scholarly journals 638. Comparative Genomics of Mycoplasma pneumoniae Isolated From Children with Pneumonia: South Korea, 2010–2016

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S295-S295
Author(s):  
Hoan J Lee ◽  
Joon Kee Lee ◽  
Yun Young Choi ◽  
Ji Young Park ◽  
Moon-Woo Seong ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome

Abstract Background This study applied high-throughput whole-genome sequencing (WGS) technologies to investigate the comparative genomics of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during two epidemics from 2010 to 2016 in comparison with a global collection of 48 Mycoplasma pneumoniae strains which includes seven countries ranging from 1944 to 2017. Methods A total number of 30 M. pneumoniae strains were selected for whole-genome sequence analysis from two epidemics, 2010–2012 and 2014–2016. Next-generation sequencing (NGS) of all M. pneumoniae strains was performed using the Illumina MiSeq desktop sequencer. Comparative genomic analysis was performed using BLAST Ring Image Generator (BRIG), MAUVE, MAFFT, CLC Phylogeny Module, SnpEff, and Pathosystems Resource Integration Center (PATRIC). 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 of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. 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. Conclusion The comparative genomics 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. Disclosures All authors: No reported disclosures.

scholarly journals Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Whole Genome ◽  
Base Pairs ◽  
Tract Infections ◽  
Phylogenetic Associations

Abstract 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 one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains. Conclusions The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.

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

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract 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.

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

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Eun Hwa Choi ◽  
Moon-Woo Seong ◽  
Youbin Yeon ◽  
Sung Im Cho ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract 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.

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

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract 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.

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

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract 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.

scholarly journals Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

2020 ◽  
Author(s):  
Xueping LI ◽  
Jianhong Li ◽  
Yonghong Qi ◽  
Yonggang Liu ◽  
Minquan Li
Keyword(s):  
Molecular Mechanisms ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Effective Control ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Fusarium Equiseti ◽  
Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

Comparison of three species of Elizabethkingia genus by whole-genome sequence analysis

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Information Storage ◽  
Whole Genome Sequence ◽  
Neonatal Meningitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Significant Finding ◽  
Beta Lactams ◽  
Clusters Of Orthologous Groups

Abstract Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that ‘metabolism’ occupied the largest part in core genome, ‘information storage and processing’ was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.

scholarly journals Draft Genome Sequence of Aspergillus oryzae BP2-1, Isolated from Traditional Malted Rice in South Korea

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Jongbum Jeon ◽  
Jung A Kim ◽  
Sook-Young Park ◽  
Gye-Won Kim ◽  
Cheon-Seok Park ◽  
...  
Keyword(s):  
South Korea ◽  
Aspergillus Oryzae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Starter Culture ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

The fungus Aspergillus oryzae strain BP2-1 was isolated from the traditional malted starter culture nuruk. We report here the draft whole-genome sequence of A. oryzae BP2-1, which is comprised of 14 scaffolds with a total length of 39,455,382 bp and a GC content of 47.13%.

scholarly journals Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

2019 ◽  
Vol 9 (10) ◽  
pp. 3057-3066 ◽  
Author(s):  
Eoin O’Connor ◽  
Jamie McGowan ◽  
Charley G. P. McCarthy ◽  
Aniça Amini ◽  
Helen Grogan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agaricus Bisporus ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Single Strain ◽  
Protein Coding Genes ◽  
Starting Point

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

scholarly journals Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Diversity ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 113 ◽  
Author(s):  
Sunitha Joseph ◽  
Rebecca O’Connor ◽  
Abdullah Al Mutery ◽  
Mick Watson ◽  
Denis Larkin ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chicken Genome ◽  
Read Depth ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Peregrine Falcon ◽  
Whole Genome ◽  
Level Sequence ◽  
Wide Range ◽  
Chromosome Level

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.

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