Characterization and comparative genomic analysis of virulent and temperateBacillus megateriumbacteriophages

Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. SeveralBacillusbacteriophages have been isolated, but very fewBacillus megateriumbacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of theB. megateriumbacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical forBacillusphages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with otherB. megateriumbacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated withBacilluspathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.

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Characterization and Comparative Genomics Analysis of two Bacillus megaterium lytic bacteriophages

10.7287/peerj.preprints.27171v1 ◽

2018 ◽

Author(s):

Abdoallah Sharaf ◽

Miroslav Obornik ◽

Adel Hammad ◽

Sohair El-Afifi ◽

Eman Marei

Keyword(s):

Bacillus Megaterium ◽

Burst Size ◽

Phylogenetic Analyses ◽

Modular Organization ◽

Environmental Diversity ◽

Egyptian Soil ◽

Comparative Genomics Analysis ◽

Next Generation Sequencing Ngs ◽

Growth Analyses ◽

Generation Sequencing

Next Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and their annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 minutes respectively) and a smaller burst size (103 and 117 PFU respectively), in comparison to that which is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with a modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7 respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.

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Characterization and Comparative Genomics Analysis of two Bacillus megaterium lytic bacteriophages

10.7287/peerj.preprints.27171 ◽

2018 ◽

Author(s):

Abdoallah Sharaf ◽

Miroslav Obornik ◽

Adel Hammad ◽

Sohair El-Afifi ◽

Eman Marei

Keyword(s):

Bacillus Megaterium ◽

Burst Size ◽

Phylogenetic Analyses ◽

Modular Organization ◽

Environmental Diversity ◽

Egyptian Soil ◽

Comparative Genomics Analysis ◽

Next Generation Sequencing Ngs ◽

Growth Analyses ◽

Generation Sequencing

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A68 Characterization and comparative genomic analysis of two Bacillus megaterium lytic bacteriophages

Virus Evolution ◽

10.1093/ve/vez002.067 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

A Sharaf ◽

M Oborník ◽

A Hammad ◽

S El-Afifi ◽

E Marei

Keyword(s):

Bacillus Megaterium ◽

Thermal Inactivation ◽

Burst Size ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Modular Organization ◽

Comparative Genomic ◽

Environmental Diversity ◽

Ph Tolerance

Abstract Next-generation sequencing technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Many Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. Here, we describe biological characteristics and whole-genome sequences and their annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), isolated from Egyptian soil samples and representing two different groups according to their host range and amplified fragment length polymorphism profiles. Both phages have been displaying different thermal inactivation points (82 and 78 °C) and pH tolerance range (5–9.2 and 5–8.4 pH) while having the same longevity in vitro (192 h). Electron microscopy observation has proved that both phages belonged to the Myoviridiae family. Furthermore, growth analyses indicated that phages BM5 and BM10 have a shorter latent period (20 and 25 min) and smaller burst size (103 and 117 PFU) than is typical for Bacillus phages. The genome sizes of phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with a modular organization. Bioinformatic analyses of BM5 and BM10 genomes enabled assignments of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of BM5 and BM10 genome structures with other B. megaterium bacteriophages revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7) within L cluster and display different lifestyles (lysogenic and lytic). Sequenced phages encode proteins associated with Bacillus pathogenesis. BM5 does not contain any tRNA sequences, while BM10 genome codes for 17 tRNAs.

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Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

Frontiers in Genetics ◽

10.3389/fgene.2021.740940 ◽

2021 ◽

Vol 12 ◽

Author(s):

Felipe Cabarcas ◽

Ana Luz Galvan-Diaz ◽

Laura M. Arias-Agudelo ◽

Gisela María García-Montoya ◽

Juan M. Daza ◽

...

Keyword(s):

De Novo ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Cryptosporidium Hominis ◽

Stool Samples ◽

Metagenomic Assembly ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.

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Next-Generation Sequencing in Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms20122929 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2929 ◽

Cited By ~ 17

Author(s):

Nicoletta Coccaro ◽

Luisa Anelli ◽

Antonella Zagaria ◽

Giorgina Specchia ◽

Francesco Albano

Keyword(s):

Next Generation Sequencing ◽

Acute Lymphoblastic Leukemia ◽

Residual Disease ◽

Age Of Onset ◽

Lymphoblastic Leukemia ◽

Genomic Analysis ◽

Next Generation ◽

Acute Leukemias ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.

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Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000226 ◽

2015 ◽

Vol 65 (Pt_7) ◽

pp. 2104-2109 ◽

Cited By ~ 48

Author(s):

Christopher A. Dunlap ◽

Soo-Jin Kim ◽

Soon-Wo Kwon ◽

Alejandro P. Rooney

Keyword(s):

Bacillus Amyloliquefaciens ◽

Type Strain ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Growth Promoters ◽

Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

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Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12080754 ◽

2021 ◽

Vol 12 (8) ◽

pp. 754

Author(s):

Yupeng Wu ◽

Hui Fang ◽

Jiping Wen ◽

Juping Wang ◽

Tianwen Cao ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Trna Genes ◽

Cox1 Gene ◽

Protein Coding ◽

Phylogenetic Implications ◽

Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

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Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage

Scientific Reports ◽

10.1038/s41598-021-01419-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Prince Kumar ◽

Mukesh K. Meghvansi ◽

D. V. Kamboj

Keyword(s):

Sequence Data ◽

Burst Size ◽

Genomic Analysis ◽

Dna Helicase ◽

Shigella Dysenteriae ◽

Whole Genome Sequence ◽

Phenotypic Characterization ◽

Comparative Genomic ◽

Tail Fiber ◽

Parsimony Method

AbstractShigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae

10.1101/2020.02.06.936641 ◽

2020 ◽

Author(s):

Andy O. Leu ◽

Simon J. McIlroy ◽

Jun Ye ◽

Donovan H. Parks ◽

Victoria J. Orphan ◽

...

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Comparative Genomic ◽

Anaerobic Oxidation Of Methane ◽

Metabolic Potential ◽

Oxidation Of Methane ◽

Oxidation Of Hydrogen ◽

Global Biogeochemical Cycles

AbstractAnaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners.ImportanceAOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance to the global carbon cycle and climate change modelling. While the oxidation of methane coupled to sulphate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae as they are absent in related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.

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