Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

Wattam, Alice R.; Brettin, Thomas; Davis, James J.; Gerdes, Svetlana; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Stevens, Rick; Vonstein, Veronika; Warren, Andrew S.; Xia, Fangfang; Yoo, Hyunseung

doi:10.1007/978-1-4939-7463-4_4

“…For the analysis of proteins and functional annotation, PATRIC was used, and a heatmap was generated based on annotations (41). Gene translation, multiple sequence alignment and visualization of proteins were performed using Clustal Omega (42).…”

Section: Proteins and Functional Analysismentioning

confidence: 99%

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Lee

¹

,

Seong

²

,

Shin

³

et al. 2019

Preprint

0

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Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

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“…For the analysis of proteins and functional annotation, PATRIC was used, and a heatmap was generated based on annotations (43). Gene translation, multiple sequence alignment and visualization of proteins were performed using Clustal Omega (44).…”

Section: Proteins and Functional Analysismentioning

confidence: 99%

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Lee

¹

,

Seong

²

,

Shin

³

et al. 2019

Preprint

0

View full text Add to dashboard Cite

Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

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“…Based on the RAST system, the Pathosystems Resource Integration Center (PATRIC) improved the data collection of ARGs, and provided users a more powerful analysis for both genomes and individual genes [6]. Another available annotation server is Resfinder which is managed by the Center for Genomic Epidemiology; it provides a convenient way of identifying acquired ARGs in sequenced bacterial isolates [7].…”

Section: Introductionmentioning

confidence: 99%

BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements

Hua

¹

,

Liang

²

,

Deng

³

et al. 2020

Preprint

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Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the most exciting advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in a variety of bacteria, which may allow comprehensive investigations of genetic features but also serve for epidemiological studies. A plethora of softwares have been developed for the detailed annotation of DNA sequences, such as RAST (Rapid Annotation using Subsystem Technology), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, up to now, a reliable annotation tool of the combination of ARGs and MGEs is not available to researchers, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, ISs, integron, and transposable elements at the same time. The algorithm generates genbank files automatically, which are compatible with easyfig for comparative genomic analysis.

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Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

Cited by 89 publications

References 20 publications

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements

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