ups type) and chromosomal location. Partial (p) and pseudogenes (Ψ) are labeled. Bolded domain structure types are unique to the HB3 parasite line. Binding properties have not been mapped to HB3 PfEMP1 proteins.

Article Snippet: Analysis of the HB3 sequence contigs obtained from the 10× coverage genome sequence at the Broad Institute[ ] identified 52 var genes that contain a DBLα domain as well as two var2csa homologs; 39 of the 54 var genes are full-length, 9 are incomplete and six are pseudogenes containing stops or frame-shifts (Figure ).

Techniques: Sequencing, Labeling, Binding Assay

Journal: BMC Genomics

Article Title: Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

doi: 10.1186/1471-2164-8-45

Figure Lengend Snippet: Var gene chromosomal locations and domain architectures across isolates.

Article Snippet: Analysis of the HB3 sequence contigs obtained from the 10× coverage genome sequence at the Broad Institute[ ] identified 52 var genes that contain a DBLα domain as well as two var2csa homologs; 39 of the 54 var genes are full-length, 9 are incomplete and six are pseudogenes containing stops or frame-shifts (Figure ).

Techniques:

Journal: BMC Genomics

Article Title: Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

doi: 10.1186/1471-2164-8-45

Figure Lengend Snippet: Phylogenetic comparison of var gene flanking regions from IT4, HB3, and 3D7 parasite isolates . A neighbor-joining tree was generated based upon 500 bp of 5' gene flanking sequence. Upstream groupings (Ups groups) with bootstrap support out of 1000 replicates are color shaded and labeled. Gene names have been removed from the figure for simplification.

Article Snippet: Analysis of the HB3 sequence contigs obtained from the 10× coverage genome sequence at the Broad Institute[ ] identified 52 var genes that contain a DBLα domain as well as two var2csa homologs; 39 of the 54 var genes are full-length, 9 are incomplete and six are pseudogenes containing stops or frame-shifts (Figure ).

Techniques: Comparison, Generated, Sequencing, Labeling

Journal: BMC Genomics

Article Title: Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

doi: 10.1186/1471-2164-8-45

Figure Lengend Snippet: Chromosomal distribution of var genes in the 3D7 and HB3 parasite isolates . Var genes are color shaded according to 5' gene flanking Ups type (U indicates unknown) and labeled according to protein architecture. The chromosomal locations were predicted for 36 of the 54 HB3 PfEMP1 proteins based upon gene flanking sequence and comparison to the 3D7 reference genome (see methods). Arrows without an outline indicate pseudogenes.

Article Snippet: Analysis of the HB3 sequence contigs obtained from the 10× coverage genome sequence at the Broad Institute[ ] identified 52 var genes that contain a DBLα domain as well as two var2csa homologs; 39 of the 54 var genes are full-length, 9 are incomplete and six are pseudogenes containing stops or frame-shifts (Figure ).

Techniques: Labeling, Sequencing, Comparison