Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains

Clément, Julie; Toulza, Ève; Gautier, Mathieu; Parrinello, Hugues; Roquis, David; Boissier, Jérôme; Rognon, Anne; Moné, Hélène; Mouahid, Gabriel; Buard, Jérǒme; Mitta, Guillaume; Grunau, Christoph

doi:10.1371/journal.pntd.0002591

Cited by 19 publications

(21 citation statements)

References 64 publications

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“…Next generation sequencing (NGS) is popular in transcriptomics because of its ability to generate highly accurate sequencing results. For example, great progress has been made in gene expression profiling (Gould et al, 2013;Huang et al, 2014), microRNA discovery (Huang et al, 2012), and single nucleotide polymorphism identification (Clément et al, 2013) due to NGS. However, we primarily focused on the RNA expression levels in this Big Data.…”

Section: Introductionmentioning

confidence: 99%

Responding to a Zoonotic Emergency with Multi-omics Research:Pentatrichomonas hominisHydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics

Fang

Chien

Huang

et al. 2016

OMICS: A Journal of Integrative Biology

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Pentatrichomonas hominis is an anaerobic flagellated protist that colonizes the large intestine of a number of mammals, including cats, dogs, nonhuman primates, and humans. The wide host range of this organism is alarming and suggests a rising zoonotic emergency. However, knowledge on in-depth biology of this protist is still limited. Similar to the human pathogen, Trichomonas vaginalis, P. hominis possesses hydrogenosomes instead of mitochondria. Studies in T. vaginalis indicated that hydrogenosome is essential for cell survival and associated with numerous pivotal biological functions, including drug resistance. To further decipher the biology of this important organelle, we undertook proteomic research in P. hominis hydrogenosomes. Lacking a decoded P. hominis genome, we utilized an RNA sequencing (RNA-seq) data set generated from P. hominis axenic culture as the reference for proteome analysis. Using this in-house reference data set and mass spectrometry (MS), we identified 442 putative hydrogenosomal proteins. Interestingly, the composition of the P. hominis hydrogenosomal proteins is very similar to that of T. vaginalis, but proteins such as Hmp36, Pam16, Pam18, and Isd11 are absent based on both MS and the RNA-seq. Our data underscore that P. hominis expresses different homologs of multiple gene families from T. vaginalis. To the best of our knowledge, we present here the first hydrogenosome proteome in a protist other than T. vaginalis that offers crucial new scholarship for global health, therapeutics, diagnostics, and veterinary medicine research. In addition, the research strategy used here using RNA sequencing and proteomics might inform future multi-omics research in other understudied organisms without decoded genomes.

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Section: Introductionmentioning

confidence: 99%

Responding to a Zoonotic Emergency with Multi-omics Research:Pentatrichomonas hominisHydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics

Fang

Chien

Huang

et al. 2016

OMICS: A Journal of Integrative Biology

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“…Pool‐Seq is now commonly adopted in many studies, including population genomics studies (Clément et al., ; Ferretti et al., ; Fischer et al., ; Rubin et al., , ), because it provides more accurate estimation of allele frequencies, at reduced sequencing and library preparation costs (Futschik & Schlötterer, ; Gautier et al., ; Rellstab, Zoller, Tedder, Gugerli, & Fischer, ; Schlötterer et al., ; Zhu et al., ). Here, we emphasize the interest of using such an approach for population genomic studies of nonclonal microorganisms, as it allowed to increase the amount of DNA while keeping information about allele frequencies.…”

Section: Discussionmentioning

confidence: 99%

“…As the amount of DNA in a single G. pallida individual is very low, pooling individuals from a same lineage was an efficient way to increase the amount of DNA while allowing the accurate estimation of population allele frequencies (e.g., Gautier et al, 2013). To accurately represent the genetic variability of each lineage, we chose to sample individuals from different cysts, rather than different individuals from a same cyst, to constitute the pools.…”

Section: Pool Sequencingmentioning

confidence: 99%

“…Here, we took advantage of the same biological material to perform a high-density genome scan using data from a wholegenome resequencing of pools of individuals (Pool-Seq, Ferretti, EOCHE-BOSY ET AL. -Onsins, & P erez-Enciso, 2013;Futschik & Schl€ otterer, 2010;Gautier et al, 2013;Schl€ otterer, Tobler, Kofler, & Nolte, 2014;Zhu, Bergland, Gonz alez, & Petrov, 2012) and a recent model testing for adaptive differentiation and association to population-specific covariables (BayPass, Gautier, 2015).…”

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confidence: 99%

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Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida

et al. 2017

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Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.

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“…2013), and selective sweeps (e.g., Boitard and Rocha 2013; Clement et al. 2013; Harris et al. 2013; Hubner et al.…”

Section: Introductionmentioning

confidence: 99%

Identifying signatures of sexual selection using genomewide selection components analysis

Flanagan

Jones

2015

Ecology and Evolution

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Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome-wide allele frequencies in adults and offspring were compared using weighted FST values. The average number of outlier peaks (i.e., those with significantly large FST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the FST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome-wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection.

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Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains

Cited by 19 publications

References 64 publications

Responding to a Zoonotic Emergency with Multi-omics Research:Pentatrichomonas hominisHydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics

Responding to a Zoonotic Emergency with Multi-omics Research:Pentatrichomonas hominisHydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida

Identifying signatures of sexual selection using genomewide selection components analysis

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