Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Primer sequences for kompetitive allele-specific PCR (KASP) markers designed from SNP sequences that showed association with Lr49 on chromosome 4BL and SNPs discovered from the sqeuences of flow sorted chromosome 4B of parental genotypes.

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Marker

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Genetic linkage map of chromosome 4BL for the VL404/WL711 RIL population (A) Bansal et al. (2008) , (B) present study (resistance gene is shown in red text), and (C) high resolution map of VL404/Avocet S (number of recombinants is given on the left).

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques:

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Comparison of Lr49 genetic linkage map with the 585 to 617 Mbp interval of Chinese Spring chromosome 4B physical map using Pretzel, a genetic map viewing software ( http://plantinformatics.io ). Markers distal to sunKASP _26 are colinear with the physical map (green connections). The genetic map order of markers proximal to sunKASP _21 does not reflect the physical map order in Chinese Spring (black connections).

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Comparison, Software

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Diagrammatic representation of the Lr49 interval and flanking region on chromosome 4B. Both VL404 (resistant parent) and WL711 (susceptible parent) have two sequence haplotypes outside the Lr49 region, while VL404 has only one sequence haplotype within the Lr49 interval. Chinese Spring has only one sequence haplotype across entire region. Each unique sequence haplotype is represented by a different color. Markers mapping within the Lr49 interval are ordered based on their physical mapping location. The Lr49 genetic map does not reflect the physical mapping order as illustrated by comparison of genetic and physical map order across the Lr49 interval. Differences in sequence haplotype structure and physical-genetic map order in VL404 and WL711, relative to Chinese Spring, suggests structural rearrangement or copy number variation (CNV) relative to Chinese Spring.

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Sequencing, Comparison

Journal: Current biology : CB

Article Title: Expanded satellite repeats amplify a discrete CENP-A nucleosome assembly site on chromosomes that drive in female meiosis

doi: 10.1016/j.cub.2017.06.069

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Custom scripts for tandem repeat analysis of paired-end sequencing reads , This paper , https://sourceforge.net/p/blacklab-mouse-seq/code.

Techniques: Immunostaining, Virus, Recombinant, Reverse Transcription, DNA Labeling, Nick Translation, DNA Ligation, Purification, SYBR Green Assay, Sequencing, Cloning, Plasmid Preparation, Software

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: (a) Leaf-like thallus visualization of bacteria on a cross-section by 3D reconstruction of FISH image stacks. Eubacteria (red) and Alphaproteobacteria (yellow) were found widespread on both, the upper and the lower cortex, while Betaproteobacteria (pink) were less abundant and locally contained. Fungal hyphae (blue) and algae located under the upper cortex (green) were visualized without specific FISH probes, due to the naturally occurring fluorescence of the internal structures. (b) Model of the lichen symbiosis depicting the functional network of the participants. The model includes relevant functions of the colonizing bacteria, which are derived from metagenomic/metaproteomic analysis, as well as cultivation-dependent experiments.

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Bacteria, Algae, Fluorescence, Functional Assay, Derivative Assay

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Principal Coordinates Analysis (PCoA) including 20 publicly available metagenomic datasets from MG-RAST and the Lobaria metagenome (red dot). All datasets were compared with subsytems and calculated using normalized values and the Bray-Curtis distance matrix. Single metagenomes from different biomes are labeled with their MG-RAST accession numbers and grouped in colored ellipses. The full colour version of this figure is available at ISME Journal online.

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Labeling

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Functional recovery of the bacterial lichen microbiome metagenome on the metaproteomic level using Voronoi treemaps. The protein sequences were compared with metagenomic contigs by BLAST and then functionally characterized using HMMER3 and TIGRFAMs. Upper panel shows all functions covered by the metagenome (third level) and the respective subroles (second level) and main roles (first level). The mainrole labels are shown. On the lower panel, metaproteomic coverage is shown (blue cells: functions present only in the metagenome; grey cells: functions present in both metagenome and metaproteome).

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Functional Assay