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

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.

scholarly journals Eutherian comparative genomic analysis protocol

2020 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 12 major eutherian gene data sets, including 1853 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670, LT962964-LT963174 and LT990249-LT990597.

scholarly journals Candidate pathogenicity islands in the genome of ‘CandidatusRickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2806 ◽  
Author(s):  
YaDong Wang ◽  
Christopher Chandler
Keyword(s):  
Genomic Island ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Photorhabdus Luminescens ◽  
Future Studies ◽  
Terrestrial Isopod ◽  
Microbe Interactions ◽  
Host Microbe Interactions

The bacterial genusRickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus,R. grylliandR. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence forR. isopodorum, and performed a comparative genomic analysis withR. grylli. We found evidence for several candidate genomic island regions inR. isopodorum, none of which appear in the previously availableR. grylligenome sequence.Furthermore, one of these genomic island candidates inR. isopodorumcontained a gene that encodes a cytotoxin partially homologous to those found inPhotorhabdus luminescensandXenorhabdus nematophilus(Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity inRickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis inR. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature.

scholarly journals Eutherian comparative genomic analysis protocol

2019 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 11 major eutherian gene data sets, including 1504 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670 and LT962964-LT963174.

scholarly journals Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

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.

scholarly journals Eutherian comparative genomic analysis protocol

2021 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biological and medical sciences. Yet, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 14 major eutherian gene data sets, including 2615 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670, LT962964-LT963174, LT990249-LT990597, LR130242-LR130508 and LR760818-LR761312.

scholarly journals Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici

2021 ◽  
Vol 12 ◽  
Author(s):  
Joung-Ho Lee ◽  
Muhammad Irfan Siddique ◽  
Jin-Kyung Kwon ◽  
Byoung-Cheorl Kang
Keyword(s):  
Phytophthora Capsici ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic Analysis ◽  
Fruit Rot ◽  
Comparative Genomic ◽  
Related Gene ◽  
Foliar Blight ◽  
Accelerated Evolution ◽  
Oomycete Pathogen

Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.

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

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
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.

scholarly journals Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

2021 ◽  
Vol 9 (6) ◽  
pp. 1332
Author(s):  
Irene Artuso ◽  
Paolo Turrini ◽  
Mattia Pirolo ◽  
Gabriele Andrea Lugli ◽  
Marco Ventura ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Species Level ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Methyl Halides ◽  
Terrestrial Environments

Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.

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