Journal: Frontiers in Plant Science

Article Title: Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

doi: 10.3389/fpls.2023.1184112

Figure Lengend Snippet: Experimental assembly comparison.

Article Snippet: Step 4 scaffolded the assemblies to the corresponding Bionano contig-assembly hybrid scaffolds using Ragtag ‘scaffold’.

Techniques: Comparison, Software

Journal: Frontiers in Plant Science

Article Title: Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

doi: 10.3389/fpls.2023.1184112

Figure Lengend Snippet: Haplotype switching. Haplotype switching was illustrated by aligning TrioCanu binned HiFi reads of parent A (HDA149) and parent B (HDA330) to each contig level genome assembly. The x-axis shows 1 Mb windows across contigs. The contigs were arranged from longest to shortest. Vertical gray lines show the boundaries of contigs. The y-axis shows the difference in percent coverage of the binned reads over a 1 Mb window of the given assembly. Higher coverage of HDA149 is shown in pink and higher coverage of HDA330 is shown in blue. (A) Hifiasm HDA149 assembly with trio-binning. (B) Hifiasm HDA330 assembly with trio-binning. (C) TrioCanu HDA149 assembly with trio-binning. (D) TrioCanu HDA330 assembly with trio-binning. (E) Hifiasm haplotype 1 assembly in default run mode, without parental k-mers for trio-binning. (F) Hifiasm haplotype 2 assembly in default run mode, without parental k-mers for trio-binning.

Article Snippet: Step 4 scaffolded the assemblies to the corresponding Bionano contig-assembly hybrid scaffolds using Ragtag ‘scaffold’.

Techniques:

Journal: BMC Genomics

Article Title: RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

doi: 10.1186/1471-2164-13-3

Figure Lengend Snippet: Contig length distribution and the efficiency of SNP discovery . Red bars represent the portion of contigs having no SNP identified, while green bars represent contigs harbouring at least one SNP.

Article Snippet: A RAD LongRead ® contig assembly was generated by a set of algorithms developed at Floragenex Inc. Sequences having more than 5 bases with poor Illumina quality scores (Phred10 or lower) were discarded.

Techniques:

Journal: BMC Genomics

Article Title: RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

doi: 10.1186/1471-2164-13-3

Figure Lengend Snippet: Comparison of K-mer spectra in the C. cardunculus RAD contig assembly vs the full genomes of A. thaliana , V. vinifera and F. vesca . K-mer (k = 10) distribution for C. cardunculus (A) was evaluated both on pre-assembly sequence data (outer box) and contig sequences (inner box). K-mer populations have been split on the basis of their CpG content. × axis represents the number of occurrences of a given 10-mer; Y axis reports the amount of different 10-mers reporting that occurrence count.

Article Snippet: A RAD LongRead ® contig assembly was generated by a set of algorithms developed at Floragenex Inc. Sequences having more than 5 bases with poor Illumina quality scores (Phred10 or lower) were discarded.

Techniques: Comparison, Sequencing

Journal: G3: Genes|Genomes|Genetics

Article Title: Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight

doi: 10.1534/g3.120.401367

Figure Lengend Snippet: Descriptive characteristics for three draft taro genome assemblies. The pseudochromosome-level taro assembly (“Ps_chr”) was composed from a linked-read assembly (“LR”) that was gap-filled using contigs assembled from nanopore MinION long-reads (merge step, “Merged”), filtered for assembly artifacts, and then concatenated into pseudochromosomes using a linkage map. Kilobase = kb

Article Snippet: We sequenced and assembled a taro genome using a linked-read sequencing strategy, with genome contiguity improved through gap filling and scaffolding using contigs assembled from Oxford Nanopore MinIon long-reads and linkage map results from a mapping population for TLB-resistance.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight

doi: 10.1534/g3.120.401367

Figure Lengend Snippet: Repetitive content of taro ( Colocasia esculenta ) and great duckweed ( Spirodela polyrhiza ) genome assembles. Total repeat content was quantified using de novo repeat libraries constructed with RepeatModeler and screened with RepeatMasker. The percent (%) of sequence is relative to each individual assembly’s total length excluding runs of NNN”s between scaffolded contigs. Short and long interspersed elements are denoted as SINEs and LINEs

Article Snippet: We sequenced and assembled a taro genome using a linked-read sequencing strategy, with genome contiguity improved through gap filling and scaffolding using contigs assembled from Oxford Nanopore MinIon long-reads and linkage map results from a mapping population for TLB-resistance.

Techniques: Construct, Sequencing

Journal: Scientific Data

Article Title: A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches

doi: 10.1038/s41597-022-01278-6

Figure Lengend Snippet: Microreact screenshot representing the distribution of the whole LISTADAPT dataset (n = 1484) by geographic region ( a ) and time ( b ). The k-mer-based phylogenomic clustering of the complete dataset is shown in ( c ). Interactive access to strain metadata and MLST types is available through Microreact , a recently developed online tool for visualizing and sharing spacio-temporal and genetic distributions of strains (Fig. 2, accession link: https://microreact.org/project/8YtGBqEqhosJtysXTVY79M-figure-2-distribution-of-the-whole-listadapt-dataset-n1484-by-geographic-region-time-and-genetic-diversity ). The dataset interactive map was generated using either the exact GPS coordinate, regional GPS coordinate or national GPS coordinate according to the level of details available for each strain. An annual timescale was used. The core genome MLST (Moura et al .) tree was generated from the draft genome assemblies using pairwise categorical difference and single linkage method in BioNumerics. The tree revealed three main clades corresponding to Lm phylogenetic lineages. Each clade included several clusters corresponding to MLST types (CC and singleton ST). Circles in shade of blue show food product isolates (clear blue: fish product, greeblue: dairy products, blue: composite dishes, deep blue: meat products). Circles in shade of orange show animal and environment isolates (beige: soil & farm environment, golden: wild animal, deep orange: farm animals). Circles size is proportional to the number of strains included.

Article Snippet: Reads normalized to 100 × coverage, draft assemblies (contigs and scaffolds) and annotated genomes (Genome Feature Format, GFF, and Genbank format, GBK) were also centralized at the MongoDB database located at ANSES (Maisons-Alfort Laboratory for Food Safety) providing quickly available, ready-to-use data.

Techniques: Generated