Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

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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Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus

10.1101/661967 ◽

2019 ◽

Author(s):

Marian Dominguez-Mirazo ◽

Rong Jin ◽

Joshua S. Weitz

Keyword(s):

De Novo ◽

Evolutionary Relationship ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Sequence Type ◽

Comparative Genomic ◽

Candidatus Liberibacter Asiaticus ◽

Candidatus Liberibacter ◽

Liberibacter Asiaticus ◽

Prediction Approach

AbstractHuanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphapro-teobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

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Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum

BMC Genomics ◽

10.1186/s12864-015-1517-1 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 40

Author(s):

Yaqiong Guo ◽

Kevin Tang ◽

Lori A Rowe ◽

Na Li ◽

Dawn M Roellig ◽

...

Keyword(s):

Cryptosporidium Parvum ◽

Genetic Recombination ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Gene Duplications ◽

Cryptosporidium Hominis

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Comparative Genomic Analysis Reveals a Critical Role of De Novo Nucleotide Biosynthesis for Saccharomyces cerevisiae Virulence

PLoS ONE ◽

10.1371/journal.pone.0122382 ◽

2015 ◽

Vol 10 (3) ◽

pp. e0122382 ◽

Cited By ~ 5

Author(s):

Roberto Pérez-Torrado ◽

Silvia Llopis ◽

Benedetta Perrone ◽

Rocío Gómez-Pastor ◽

Bernhard Hube ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

De Novo ◽

Critical Role ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Nucleotide Biosynthesis

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Characterization and comparative genomic analysis of virulent and temperateBacillus megateriumbacteriophages

PeerJ ◽

10.7717/peerj.5687 ◽

2018 ◽

Vol 6 ◽

pp. e5687 ◽

Cited By ~ 2

Author(s):

Abdoallah Sharaf ◽

Miroslav Oborník ◽

Adel Hammad ◽

Sohair El-Afifi ◽

Eman Marei

Keyword(s):

Burst Size ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Modular Organization ◽

Comparative Genomic ◽

Environmental Diversity ◽

Egyptian Soil ◽

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. 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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Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal PathogenicEscherichia coli(ExPEC) Lineages

mBio ◽

10.1128/mbio.01596-17 ◽

2017 ◽

Vol 8 (5) ◽

Cited By ~ 39

Author(s):

Sabiha Shaik ◽

Amit Ranjan ◽

Sumeet K. Tiwari ◽

Arif Hussain ◽

Nishant Nandanwar ◽

...

Keyword(s):

Molecular Mechanisms ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Sequence Type ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

E Coli ◽

Extended Spectrum ◽

Tract Infections ◽

St131 Clone

ABSTRACTEscherichia colisequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenicE. coli(ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producingE. coliclones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131E. colistrains with 40 genomes from three other STs, including ST38 (n =12), ST405 (n =10), and ST648 (n =18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification ofE. colistrains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.IMPORTANCEE. coli, particularly the ST131 extraintestinal pathogenicE. coli(ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzesE. coliST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemicE. coliST131 clone.

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Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires betweenPyricularia oryzaeandPyricularia pennisetiisolated from aPennisetumgrass

10.1101/360016 ◽

2018 ◽

Author(s):

Huakun Zheng ◽

Zhenhui Zhong ◽

Mingyue Shi ◽

Limei Zhang ◽

Lianyu Lin ◽

...

Keyword(s):

Genetic Study ◽

Genomic Sequence ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Blast Disease ◽

Individual Species ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Avirulence Genes ◽

Related Gene

AbstractBackgroundsPyriculariais a multispecies complex that could infect and cause severe blast disease on diverse hosts, including rice, wheat and many other grasses. Although the genome size of this fungal complex is small [~40 Mbp forPyricularia oryzae(syn.Magnaporthe oryzae), and ~45 Mbp forP. grisea], the genome plasticity allows the fungus to jump and adapt to new hosts. Therefore, deciphering the genome basis of individual species could facilitate the evolutionary and genetic study of this fungus. However, except for theP. oryzaesubgroup, many other species isolated from diverse hosts, such as thePennisetumgrasses, remain largely uncovered genetically.ResultsHere, we report the genome sequence of a pyriform-shaped fungal strainP. pennisetiP1609 isolated from aPennisetumgrass (JUJUNCAO) using PacBio SMRT sequencing technology. We performed a phylogenomic analysis of 28 Magnaporthales species and 5 non-Magnaporthales species and addressed P1609 into aPyriculariasubclade that is distant fromP. oryzae. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires were fairly different between P1609 and theP. oryzaestrain 70-15, including the cloned avirulence genes, other putative secreted proteins, as well as some other predictedPathogen-Host Interaction(PHI) genes. Genomic sequence comparison also identified many genomic rearrangements.ConclusionTaken together, our results suggested that the genomic sequence of theP. pennisetiP1609 could be a useful resource for the genetic study of thePennisetum-infectingPyriculariaspecies.

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