scholarly journals Strong experimental support for the hologenome hypothesis revealed from Drosophila melanogaster selection lines

2021 ◽  
Author(s):  
Torsten Nygaard Kristensen ◽  
Anna A. Schönherz ◽  
Palle Duun Rohde ◽  
Jesper Givskov Sørensen ◽  
Volker Loeschcke
Keyword(s):  
Drosophila Melanogaster ◽  
Stress Resistance ◽  
Large Scale ◽  
Bacterial Species ◽  
Common Garden ◽  
Biological Entity ◽  
Standard Laboratory ◽  
Theory Of Evolution ◽  
Experimental Support ◽  
Control Regime

AbstractRecently it has been proposed, that the holobiont, i.e., the host and its associated microbiome, constitute a distinct biological entity, on which selection operates. This is a fascinating idea that so far has limited empirical justification. Here Drosophila melanogaster lines from a large-scale artificial selection experiment, where we selected for stress resistance traits and for longevity, were used to test the hologenome hypothesis. We raised flies from all selection regimes, including a regime where flies were kept at benign standard laboratory condition (control regime) throughout the duration of the experiment, under common garden conditions and sequenced the microbiome of the flies. We found abundant differences in microbial communities between control and selection regimes, but not between replicate lines within the regimes, and microbial diversity was higher in selected relative to control lines. Several major core Drosophila bacterial species were differentially abundant in the different selection regimes despite flies being exposed to similar nutritional and general environmental conditions. Our results support the idea that the host and microbiome genomes have evolved in concert and provide experimental support for the hologenome theory of evolution.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals INTRACISTRONIC MAPPING OF ELECTROPHORETIC SITES IN DROSOPHILA MELANOGASTER: FIDELITY OF INFORMATION TRANSFER BY GENE CONVERSION

Genetics ◽  
1974 ◽  
Vol 76 (2) ◽  
pp. 289-299
Author(s):  
Margaret McCarron ◽  
William Gelbart ◽  
Arthur Chovnick
Keyword(s):  
Drosophila Melanogaster ◽  
Information Transfer ◽  
Large Scale ◽  
Genetic Basis ◽  
Xanthine Dehydrogenase ◽  
Specific Protein ◽  
Wild Type ◽  
Electrophoretic Variation ◽  
The Stability ◽  
Recombination Experiments

ABSTRACT A convenient method is described for the intracistronic mapping of genetic sites responsible for electrophoretic variation of a specific protein in Drosophila melanogaster. A number of wild-type isoalleles of the rosy locus have been isolated which are associated with the production of electrophoretically distinguishable xanthine dehydrogenases. Large-scale recombination experiments were carried out involving null enzyme mutants induced on electrophoretically distinct wild-type isoalleles, the genetic basis for which is followed as a nonselective marker in the cross. Additionally, a large-scale recombination experiment was carried out involving null enzyme rosy mutants induced on the same wild-type isoallele. Examination of the electrophoretic character of crossover and convertant products recovered from the latter experiment revealed that all exhibited the same parental electrophoretic character. In addition to documenting the stability of the xanthine dehydrogenase electrophoretic character, this observation argues against a special mutagenesis hypothesis to explain conversions resulting from allele recombination studies.

scholarly journals Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Matthew R. Olm ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Proteins ◽  
Large Scale ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Discrimination ◽  
Bacterial Genomes ◽  
Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

The Effects of Stress-Related Hormones on the Stress Resistance in Drosophila melanogaster Carrying Mutation in the Dilp6 Gene

2018 ◽  
Vol 54 (2) ◽  
pp. 259-261
Author(s):  
E. V. Burdina ◽  
N. V. Adonyeva ◽  
N. E. Gruntenko ◽  
I. Yu. Rauschenbach
Keyword(s):  
Drosophila Melanogaster ◽  
Stress Resistance ◽  
Effects Of Stress

scholarly journals RAPID LOSS OF STRESS RESISTANCE IN DROSOPHILA MELANOGASTER UNDER ADAPTATION TO LABORATORY CULTURE

Evolution ◽  
2001 ◽  
Vol 55 (2) ◽  
pp. 436-438 ◽  
Author(s):  
Ary A. Hoffmann ◽  
Rebecca Hallas ◽  
Chantelle Sinclair ◽  
Linda Partridge
Keyword(s):  
Drosophila Melanogaster ◽  
Stress Resistance ◽  
Laboratory Culture ◽  
Rapid Loss

scholarly journals Cross-Species RNAi Rescue Platform in Drosophila melanogaster

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1165-1173 ◽  
Author(s):  
Shu Kondo ◽  
Matthew Booker ◽  
Norbert Perrimon
Keyword(s):  
Cell Culture ◽  
Drosophila Melanogaster ◽  
Large Scale ◽  
Transgenic Animals ◽  
Selection Marker ◽  
Bacterial Artificial Chromosomes ◽  
Loss Of Function ◽  
Artificial Chromosomes ◽  
Target Effects

RNAi-mediated gene knockdown in Drosophila melanogaster is a powerful method to analyze loss-of-function phenotypes both in cell culture and in vivo. However, it has also become clear that false positives caused by off-target effects are prevalent, requiring careful validation of RNAi-induced phenotypes. The most rigorous proof that an RNAi-induced phenotype is due to loss of its intended target is to rescue the phenotype by a transgene impervious to RNAi. For large-scale validations in the mouse and Caenorhabditis elegans, this has been accomplished by using bacterial artificial chromosomes (BACs) of related species. However, in Drosophila, this approach is not feasible because transformation of large BACs is inefficient. We have therefore developed a general RNAi rescue approach for Drosophila that employs Cre/loxP-mediated recombination to rapidly retrofit existing fosmid clones into rescue constructs. Retrofitted fosmid clones carry a selection marker and a phiC31 attB site, which facilitates the production of transgenic animals. Here, we describe our approach and demonstrate proof-of-principle experiments showing that D. pseudoobscura fosmids can successfully rescue RNAi-induced phenotypes in D. melanogaster, both in cell culture and in vivo. Altogether, the tools and method that we have developed provide a gold standard for validation of Drosophila RNAi experiments.

scholarly journals Comparative Genomics ofH. pyloriand Non-PyloriHelicobacterSpecies to Identify New Regions Associated with Its Pathogenicity and Adaptability

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
De-Min Cao ◽  
Qun-Feng Lu ◽  
Song-Bo Li ◽  
Ju-Ping Wang ◽  
Yu-Li Chen ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Functional Annotation ◽  
Human Population ◽  
Large Scale ◽  
Bacterial Species ◽  
Human Beings ◽  
Gram Negative ◽  
Protein Protein Interaction ◽  
H Pylori ◽  
Cooperation Relationship

The genusHelicobacteris a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species.Helicobacter pylori(H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings ofH. pylorithat are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representativeH. pyloriand 24 non-pylori Helicobactergenomes. There were 1173 conserved protein families ofH. pyloriand 673 of all 99Helicobactergenus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of theH. pyloribut lacked in non-pylori Helicobacterspecies. The operons, genes, and sRNAs within theH. pyloriunique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.

scholarly journals Expression of heat shock protein 70 is insufficient to extend Drosophila melanogaster longevity

2019 ◽  
Author(s):  
Chengfeng Xiao ◽  
Danna Hull ◽  
Shuang Qiu ◽  
Joanna Yeung ◽  
Jie Zheng ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Stress Resistance ◽  
Heat Shock Protein 70 ◽  
Biological Effect ◽  
Hsp70 Expression ◽  
Gene Encoding ◽  
Shock Proteins

AbstractIt has been known for over 20 years that Drosophila melanogaster flies with twelve additional copies of the hsp70 gene encoding the 70 kDa heat shock protein lives longer after a non-lethal heat treatment. Since the heat treatment also induces the expression of additional heat shock proteins, the biological effect can be due either to HSP70 acting alone or in combination. This study used the UAS/GAL4 system to determine whether hsp70 is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation of Hsp70 using RNAi did not affect longevity.

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