scholarly journals Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Zigang Qu ◽  
Wenhui Li ◽  
Nianzhang Zhang ◽  
Li Li ◽  
Hongbin Yan ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Vaccine Development ◽  
Trichinella Spiralis ◽  
Cell Formation ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Effective Control ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Low Oxygen

Trichinellosis caused by parasitic nematodes of the genus Trichinella may result in human morbidity and mortality worldwide. Deciphering processes that drive species diversity and adaptation are key to understanding parasitism and developing effective control strategies. Our goal was to identify genes that are under positive selection and possible mechanisms of adaptive evolution of Trichinella spiralis genes using a comparative genomic analysis with the genomes of Brugia malayi, Trichuris suis, Ancylostoma ceylanicum, and Caenorhabditis elegans. The CODEML program derived from the PAML package was used to deduce the most probable dN/dS ratio, a measurement to detect genes/proteins undergoing adaptation. For each pair of sequences, those with a dN/dS ratio > 1 were considered positively selected genes (PSGs). Altogether, 986 genes were positively selected (p-value < 0.01). Genes involved in metabolic pathways, signaling pathways, and cytosolic DNA-sensing pathways were significantly enriched among the PSGs. Several PSGs are associated with exploitation of the host: modification of the host’s metabolism, creation of new parasite-specific morphological structures between T. spiralis and the host interface, xenobiotic metabolism to combat low oxygen concentrations and host toxicity, muscle cell transformation, cell cycle arrest, DNA repair processes during nurse cell formation, antiapoptotic factors, immunomodulation, and regulation of epigenetic processes. Some of the T. spiralis PSGs have C. elegans orthologs that confer severe or lethal RNAi phenotypes. Fifty-seven PSGs in T. spiralis were analyzed to encode differentially expressed proteins. The present study utilized an overall comparative genomic analysis to discover PSGs within T. spiralis and their relationships with biological function and organism fitness. This analysis adds to our understanding of the possible mechanism that contributes to T. spiralis parasitism and biological adaptation within the host, and thus these identified genes may be potential targets for drug and vaccine development.

scholarly journals Comparative Genomic Analysis Provides Insights into the Phylogeny, Resistome, Virulome, and Host Adaptation in the Genus Ewingella

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 330 ◽  
Author(s):  
Zhenghui Liu ◽  
Hongyan Sheng ◽  
Benjamin Azu Okorley ◽  
Yu Li ◽  
Frederick Leo Sossah
Keyword(s):  
Antibiotic Resistance ◽  
Control Strategies ◽  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Defense Responses ◽  
Host Adaptation ◽  
Comparative Genomic Analysis ◽  
Effective Control ◽  
Comparative Genomic ◽  
Temperature Oxidation

Ewingella americana is a cosmopolitan bacterial pathogen that has been isolated from many hosts. Here, we sequenced a high-quality genome of E. americana B6-1 isolated from Flammulina filiformis, an important cultivated mushroom, performed a comparative genomic analysis with four other E. americana strains from various origins, and tested the susceptibility of B6-1 to antibiotics. The genome size, predicted genes, and GC (guanine-cytosine) content of B6-1 was 4.67 Mb, 4301, and 53.80%, respectively. The origin of the strains did not significantly affect the phylogeny, but mobile genetic elements shaped the evolution of the genus Ewingella. The strains encoded a set of common genes for type secretion, virulence effectors, CAZymes, and toxins required for pathogenicity in all hosts. They also had antibiotic resistance, pigments to suppress or evade host defense responses, as well as genes for adaptation to different environmental conditions, including temperature, oxidation, and nutrients. These findings provide a better understanding of the virulence, antibiotic resistance, and host adaptation strategies of Ewingella, and they also contribute to the development of effective control strategies.

scholarly journals Comparative genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira

2017 ◽  
Author(s):  
Alejandro Palomo ◽  
Anders G Pedersen ◽  
S Jane Fowler ◽  
Arnaud Dechesne ◽  
Thomas Sicheritz-Pontén ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Nitrite Reduction ◽  
Ammonium Uptake ◽  
Comparative Genomic ◽  
Ammonium Oxidation ◽  
Low Oxygen ◽  
Oxidation Pathway ◽  
History Of

AbstractThe description of comammoxNitrospiraspp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammoxNitrospiraand the evolutionary history of their ammonium oxidation pathway. We report four new comammoxNitrospiragenomes, constituting two novel species, and the first comparative genomic analysis on comammoxNitrospira.ComammoxNitrospirahas lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizingNitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to otherNitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammoxNitrospiragenomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammoxNitrospiraseems attuned to oligotrophy and hypoxia compared to β-AOB.β-AOBs are the clear origin of the ammonium oxidation pathway in comammoxNitrospira: reconciliation analysis indicates two separate earlyamoAgene transfer events from β-AOB to an ancestor of comammoxNitrospira, followed by clade specific losses. ForhaoA, one early transfer from β-AOB to comammoxNitrospirais predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in mostNitrospiragenomes is the result of subsequent loss.SignificanceThe recent discovery of comammox bacteria - members of theNitrospiragenus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammoxNitrospiraand related nitrifiers. Ammonium oxidation genes in comammoxNitrospirahad a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

scholarly journals Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible

2021 ◽  
pp. 100015
Author(s):  
Eamon O. Murchu ◽  
Sinead O'Neill ◽  
Paula Byrne ◽  
Cillian De Gascun ◽  
Michelle O'Neill ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis

3 Biotech ◽  
2021 ◽  
Vol 11 (6) ◽  
Author(s):  
Kai Huang ◽  
Bo Zhang ◽  
Yu Chen ◽  
Zhe-Ming Wu ◽  
Zhi-Qiang Liu ◽  
...  
Keyword(s):  
Amphotericin B ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic
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