Genomic evolution of the marine bacterium Phaeobacter inhibens during biofilm growth

2021 ◽  
Author(s):  
Marwan E. Majzoub ◽  
Kerensa McElroy ◽  
Michael Maczka ◽  
Stefan Schulz ◽  
Torsten Thomas ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Phenotypic Variation ◽  
Phenotypic Diversity ◽  
Survival Strategies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Biofilm Growth ◽  
Tropodithietic Acid ◽  
Biofilm Dispersal ◽  
Phaeobacter Inhibens

P. inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded, secondary metabolite tropodithietic acid (TDA). P. inhibens 2.10 biofilms produce phenotypic variants with reduced competitiveness compared to the wild-type. In the present study, we used longitudinal, genome-wide deep sequencing to uncover the genetic foundation that contributes to the emergent phenotypic diversity in P. inhibens 2.10 biofilm dispersants. Our results show that phenotypic variation is not due to the loss of plasmid that encodes the genes for the TDA synthesis, but instead show that P. inhibens 2.10 biofilm populations become rapidly enriched in single nucleotide variations in genes involved in the synthesis of TDA. While variants in genes previously linked to other phenotypes, such as lipopolysaccharide production (i.e. rfbA ) and celluar persistence (i.e. metG ), also appear to be selected for during biofilm dispersal, the number and consistency of variations found for genes involved in TDA production suggest that this metabolite imposes a burden for P. inhibens 2.10 cells. Our results indicate a strong selection pressure for the loss of TDA in mono-species biofilm populations and provide insight into how competition (or lack thereof) in biofilms might shape genome evolution in bacteria. Importance Statement Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal cells often display stable and heritable variants from the parental biofilm. Phaeobacter inhibens is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a non-competitive phenotype. This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens , little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens , including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it reveals how the biofilm-lifestyle might shape genome evolution in a cosmopolitan bacterium.

scholarly journals Proprioceptive Genes as a Source of Genetic Variation Underlying Robustness for Flight Performance in Drosophila

2021 ◽  
Author(s):  
Adam N Spierer ◽  
David M. Rand
Keyword(s):  
Phenotypic Variation ◽  
Flight Performance ◽  
Nucleotide Polymorphisms ◽  
Genetic Modifiers ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Genetic Components ◽  
Trait Variance ◽  
External Stimuli ◽  
Drosophila Genetic Reference Panel

A central challenge of quantitative genetics is partitioning phenotypic variation into genetic and non-genetic components. These non-genetic components are usually interpreted as environmental effects; however, variation between genetically identical individuals in a common environment can still exhibit phenotypic variation. A trait's resistance to variation is called robustness, though the genetics underlying it are poorly understood. Accordingly, we performed an association study on a previously studied, whole organism trait: robustness for flight performance. Using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, we surveyed variation across single nucleotide polymorphisms, whole genes, and epistatic interactions to find genetic modifiers robustness for flight performance. There was an abundance of genes involved in the development of sensory organs and processing of external stimuli, supporting previous work that processing proprioceptive cues is important for affecting variation in flight performance. Additionally, we tested insertional mutants for their effect on robustness using candidate genes found to modify flight performance. These results suggest several genes involved in modulating a trait mean are also important for affecting trait variance, or robustness, as well.

scholarly journals A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

2020 ◽  
Vol 12 (4) ◽  
pp. 345-357 ◽  
Author(s):  
Niko Popitsch ◽  
Christian D Huber ◽  
Ilana Buchumenski ◽  
Eli Eisenberg ◽  
Michael Jantsch ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Single Nucleotide Polymorphisms ◽  
Genome Evolution ◽  
Rna Editing ◽  
Adaptive Evolution ◽  
Population Genomics ◽  
Common Type ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cellular Machinery

Abstract In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

scholarly journals Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pornpen Tantivitayakul ◽  
Wuthiwat Ruangchai ◽  
Tada Juthayothin ◽  
Nat Smittipat ◽  
Areeya Disratthakit ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Phenotypic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

2016 ◽  
Author(s):  
Daniel C. Jeffares ◽  
Clemency Jolly ◽  
Mimoza Hoti ◽  
Doug Speed ◽  
Liam Shaw ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reproductive Isolation ◽  
Cell Shape ◽  
Quantitative Traits ◽  
Phenotypic Diversity ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Sugar Utilization

AbstractLarge structural variations (SVs) in the genome are harder to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. Here we analyze the effects of SVs on gene expression, quantitative traits, and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalog of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) frequently segregate within closely related clonal populations, are weakly linked to single nucleotide polymorphisms (SNPs), and show other genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits such as cell shape, cell growth under diverse conditions, sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.

scholarly journals Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Minqiang Tang ◽  
Juanling Li ◽  
Xu Hu ◽  
Lu Sun ◽  
MMU Helal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Brassica Napus ◽  
Genome Evolution ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expression Levels ◽  
Dna And Rna ◽  
Polyploid Genome ◽  
Gene Expression Levels

The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.

scholarly journals Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars

2021 ◽  
Author(s):  
Dominique D A Pincot ◽  
Mirko Ledda ◽  
Mitchell J Feldmann ◽  
Michael A Hardigan ◽  
Thomas J Poorten ◽  
...  
Keyword(s):  
Overlapping Generations ◽  
Phenotypic Diversity ◽  
Allelic Diversity ◽  
Nucleotide Polymorphisms ◽  
Fragaria Ananassa ◽  
Single Nucleotide ◽  
Day Range ◽  
History Of ◽  
Cycle Lengths ◽  
Shed Light

Abstract The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three century long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying exclusion analysis to array-genotyped single nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the last 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation) but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations and shed light on forces that have shaped phenotypic diversity in F. × ananassa.

Functional markers for selection of potyvirus resistance alleles at the pvr2-eIF4E locus in pepper using tetra-primer ARMS–PCR

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 767-771 ◽  
Author(s):  
Manuel Rubio ◽  
Carole Caranta ◽  
Alain Palloix
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Phenotypic Variation ◽  
Marker Assisted Selection ◽  
Functional Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Arms Pcr ◽  
Codominant Markers ◽  
The World ◽  
Selection Of

Functional markers targeted on single nucleotide polymorphisms (SNPs) responsible for phenotypic variation constitute optimal tools for marker-assisted selection (MAS) of resistance alleles with different specificities. Here, we used the tetra-primer ARMS–PCR procedure to assay SNP signatures of four distinct alleles at the pvr2-eIF4E locus, which controls pepper resistance to several potyviruses. These simple, economical, and codominant markers open the way for MAS of pepper genotypes resistant to the potyviral strains and species that are prevalent in distinct cultivation areas across the world.

scholarly journals Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars

2020 ◽  
Author(s):  
Dominique D.A. Pincot ◽  
Mirko Ledda ◽  
Mitchell J. Feldmann ◽  
Michael A. Hardigan ◽  
Thomas J. Poorten ◽  
...  
Keyword(s):  
Overlapping Generations ◽  
Phenotypic Diversity ◽  
Allelic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Day Range ◽  
History Of ◽  
Cycle Lengths ◽  
Shed Light ◽  
European Populations

ABSTRACTThe widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three century long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying exclusion analysis to array-genotyped single nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the last 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation) but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations and shed light on forces that have shaped phenotypic diversity in F. × ananassa.

scholarly journals Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

2014 ◽  
Author(s):  
Jason G Wallace ◽  
Peter Bradbury ◽  
Nengyi Zhang ◽  
Yves Gibon ◽  
Mark Stitt ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Copy Number Variants ◽  
Natural Populations ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Single Nucleotide ◽  
Gene By Environment Interactions ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Regulatory Functions

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.

scholarly journals Adaptations to new environments in humans: the role of subtle allele frequency shifts

2010 ◽  
Vol 365 (1552) ◽  
pp. 2459-2468 ◽  
Author(s):  
Angela M. Hancock ◽  
Gorka Alkorta-Aranburu ◽  
David B. Witonsky ◽  
Anna Di Rienzo
Keyword(s):  
Phenotypic Diversity ◽  
Human Populations ◽  
Strongly Correlated ◽  
Nucleotide Polymorphisms ◽  
Environmental Correlation ◽  
Single Nucleotide ◽  
Environmental Pressures ◽  
Genome Wide ◽  
Geographically Distributed

Humans show tremendous phenotypic diversity across geographically distributed populations, and much of this diversity undoubtedly results from genetic adaptations to different environmental pressures. The availability of genome-wide genetic variation data from densely sampled populations offers unprecedented opportunities for identifying the loci responsible for these adaptations and for elucidating the genetic architecture of human adaptive traits. Several approaches have been used to detect signals of selection in human populations, and these approaches differ in the assumptions they make about the underlying mode of selection. We contrast the results of approaches based on haplotype structure and differentiation of allele frequencies to those from a method for identifying single nucleotide polymorphisms strongly correlated with environmental variables. Although the first group of approaches tends to detect new beneficial alleles that were driven to high frequencies by selection, the environmental correlation approach has power to identify alleles that experienced small shifts in frequency owing to selection. We suggest that the first group of approaches tends to identify only variants with relatively strong phenotypic effects, whereas the environmental correlation methods can detect variants that make smaller contributions to an adaptive trait.

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