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

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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The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals

Genome Biology and Evolution ◽

10.1093/gbe/evaa089 ◽

2020 ◽

Vol 12 (6) ◽

pp. 878-889

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

Abstract Phages can fundamentally alter the physiology and metabolism of their hosts. Although these phages are ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception is 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 ten 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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The evolutionary origins of the cat attractant nepetalactone in catnip

Science Advances ◽

10.1126/sciadv.aba0721 ◽

2020 ◽

Vol 6 (20) ◽

pp. eaba0721 ◽

Cited By ~ 6

Author(s):

Benjamin R. Lichman ◽

Grant T. Godden ◽

John P. Hamilton ◽

Lira Palmer ◽

Mohamed O. Kamileen ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Evolution ◽

Gene Cluster ◽

Phylogenetic Analyses ◽

Chemical Diversity ◽

Flowering Plant ◽

Present Evidence ◽

Metabolic Gene ◽

Evolutionary Origins ◽

Plant Chemical

Catnip or catmint (Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This phenomenon is caused by the compound nepetalactone, a volatile iridoid that also repels insects. Iridoids are present in many Lamiaceae species but were lost in the ancestor of the Nepetoideae, the subfamily containing Nepeta. Using comparative genomics, ancestral sequence reconstructions, and phylogenetic analyses, we probed the re-emergence of iridoid biosynthesis in Nepeta. The results of these investigations revealed mechanisms for the loss and subsequent re-evolution of iridoid biosynthesis in the Nepeta lineage. We present evidence for a chronology of events that led to the formation of nepetalactone biosynthesis and its metabolic gene cluster. This study provides insights into the interplay between enzyme and genome evolution in the origins, loss, and re-emergence of plant chemical diversity.

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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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Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi

New Phytologist ◽

10.1111/nph.17160 ◽

2020 ◽

Author(s):

Lotus A. Lofgren ◽

Nhu H. Nguyen ◽

Rytas Vilgalys ◽

Joske Ruytinx ◽

Hui‐Ling Liao ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Evolution ◽

Ectomycorrhizal Fungi ◽

Dynamic Genome

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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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Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

10.1101/2020.01.29.924464 ◽

2020 ◽

Author(s):

Andrés Moya ◽

José L. Oliver ◽

Miguel Verdú ◽

Luis Delaye ◽

Vicente Arnau ◽

...

Keyword(s):

Natural Selection ◽

Genome Evolution ◽

Biological Function ◽

Phylogenetic Analyses ◽

Controversial Issue ◽

Diverse Group ◽

Evolutionary Trends ◽

Genome Complexity ◽

Environmental Interactions

AbstractProgressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.

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The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire

Microorganisms ◽

10.3390/microorganisms9091842 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1842

Author(s):

Sara Laetitia Elphège Gnangui ◽

Romain Kouakou Fossou ◽

Anicet Ebou ◽

Chiguié Estelle Raïssa Amon ◽

Dominique Kadio Koua ◽

...

Keyword(s):

Cote D'ivoire ◽

Côte D’Ivoire ◽

Phylogenetic Analyses ◽

Variable Region ◽

Soil Microbiome ◽

National Study ◽

Rrna Gene ◽

Cote D’Ivoire ◽

Variable Regions ◽

Côte D'ivoire

Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.

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Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

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Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

BMC Genomics ◽

10.1186/1471-2164-11-688 ◽

2010 ◽

Vol 11 (1) ◽

Cited By ~ 137

Author(s):

Henk C den Bakker ◽

Craig A Cummings ◽

Vania Ferreira ◽

Paolo Vatta ◽

Renato H Orsi ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Evolution ◽

Gene Loss ◽

Bacterial Genus ◽

Gene Acquisition

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Development and Application of a Multiplex Reverse-Transcription Polymerase Chain Reaction Assay for Screening a Global Collection of Citrus tristeza virus Isolates

Phytopathology ◽

10.1094/phyto-04-10-0102 ◽

2010 ◽

Vol 100 (10) ◽

pp. 1077-1088 ◽

Cited By ~ 25

Author(s):

Avijit Roy ◽

G. Ananthakrishnan ◽

John S. Hartung ◽

R. H. Brlansky

Keyword(s):

Polymerase Chain Reaction ◽

Reverse Transcription ◽

Citrus Tristeza Virus ◽

Phylogenetic Analyses ◽

Rt Pcr ◽

Chain Reaction ◽

Variable Regions ◽

Polymerase Chain ◽

Tristeza Virus ◽

Citrus Tristeza

The emerging diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures and prompted the search for new differentiation methods. To simplify the identification and differentiation of CTV genotypes, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) technique for the screening of CTV isolates was developed. Variable regions within the open reading frame (ORF)-1a of diverse CTV genotypes were identified to develop first a simplex (S) and then a hexaplex (H) RT-PCR. CTV isolates have been grouped previously into five genotypes (namely, T3, T30, T36, VT, and B165) based on the nucleotide sequence comparisons and phylogenetic analyses. Nucleotide sequences from GenBank were used to design species and genotype-specific primers (GSPs). The GSPs were initially used for reliable detection of all CTV genotypes using S-RT-PCR. Furthermore, detection of all five recognized CTV genotypes was established using the H-RT-PCR. Six amplicons, one generic to all CTV isolates and one for each of the five recognized genotypes, were identified on the basis of their size and were confirmed by sequence analysis. In all, 175 CTV isolates from 29 citrus-growing countries were successfully analyzed by S- and H-RT-PCR. Of these, 97 isolates contained T36 genotypes, 95 contained T3 genotypes, 76 contained T30 genotypes, 71 contained VT genotypes, and 24 contained B165 genotype isolates. In total, 126 isolates contained mixed infections of 2 to 5 of the known CTV genotypes. Two of the CTV isolates could not be assigned to a known genotype. H-RT-PCR provides a sensitive, specific, reliable, and rapid way to screen for CTV genotypes compared with other methods for CTV genotype detection. Efficient identification of CTV genotypes will facilitate a better understanding of CTV isolates, including the possible interaction of different genotypes in causing or preventing diseases. The methods described can also be used in virus-free citrus propagation programs and in the development of CTV-resistant cultivars.

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