DNA Features Viewer: a sequence annotation formatting and plotting library for Python

Zulkower, Valentin; Rosser, Susan J.

doi:10.1093/bioinformatics/btaa213

Cited by 112 publications

(72 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gene functions are distinguished by different colors. The visualization of gene arrangement is performed with dna-features-viewer v3.0.3 [64]. The structures of the gene arrangement classified the nif clusters into three types: those belonging to the Cluster FL or Cluster PB (A), those found in the symbiosis island in most symbiotic strains or in FL nif strains that cluster with symbiotic strains (B), and those from outgroup species (C).…”

Section: Resultsmentioning

confidence: 99%

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium

Jiang

Wang

Liao

et al. 2021

Preprint

View full text Add to dashboard Cite

The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world's soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world's soils, our findings have implications for global nitrogen cycles and agricultural research.

show abstract

Section: Resultsmentioning

confidence: 99%

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium

Jiang

Wang

Liao

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…S4A). Whole-plasmid visualization was performed using a python module for prokaryotic genome analyses – DnaFeaturesView – and matplotlib module combined, as well as ARG-ANNOT and Prokka’s results (57). B ) Plasmid pKP508BN15 (136.8 kb) from K. pneumoniae 508B transports a sul2 and an rRNA adenine n-6-methyltransferase ( ermC ) resistance markers.…”

Section: Resultsmentioning

confidence: 99%

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

Aft

et al. 2020

Preprint

View full text Add to dashboard Cite

The rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative and Gram-positive bacteria, including the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. We identify a high abundance of beta-lactamase genes in highly resistant organisms, including seven extended-spectrum β-lactamases shared between organisms from different species. Additionally, we identify several ARGs-carrying plasmids indicating the potential for fast transmission of resistance mechanism between bacterial strains, comprising a novel IncFII plasmid recently introduced in Brazil from Asia. Through comparative genomic analysis, we demonstrate that some pathogens identified here are very distantly related to other bacteria isolated worldwide, demonstrating the potential existence of endemic bacterial pathogens in Brazil. Also, we uncovered at least two couples of (near)-identical plasmids exhibiting multi-drug resistance, suggesting that plasmids were transmitted between bacteria of the same or different species in the hospital studied. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identify six beta-lactamase genes out of 15 predicted in silico as the main responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms.

show abstract

“…Phylogenetic data visualization was done using auspice (interactive view) 61 and baltic 0.1.0 (static view). The search for polymorphisms in comparison with the reference genome (MN908947.3) was performed using Python scripts, and visualization of genome annotations were done using DNA Features Viewer 3.0.1 63 . The structure in Extended Data Fig.…”

Section: Methods Detailsmentioning

confidence: 99%

Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient

Klein

Trubin

et al. 2021

Preprint

View full text Add to dashboard Cite

Prior to the emergence of antigenically distinct SARS-CoV-2 variants, reinfections were reported infrequently - presumably due to the generation of durable and protective immune responses. However, case reports also suggested that rare, repeated infections may occur as soon as 48 days following initial disease onset. The underlying immunologic deficiencies enabling SARS-CoV-2 reinfections are currently unknown. Here we describe a renal transplant recipient who developed recurrent, symptomatic SARS-CoV-2 infection - confirmed by whole virus genome sequencing - 7 months after primary infection. To elucidate the immunological mechanisms responsible for SARS-CoV-2 reinfection, we performed longitudinal profiling of cellular and humoral responses during both primary and recurrent SARS-CoV-2 infection. We found that the patient responded to the primary infection with transient, poor-quality adaptive immune responses. The patients immune system was further compromised by intervening treatment for acute rejection of the renal allograft prior to reinfection. Importantly, we also identified the development of neutralizing antibodies and the formation of humoral memory responses prior to SARS-CoV-2 reinfection. However, these neutralizing antibodies failed to confer protection against reinfection, suggesting that additional factors are required for efficient prevention of SARS-CoV-2 reinfection. Further, we found no evidence supporting viral evasion of primary adaptive immune responses, suggesting that susceptibility to reinfection may be determined by host factors rather than pathogen adaptation in this patient. In summary, our study suggests that a low neutralizing antibody presence alone is not sufficient to confer resistance against reinfection. Thus, patients with solid organ transplantation, or patients who are otherwise immunosuppressed, who recover from infection with SARS-CoV-2 may not develop sufficient protective immunity and are at risk of reinfection.

show abstract

DNA Features Viewer: a sequence annotation formatting and plotting library for Python

Abstract: Abstract Motivation While the Python programming language counts many Bioinformatics and Computational Biology libraries, none offers customizable sequence annotation visualizations with layout optimization. Results DNA Features Viewer is a sequence annotation plo… Show more

Cited by 112 publications

References 6 publications

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient

Contact Info

Product

Resources

About

DNA Features Viewer: a sequence annotation formatting and plotting library for Python

Abstract: Abstract Motivation While the Python programming language counts many Bioinformatics and Computational Biology libraries, none offers customizable sequence annotation visualizations with layout optimization. Results DNA Features Viewer is a sequence annotation plo… Show more

Cited by 112 publications

References 6 publications

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N2-fixingBradyrhizobium

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N2-fixingBradyrhizobium

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient

Contact Info

Product

Resources

About

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium

Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N₂-fixingBradyrhizobium