The population genetic test Tajima's <i>D</i> identifies genes encoding pathogen‐associated molecular patterns and other virulence‐related genes in <i>Ralstonia solanacearum</i>

Eckshtain‐Levi, Noam; Weisberg, Alexandra J.; Vinatzer, Boris A.

doi:10.1111/mpp.12688

Cited by 22 publications

(16 citation statements)

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“…To compare the previously simulated and observed data based on summary statistics, we used the ape [100] and pegas [101] libraries in R to estimate the number of polymorphic sites and the Tajima's D based on the entire genomes. Tajima's D is commonly used to estimate demographic changes in populations [102,103]. Also, we obtained 1000 sliding windows frames to estimate the Tajima's D along the genomes, as well as the mean and standard deviation of Tajima's D. Tajima's D, π, and Watterson's theta (θw) were estimated for each clade as well as for Sub-clades A, B and G. Since Clades I and VI had three sequences and it was not possible to obtain Tajima's D, we did 1000 replicates in which we subsampled with replacement 10 sequences.…”

Section: Effective Population Size Estimationmentioning

confidence: 99%

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

et al. 2020

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Background: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (N e), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. Results: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high N e estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pangenome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.

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Section: Effective Population Size Estimationmentioning

confidence: 99%

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

et al. 2020

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“…In silico or experimental evolution is another strategy used to screen pathogenicity genes in R. solanacearum . Forty-nine genes in 37 R. solanacearum genomes were identified as nonneutrally evolving and maybe virulence related using Tajima’s D population genetic test ( 13 ). The multihost experimental evolution of selected independent mutations in the regulatory gene efpR revealed that it is a determinant conditioning host adaptation of R. solanacearum ( 14 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Ralstonia solanacearum Genes Required for Survival in Tomato Plants

Liang

et al. 2021

mSystems

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“…To compare the previously simulated and observed data based on summary statistics, we used the ape [98] and pegas [99] libraries in R to estimate the number of polymorphic sites and the Tajima’s D based on the entire genomes. Tajima’s D is commonly used to estimate demographic changes in populations [100, 101]. Also, we obtained 1,000 sliding windows frames to estimate the Tajima’s D along the genomes, as well as the mean and standard deviation of Tajima’s D .…”

Section: Methodsmentioning

confidence: 99%

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Vázquez-Rosas-Landa

Ponce-Soto

Aguirre‐Liguori

et al. 2019

Preprint

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323 words). 27 Background: In bacteria, pan-genomes are the result of the evolutionary "tug of 28 war" between selection and horizontal gene transfer (HGT). High rates of HGT 29 increase the genetic pool and the effective population size, resulting in open pan-30 genomes. In contrast, selective pressures can lead to local adaptation by purging 31 the variation introduced by HGT, resulting in closed pan-genomes and clonal 32 lineages. In this study, we explored both hypotheses elucidating the pan-genome 33 of Vibrionaceae isolates after a perturbation event in the endangered oasis of 34 Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the 35 environments in their genomes.36Results: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two 37 of them did not showed any close reference strain in databases. Five of the 38 lineages showed closed pan-genomes and were associated to either water or 39 sediment environment; their high effective population size (Ne) estimates suggest 40 that these lineages are not from a recent origin. The only clade with an open pan-41 genome was found in both environments and was formed by ten genetic groups 42 with low Ne, suggesting a recent origin. The recombination and mutation estimators 43 (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae 44 estimations; however, we identified 367 gene families with signals of positive 45 selection, most of them found in the core genome; suggesting that despite 46 recombination, natural selection moves the Vibrionaceae CCB lineages to local 47 adaptation purging the genomes and keeping closed pan-genome patterns. 48 Moreover, we identify 598 SNPs associated with an unstructured environment; 49 some of the genes under this SNPs were related to sodium transport. 50 Conclusions: Different lines of evidence suggest that the sampled Vibrionaceae, 51 are part of the rare biosphere usually living under famine conditions. Two of these 52 lineages were reported by the first time. Most Vibrionaceae lineages of CCB are 53 adapted to their microhabitats rather than to the sampled environments. This 54 pattern of adaptation agrees with the association of closed pan-genomes and local 55 adaptation. 56 57 3Comparative genomics analyses have shown a wide range of genomic 78 variation within bacteria from different phylogenetic groups [1][2][3]. This variation 79 range has been explained in part by the wide ecological niche occupied by different 80 bacterial groups [4][5][6][7][8]. Bacterial genomes, in contrast to eukaryotic genomes, 81 usually maintain constant genome sizes [9, 10], suggesting that while horizontal 82 gene transfer (HGT) increases the genome size by adding new genes, selection 83 maintains the genome size by removing deleterious, non-functional or non-useful 84 genes [11][12][13]. Therefore, bacteria can present very different genomic 85 compositions even within a species, with HGT creating a flexible genome and 86 natural selection purging or maintaining it [10, 14]. 87...

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The population genetic test Tajima's D identifies genes encoding pathogen‐associated molecular patterns and other virulence‐related genes in Ralstonia solanacearum

Cited by 22 publications

References 44 publications

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Genome-Wide Identification of Ralstonia solanacearum Genes Required for Survival in Tomato Plants

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

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