Vcflib and tools for processing the VCF variant call format

Garrison, Erik; Kronenberg, Zev; Dawson, Eric T.; Pedersen, Brent S.; Prins, Pjotr

doi:10.1101/2021.05.21.445151

Cited by 104 publications

(111 citation statements)

References 34 publications

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“…The trimmed reads were then re-used to call SNPs to assess heterozygosity using freebayes under default settings (Garrison and Marth, 2012). We then used vcflib packages vcffilter to filter the results for a minimum quality of 20 (-f "QUAL >20") and vcfstats to count the number of SNPs (Garrison et al, 2021). Transcriptome sequencing.…”

Section: Discussionmentioning

confidence: 99%

The whale shark genome reveals patterns of vertebrate gene family evolution

Tan

Redmond

Dooley

et al. 2021

eLife

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Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.

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Section: Discussionmentioning

confidence: 99%

The whale shark genome reveals patterns of vertebrate gene family evolution

Tan

Redmond

Dooley

et al. 2021

eLife

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“…Graphtyper (v 2.6.2; accessed on 20 August 2021) was run on the dataset with the default parameters [31]. SNPs were filtered using vcffilter in vcflib (v 1.0.0; accessed on 20 August 2021 [32]) with the options '-f "ABHet < 0.0 | ABHet > 0.33" -f "ABHom < 0.0 | ABHom > 0.97" -f "MaxAASR > 0.4" -f "MQ > 30". SNP calls annotated as "FAIL" or "heterozygous" were filtered to "no-call".…”

Section: Whole Genome Snp and Pangenome Analysesmentioning

confidence: 99%

Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Bland

Johnson

Waite‐Cusic

et al. 2021

Foods

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Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0–2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings.

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“…Resulting reads were mapped against the GenBank AX955019.1 S-2L reference sequence using Minimap2 v2.17 39 . Variant calling was carried out by Freebayes v1.3.2 40 and later filtered by VCFLIB 41 . A consensus sequence was generated using VCF Consensus Builder v0.1.0 42 .…”

Section: Methodsmentioning

confidence: 99%

Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA

et al. 2021

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Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes – datZ, mazZ and purZ – was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.

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Vcflib and tools for processing the VCF variant call format

Cited by 104 publications

References 34 publications

The whale shark genome reveals patterns of vertebrate gene family evolution

The whale shark genome reveals patterns of vertebrate gene family evolution

Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA

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