1P230 Phylogenetic Analyses of Essential Genes by Using ORI-GENE(Bioinformatics-comparative genomics and molecular evolution,Poster Presentations)

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

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Evolutionary Analyses of Protein Interaction Networks

Biological Data Mining in Protein Interaction Networks ◽

10.4018/978-1-60566-398-2.ch010 ◽

2009 ◽

pp. 169-181 ◽

Cited By ~ 2

Author(s):

Takashi Makino ◽

Aoife McLysaght

Keyword(s):

Molecular Evolution ◽

Comparative Genomics ◽

Protein Interaction ◽

Protein Interaction Networks ◽

Evolutionary Rates ◽

Interaction Networks ◽

Evolutionary Mechanisms ◽

Ancestral Gene ◽

Protein Protein Interaction ◽

A Genome

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evolutionary mechanisms acting on the interactome it is necessary to compare PPIs across species. Investigation of co-localization of interacting genes in a genome shows that PPIs have an important role in the maintenance of a physical link between neighboring genes. The purpose of this chapter is to introduce methodologies for analyzing PPI data and to describe molecular evolution and comparative genomics insights gained from such studies.

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Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02873-19 ◽

2020 ◽

Vol 86 (6) ◽

Cited By ~ 3

Author(s):

Ebrahim Osdaghi ◽

Touraj Rahimi ◽

S. Mohsen Taghavi ◽

Maryam Ansari ◽

Sadegh Zarei ◽

...

Keyword(s):

Genetic Diversity ◽

Comparative Genomics ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sensu Stricto ◽

Bacterial Canker ◽

Agricultural Crops ◽

Content Type ◽

Canker Disease

ABSTRACT Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections. IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.

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Molecular evolution of the natriuretic peptide system as revealed by comparative genomics

Comparative Biochemistry and Physiology Part D Genomics and Proteomics ◽

10.1016/j.cbd.2005.10.002 ◽

2006 ◽

Vol 1 (1) ◽

pp. 69-76 ◽

Cited By ~ 2

Author(s):

Koji Inoue ◽

Yoshio Takei

Keyword(s):

Molecular Evolution ◽

Comparative Genomics ◽

Natriuretic Peptide ◽

Peptide System ◽

Natriuretic Peptide System

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Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

10.1101/2020.04.23.055285 ◽

2020 ◽

Author(s):

Camilla Fagorzi ◽

Alexandru Ilie ◽

Francesca Decorosi ◽

Lisa Cangioli ◽

Carlo Viti ◽

...

Keyword(s):

Nitrogen Fixation ◽

Comparative Genomics ◽

Phylogenetic Analyses ◽

Carbon Sources ◽

Associated Bacteria ◽

Phenotypic Differences ◽

Genetic Features ◽

Alkaline Conditions ◽

High Throughput Phenotyping ◽

Acidic Conditions

ABSTRACTRhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF emerged several times within the genus Ensifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

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The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

10.1101/2020.03.17.996009 ◽

2020 ◽

Author(s):

Jeff Rouïl ◽

Emmanuelle Jousselin ◽

Armelle Coeur d’acier ◽

Corinne Cruaud ◽

Alejandro Manzano-Marín

Keyword(s):

Comparative Genomics ◽

Genome Evolution ◽

Phylogenetic Analyses ◽

Insect Species ◽

Parasitoid Wasps ◽

Valuable Resource ◽

Variable Regions ◽

New Genes ◽

Endosymbiotic Bacteria ◽

Hamiltonella Defensa

ABSTRACTPhages can fundamentally alter the physiology and metabolism of their hosts. While ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception in the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa, hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called ”types”. In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across 10 insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts.

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In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes

Microbial Genomics ◽

10.1099/mgen.0.000546 ◽

2021 ◽

Author(s):

Lucas Morinière ◽

Solène Lecomte ◽

Erwan Gueguen ◽

Franck Bertolla

Keyword(s):

Comparative Genomics ◽

Plant Pathogen ◽

Type Species ◽

Essential Genes ◽

Content Type ◽

Link Type ◽

Transposon Insertion ◽

Ecological Features ◽

Genomic Study ◽

Transposon Insertion Sequencing

The essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome ofXanthomonas hortorumpv.vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativaL.) which belongs to the plant-pathogen reservoir genusXanthomonasand is affiliated to the familyXanthomonadaceae. No practical means of disease control or prevention against this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome ofX. hortorumpv.vitiansLM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features ofXanthomonasorXanthomonadaceaespecies, or acquired through horizontal gene transfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study ofX. hortorumpv.vitians.

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Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction

Journal of General Virology ◽

10.1099/vir.0.81309-0 ◽

2006 ◽

Vol 87 (4) ◽

pp. 885-893 ◽

Cited By ~ 83

Author(s):

Shannon N. Bennett ◽

Edward C. Holmes ◽

Maritza Chirivella ◽

Dania M. Rodriguez ◽

Manuela Beltran ◽

...

Keyword(s):

Puerto Rico ◽

Molecular Evolution ◽

Positive Selection ◽

Disease Incidence ◽

Phylogenetic Analyses ◽

Acid Sites ◽

Viral Envelope ◽

Envelope Gene ◽

Structural Genes ◽

Phylogenetic Structure

Dengue virus is a circumtropical, mosquito-borne flavivirus that infects 50–100 million people each year and is expanding in both range and prevalence. Of the four co-circulating viral serotypes (DENV-1 to DENV-4) that cause mild to severe febrile disease, DENV-2 has been implicated in the onset of dengue haemorrhagic fever (DHF) in the Americas in the early 1980s. To identify patterns of genetic change since DENV-2's reintroduction into the region, molecular evolution in DENV-2 from Puerto Rico (PR) and surrounding countries was examined over a 20 year period of fluctuating disease incidence. Structural genes (over 20 % of the viral genome), which affect viral packaging, host-cell entry and immune response, were sequenced for 91 DENV-2 isolates derived from both low- and high-prevalence years. Phylogenetic analyses indicated that DENV-2 outbreaks in PR have been caused by viruses assigned to subtype IIIb, originally from Asia. Variation amongst DENV-2 viruses in PR has since largely arisen in situ, except for a lineage-replacement event in 1994 that appears to have non-PR New World origins. Although most structural genes have remained relatively conserved since the 1980s, strong evidence was found for positive selection acting on a number of amino acid sites in the envelope gene, which have also been important in defining phylogenetic structure. Some of these changes are exhibited by the multiple lineages present in 1994, during the largest Puerto Rican outbreak of dengue, suggesting that they may have altered disease dynamics, although their functional significance will require further investigation.

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