scholarly journals A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals

2017 ◽  
Author(s):  
Niko Popitsch ◽  
Christian D. Huber ◽  
Ilana Buchumenski ◽  
Eli Eisenberg ◽  
Michael Jantsch ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genome Evolution ◽  
Rna Editing ◽  
Adaptive Evolution ◽  
Base Pair ◽  
Population Genomics ◽  
Common Type ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cellular Machinery

AbstractIn animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines base-pair 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 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 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 Differences in mate pairings of hatchery and natural origin coho salmon inferred from offspring genotypes

2021 ◽  
Author(s):  
H L Auld ◽  
D P Jacobson ◽  
A C Rhodes ◽  
M A Banks
Keyword(s):  
Mate Choice ◽  
Captive Breeding ◽  
Population Genomics ◽  
Coho Salmon ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Natural Origin ◽  
In Captivity ◽  
Genetic Level

Abstract Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery and natural origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared to natural origin fish at a genetic level. Using genotyping-by-sequencing (GBS), we identify single nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery and natural origin coho salmon (Oncorhynchus kisutch). In both natural origin and hatchery mate pairs, we observed more SNPs with negative assortment, than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.

scholarly journals AURKA rs8173 G>C Polymorphism Decreases Wilms Tumor Risk in Chinese Children

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Tongyi Lu ◽  
Li Li ◽  
Jinhong Zhu ◽  
Jiabin Liu ◽  
Ao Lin ◽  
...  
Keyword(s):  
Haplotype Analysis ◽  
Wilms Tumor ◽  
Clinical Stage ◽  
Common Type ◽  
Chinese Children ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tumor Susceptibility ◽  
Tumor Risk ◽  
Strength Of Association

Wilms tumor is the most common type of renal malignancy in children. Previous studies have demonstrated that single nucleotide polymorphisms (SNPs) in the AURKA gene could predispose to several human malignancies. We recruited 145 cases and 531 cancer-free controls to investigate whether AURKA gene variants modify Wilms tumor susceptibility. Three AURKA SNPs (rs1047972 C>T, rs2273535 T>A, and rs8173 G>C) were genotyped by the Taqman methodology. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of association between AURKA SNPs and Wilms tumor risk. We found that only the rs8173 G>C polymorphism was significantly associated with Wilms tumor risk (GC vs. GG: adjusted OR (AOR) = 0.50, 95% CI = 0.35–0.73, P=0.0002; GC/CC vs. GG: AOR = 0.60, 95% CI = 0.42–0.88, P=0.008). Stratification analysis revealed that rs8173 GC/CC genotypes were associated with Wilms tumor risk among children aged >18 months (AOR = 0.56, 95% CI = 0.34–0.93, P=0.024), male children (AOR = 0.54, 95% CI = 0.33–0.90, P=0.017), and children with clinical stage III + IV diseases (AOR = 0.56, 95% CI = 0.35–0.90, P=0.017). Haplotype analysis indicated that the CAG haplotype was significantly associated with increased Wilms tumor risk. In conclusion, our findings indicated that the AURKA rs8173 G>C polymorphism was associated with decreased Wilms tumor risk in Chinese children.

scholarly journals Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190341 ◽  
Author(s):  
Judit Salces-Ortiz ◽  
Carlos Vargas-Chavez ◽  
Lain Guio ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Organophosphate Insecticide ◽  
Single Nucleotide ◽  
Insecticide Exposure ◽  
Genomic Response

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis -regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

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.

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.

SSCP Analysis of cDNA Markers Provides a Dense Linkage Map of theAedes aegyptiGenome

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 715-726 ◽  
Author(s):  
Ruth E Fulton ◽  
Michael L Salasek ◽  
Nancy M DuTeau ◽  
William C Black
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Linkage Map ◽  
Single Strand Conformation Polymorphism ◽  
Genome Project ◽  
Sscp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
F2 Progeny ◽  
Conformation Polymorphism

AbstractAn intensive linkage map of the yellow fever mosquito, Aedes aegypti, was constructed using single-strand conformation polymorphism (SSCP) analysis of cDNA markers to identify single nucleotide polymorphisms (SNPs). A total of 94 A. aegypti cDNAs were downloaded from GenBank and primers were designed to amplify fragments <500 bp in size. These primer pairs amplified 94 loci, 57 (61%) of which segregated in a single F1 intercross family among 83 F2 progeny. This allowed us to produce a dense linkage map of one marker every 2 cM distributed over a total length of 134 cM. Many A. aegypti cDNAs were highly similar to genes in the Drosophila melanogaster genome project. Comparative linkage analysis revealed areas of synteny between the two species. SNP polymorphisms are abundant in A. aegypti genes and should prove useful in both population genetics and mapping studies.

scholarly journals Differentiating Genomic SNPs Using Allele Depth and Predicted Genotype

2018 ◽  
Author(s):  
Saam Hasan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Rna Editing ◽  
Editing Site ◽  
Biological Processes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide Variants ◽  
Accuracy Rate ◽  
Single Nucleotide

AbstractDifferentiating between genomic SNPs and other types of single nucleotide variants becomes a key issue in research aimed at studying the importance of these variants of a particular type in biological processes. Here we present an R based method for differentiating between genomic single nucleotide polymorphisms (SNPs) and RNA editing sites. We use data from an earlier study of ours and target only the known dbsnp SNPs that we found in our study. Our method involves calculating the ratio of allele depth for ref and alt alleles and comparing that to the predicted genotype. We use the concept that editing levels should be different for each allele and thus should not reflect the ratio predicted by the genotype. The study yielded an accuracy rate ranging from 86 to over 90 percent at successfully predicted dbsnp entries as SNPs. Albeit this is in the absence of known RNA editing site vcf data to compare as a reference.

scholarly journals Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

2016 ◽  
Author(s):  
John E. Pool ◽  
Dylan T. Braun ◽  
Justin B. Lack
Keyword(s):  
Drosophila Melanogaster ◽  
Cold Tolerance ◽  
South African ◽  
Climate Adaptation ◽  
Parallel Evolution ◽  
Frequency Change ◽  
Nucleotide Polymorphisms ◽  
Tropical Africa ◽  
Single Nucleotide ◽  
Cold Adapted

ABSTRACTDrosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we show that elevated cold tolerance has arisen at least three times within this species: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ~4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation.

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