Jumping genes: Genomic ballast or powerhouse of biological diversification

Choudhury, Rimjhim Roy; Parisod, Christian

doi:10.1111/mec.14247

Cited by 7 publications

(3 citation statements)

References 15 publications

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“…Transposable elements have been noted to play a key role in evolution (Oliver & Greene, 2009). TEs have been proposed to contribute to introgression (Choudhury & Parisod, 2017) as well as reproductive isolation and speciation (Naciri & Linder, 2020; Serrato‐Capuchina & Matute, 2018). TEs may also play a possible role in bird diversification (Suh et al., 2018) and in speciation in amniotes (Zeng et al., 2018), mammals (Ricci et al., 2018), and fishes (Volff, 2005).…”

Section: Discussionmentioning

confidence: 99%

Movement of transposable elements contributes to cichlid diversity

et al. 2020

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African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.

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Section: Discussionmentioning

confidence: 99%

Movement of transposable elements contributes to cichlid diversity

et al. 2020

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“…Variation associated with TEs is often ignored because TE‐rich genomic regions are difficult to assemble and annotate in genome drafts (Hoban et al, ; Treangen & Salzberg, ). The genotyping of polymorphic TEs (i.e., presence/absence of TE insertions at specific loci) benefits from the availability of high‐quality TE annotation and, thus, allows for the assessment of their significance (Choudhury & Parisod, ). In contrast to the detection of SNPs, the development of appropriate computational tools to detect polymorphic TEs from current sequence data is still in its infancy.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Rogivue

Choudhury

Zoller

et al. 2019

Molecular Ecology Resources

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Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

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“…The vast majority of new TE insertions are neutral or deleterious, and purifying selection is expected to remove them or favours their silencing [9][10][11]. However, some TE insertions may be advantageous and facilitate adaptation in different environments [6,[12][13][14][15][16][17][18][19][20][21][22]. Such adaptive effects have been previously observed in response to both biotic (e.g., virus infection) and abiotic (e.g., oxidative stress) stress [19,20].…”

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Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species

St.Pierre

Jaquet

Picarle

et al. 2020

Preprint

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BackgroundAdaptation to rapid environmental changes must occur within a short time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and successfully adapted to novel environmental conditions. Here we investigated how invasive and non-invasive populations of D. suzukii deal with an oxidative stress at both the phenotypic and molecular level. We also investigated the impact of transposable element insertions on the differential gene expression between genotypes in response to oxidative stress.ResultsInvasive populations lived longer in the untreated condition than non-invasive Japanese populations. As expected, lifespan was greatly reduced following exposure to paraquat, but this reduction varied among genotypes (a genotype by environment interaction, GEI) with invasive genotypes appearing more affected by exposure than non-invasive genotypes. We also performed transcriptomic sequencing of selected genotypes upon and without paraquat and detected a large number of genes differentially expressed, distinguishing the genotypes in the untreated environment. While a small core set of genes were differentially expressed by all genotypes following paraquat exposure, much of the response of each population was unique. Interestingly, we identified a set of genes presenting genotype by environment interaction (GEI). Many of these differences may reflect signatures of history of past adaptation. Transposable elements (TEs) were not activated after oxidative stress and differentially expressed (DE) genes were significantly depleted of TEs.ConclusionIn the decade since the invasion from the south of Asia, invasive populations of D. suzukii have diverged from populations in the native area regarding their genetic response to oxidative stress. This suggests that such transcriptomic changes could be involved in the rapid adaptation to local environments.

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Jumping genes: Genomic ballast or powerhouse of biological diversification

Cited by 7 publications

References 15 publications

Movement of transposable elements contributes to cichlid diversity

Movement of transposable elements contributes to cichlid diversity

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species

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