scholarly journals Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

2020 ◽  
Vol 8 (11) ◽  
pp. 1713
Author(s):  
Zhi Yong Shen ◽  
Xiu Pei Koh ◽  
Yan Ping Yu ◽  
Stanley C. K. Lau
Keyword(s):  
Functional Divergence ◽  
Low Frequency ◽  
Independent Set ◽  
Correct Prediction ◽  
Habitat Association ◽  
Orthologous Genes ◽  
Genomic Signatures ◽  
Environment Model ◽  
Niche Adaptation ◽  
External Environments

The evolution, habitat, and lifestyle of the cryptic clade II of Escherichia, which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other Escherichia genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments.

scholarly journals Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs

2019 ◽  
Author(s):  
Jon M. Laurent ◽  
Riddhiman K. Garge ◽  
Ashley I. Teufel ◽  
Claus O. Wilke ◽  
Aashiq H. Kachroo ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Gene Families ◽  
Evolutionary Divergence ◽  
Orthologous Genes ◽  
Specific Expression ◽  
Human Genes ◽  
Human Orthologs ◽  
Human Proteins ◽  
Yeast Genes ◽  
Opening Up

AbstractDespite over a billion years of evolutionary divergence, several thousand human genes possess clearly identifiable orthologs in yeast, and many have undergone lineage-specific duplications in one or both lineages. The ortholog conjecture postulates that orthologous genes between species retain ancestral functions despite divergence over vast timescales, but duplicated genes will be free to diverge in function. However, the retention of ancestral functions among co-orthologs between species and within gene families has been difficult to test experimentally at scale. In order to investigate how ancestral functions are retained or lost post-duplication, we systematically replaced hundreds of essential yeast genes with their human orthologs from gene families that have undergone lineage-specific duplications, including those with single duplications (one yeast gene to two human genes, 1:2) or higher-order expansions (1:>2) in the human lineage. We observe a variable pattern of replaceability across different ortholog classes, with an obvious trend towards differential replaceability inside gene families, rarely observing replaceability by all members of a family. We quantify the ability of various properties of the orthologs to predict replaceability, showing that in the case of 1:2 orthologs, replaceability is predicted largely by the divergence and tissue-specific expression of the human co-orthologs, i.e. the human proteins that are less diverged from their yeast counterpart and more ubiquitously expressed across human tissues more often replace their single yeast ortholog. These trends were consistent with in silico simulations demonstrating that when only one ortholog is replaceable, it tends to be the least diverged of the pair. Replaceability of yeast genes having more than two human co-orthologs was marked by retention of orthologous interactions in functional or protein networks as well as by more ancestral subcellular localization. Overall, we performed >400 human gene replaceability assays revealing 56 new human-yeast complementation pairs, thus opening up avenues to further functionally characterize these human genes in a simplified organismal context.

scholarly journals Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 490 ◽  
Author(s):  
Yunpeng Cao ◽  
Lan Jiang ◽  
Lihu Wang ◽  
Yongping Cai
Keyword(s):  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Different Types ◽  
Synonymous Substitution Rates ◽  
Gene Structures

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.

scholarly journals A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

2016 ◽  
pp. btw518 ◽  
Author(s):  
Nicole E. Wheeler ◽  
Lars Barquist ◽  
Robert A. Kingsley ◽  
Paul P. Gardner
Keyword(s):  
Functional Divergence ◽  
Bacterial Genomes ◽  
Orthologous Genes

scholarly journals Predicting the Depositional Environments of Mishrif Formation from Seismic Isopach Map in the Dujaila Oil Field, Southeast-Iraq

2021 ◽  
pp. 1943-1955
Author(s):  
Ahmed Muslim Khawaja ◽  
Jassim Muhammad Thabit
Keyword(s):  
Low Frequency ◽  
Depositional Environments ◽  
Oil Field ◽  
Frequency Model ◽  
Environment Model ◽  
Carbonate Formation ◽  
Porous Reservoir ◽  
Well Data ◽  
Isopach Map ◽  
Marine Basin

In this paper, we attempt to predict the depositional environments with associated lithofacies of the main reservoir of the late Cretaceous Mishrif carbonate Formation, depending on the analysis of the created seismic isopach map by integrating seismic and well data. The isopach map was created from a 3D-seismic reflection survey carried out at the Dujaila oil field in southeastern Iraq, which is of an area of 602.26 Km2, and integrated with the data of the two explored wells. Based on the interpretation of the seismic isopach map, the diagram of the 3D-depositional environment model of Mishrif Formation was constructed. It showed three distinguished depositional environments, which were graduated from a back reef lithofacies of a shallow open marine (shelf) environment in the west and NW, to a shoal environment of isolated Rudist reefal buildup in the middle, and a fore reef lithofacies of the deep open marine basin environment in the SE of the field. A 3D-instantaneous frequency model was generated to verify the capability of the seismic isopach map of predicting the depositional environments, which in turn showed that the low frequency was restricted in the region of the high thickness of Rudist reefal buildups (porous reservoir facies) in the vicinity of the productive well Dujaila-1.

scholarly journals Genomic signatures and insights into host niche adaptation of the entomopathogenic fungus Metarhizium humberi

2021 ◽  
Author(s):  
Natasha Sant′Anna Iwanicki ◽  
Ana Beatriz Riguetti Zanardo Botelho ◽  
Ingeborg Klingen ◽  
Italo Delalibera Júnior ◽  
Simeon Rossmann ◽  
...  
Keyword(s):  
Biological Control ◽  
Insect Pests ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Point Mutations ◽  
Broad Host Range ◽  
Agricultural Pests ◽  
Genomic Signatures ◽  
Host Interaction ◽  
Niche Adaptation

Abstract The genus Metarhizium is composed of species used in biological control programes of agricultural pests worldwide. This genus includes common fungal pathogen of many insects and mites and endophytes that can increase plant growth. Metarhizium humberi was recently described as a new species. This species is highly virulent against some insect pests and promotes growth in sugarcane, strawberry, and soybean crops. In the present study, we sequenced the genome of M. humberi, isolate ESALQ1638, and performed a functional analysis to determine its genomic signatures and highlight the genes and biological processes associated with its lifestyle. The genome annotation predicted 10633 genes in M. humberi, of which 92.0% are assigned putative functions, and ∼17% of the genome was annotated as repetitive sequences. We found that 18.5% of the M. humberi genome is similar to experimentally validated proteins associated with pathogen-host interaction. Compared to the genomes of eight Metarhizium species, the M. humberi ESALQ1638 genome revealed some unique traits that stood out, e.g.,, more genes functionally annotated as polyketide synthases (PKs), overrepresended GO-terms associated to transport of ions, organic and amino acid, a higher percentage of repetitive elements, and higher levels of RIP-induced point mutations. The M. humberi genome will serve as a resource for promoting studies on genome structure and evolution that can contribute to research on biological control and plant biostimulation. Thus, the genomic data supported the broad host range of this species within the generalist PARB clade and suggested that M. humberi ESALQ1638 might be particularly good at producing secondary metabolites and might be more efficient in transporting amino acids an organics compounds.

scholarly journals Ecological niche adaptation of a bacterial pathogen associated with reduced zoonotic potential

2020 ◽  
Author(s):  
Mark Kirkwood ◽  
Prerna Vohra ◽  
Matt Bawn ◽  
Gaëtan Thilliez ◽  
Hannah Pye ◽  
...  
Keyword(s):  
Food Safety ◽  
Bacterial Pathogens ◽  
Functional Divergence ◽  
Animal Health ◽  
Phage Type ◽  
Genotypic Variation ◽  
Ecological Niches ◽  
Virulence Plasmid ◽  
Zoonotic Potential ◽  
Niche Adaptation

AbstractThe emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two variants, S. Typhimurium phage type U288 and monophasic S. Typhimurium (S. 4,[5],12:i:-) ST34 emerged and have accounted for the majority of isolates from pigs in the UK in the past two decades, but have distinct host range and risk to food safety. ST34 accounts for over 50% of all S. Typhimurium infections in people while U288 less than 2%. U288 and ST34 form distinct phylogenetic clusters within S. Typhimurium, defined by approximately 600 SNPs within their 5 Mbp genomes. Evolution of the U288 clade from an LT2-like ancestor was characterised by the acquisition of AMR genes, insertions and deletions in the virulence plasmid pU288-1, and the accumulation of polymorphisms, some of which resulted in truncation of coding sequences. U288 isolates exhibited lower growth rate and viability following desiccation compared to ST34 isolates, characteristics that could affect transmission through the food chain. U288 and ST34 isolates exhibited distinct outcomes of infection in the murine model of colitis, and colonised pigs in a manner that affected the disease symptoms and distribution in organs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution of S. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential.ImportanceBacterial pathogens continually evolve to exploit new ecological niches as they emerge due to human activity including agricultural, medical or societal practice. The consequences of the emergence of new pathogens may affect outcome of infection and risk to human or animal health. Genome sequence can resolve the population structure, identify variants that are evolving as they enter a new niche, and pinpoint potential functional divergence. We report a variant S. Typhimurium that adapted to a unique niche distinct to that occupied by a second S. Typhimurium variant circulating in the same pig populations. Adaptation was accompanied by phenotypic and genotypic changes consistent with a more invasive lifestyle and a decreased zoonotic potential observed in the epidemiological record. Our findings suggest that pathogen genotypic variation may be useful in estimating zoonotic potential and threat to livestock welfare.

scholarly journals Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements

2020 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Heiko Liesegang ◽  
Olivia Roth ◽  
Carolin Charlotte Wendling
Keyword(s):  
Clonal Expansion ◽  
Mobile Genetic Elements ◽  
Vibrio Alginolyticus ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Kiel Fjord ◽  
Genetic Elements ◽  
Genomic Signatures ◽  
Accessory Genes ◽  
Niche Adaptation

Abstract Background Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate (1) those genomic signatures that characterize a habitat-specific ecotype and (2) the source of genomic variation within this ecotype. Results We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. Conclusion We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.

scholarly journals Natural Selection and Evolution of Streptococcal Virulence Genes Involved in Tissue-Specific Adaptations

2004 ◽  
Vol 186 (1) ◽  
pp. 110-121 ◽  
Author(s):  
Awdhesh Kalia ◽  
Debra E. Bessen
Keyword(s):  
Molecular Mechanisms ◽  
Virulence Genes ◽  
Intragenic Recombination ◽  
Site Preference ◽  
Strong Linkage Disequilibrium ◽  
Orthologous Genes ◽  
Gene Encoding ◽  
Tissue Specific ◽  
Niche Adaptation ◽  
Group A

ABSTRACT The molecular mechanisms underlying niche adaptation in bacteria are not fully understood. Primary infection by the pathogen group A streptococcus (GAS) takes place at either the throat or the skin of its human host, and GAS strains differ in tissue site preference. Many skin-tropic strains bind host plasminogen via the plasminogen-binding group A streptococcal M protein (PAM) present on the cell surface; inactivation of genes encoding either PAM or streptokinase (a plasminogen activator) leads to loss of virulence at the skin. Unlike PAM, which is present in only a subset of GAS strains, the gene encoding streptokinase (ska) is present in all GAS isolates. In this study, the evolution of the virulence genes known to be involved in skin infection was examined. Most genetic diversity within ska genes was localized to a region encoding the plasminogen-docking domain (β-domain). The gene encoding PAM displayed strong linkage disequilibrium (P ≪ 0.01) with a distinct phylogenetic cluster of the ska β-domain-encoding region. Yet, ska alleles of distant taxa showed a history of intragenic recombination, and high intrinsic levels of recombination were found among GAS strains having different tissue tropisms. The data suggest that tissue-specific adaptations arise from epistatic coselection of bacterial virulence genes. Additional analysis of ska genes showed that ∼4% of the codons underwent strong diversifying selection. Horizontal acquisition of one ska lineage from a commensal Streptococcus donor species was also evident. Together, the data suggest that new phenotypes can be acquired through interspecies recombination between orthologous genes, while constrained functions can be preserved; in this way, orthologous genes may provide a rich and ready source for new phenotypes and thereby play a facilitating role in the emergence of new niche adaptations in bacteria.

scholarly journals Nomadic Lifestyle of Lactobacillus plantarum Revealed by Comparative Genomics of 54 strains Isolated from Different Niches

2016 ◽  
Author(s):  
Maria Elena Martino ◽  
Jumamurat R. Bayjanov ◽  
Brian E. Caffrey ◽  
Michiel Wels ◽  
Pauline Joncour ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Lactobacillus Plantarum ◽  
Functional Divergence ◽  
High Complexity ◽  
Bacterial Genomes ◽  
Genomic Signatures ◽  
Ecological Versatility ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Ecological Constraint

AbstractThe ability of many bacteria to adapt to diverse environmental conditions is well known. Recent research has linked the process of bacterial adaptation to a niche to changes in the genome content and size, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse niches that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of niches. With the aim of unravelling the link between genome evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Phylogenomic analyses coupled with the study of genetic functional divergence and gene-trait matching analysis revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings demonstrate the high complexity of L. plantarum evolution, revealing the absence of specific genomic signatures marking adaptations of this species towards the diverse habitats it is associated with. This suggests fundamentally similar and parallel trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species.

scholarly journals Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements

2020 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Olivia Roth ◽  
Heiko Liesegang ◽  
Carolin Charlotte Wendling
Keyword(s):  
Clonal Expansion ◽  
Mobile Genetic Elements ◽  
Vibrio Alginolyticus ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Kiel Fjord ◽  
Genetic Elements ◽  
Genomic Signatures ◽  
Accessory Genes ◽  
Niche Adaptation

Abstract Background Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate (1) those genomic signatures that characterize a habitat-specific ecotype and (2) the source of genomic variation within this ecotype.Results We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. Conclusion We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.

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