Rethinking the “gypsy” retrotransposon: A roadmap for community-driven reconsideration of problematic gene names

Wei, Kevin H.-C.; Aldaimalani, Reema; Mai, Dat; Zinshteyn, Daniel; PRV, Satyaki; Blumenstiel, Justin P.; Kelleher, Erin S.; Brooks, Ethel

doi:10.31219/osf.io/fma57

Cited by 20 publications

(12 citation statements)

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“…The name we used throughout the paper for each element is shown, along with its original name in RepBase ( 21) fngrep version 25.10, the class, and the family each element belongs to. We adopted a naming convention for Ty3 (formerly Gypsy) elements, where any "GY" in the RepBase name was replaced with "Ty3" in order to use a non-discriminatory and respectful naming scheme (56). Grasshopper is the original name of the GYPSY1 RepBase element, so it is used instead (57).…”

Section: Effector Annotation and Analysismentioning

confidence: 99%

Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes

Nakamoto

Joubert

Krasileva

2022

Preprint

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Fungal plant pathogens pose a significant threat to biodiversity and food security worldwide. This threat is aggravated by their rapidly evolving genomes that adapt to evade host plant defenses, reducing the efficacy of deployed resistant crops.Magnaporthe oryzaeinfects rice, wheat, and many other grasses, resulting in significant crop losses each year. Transposable elements (TEs) are hypothesized to be involved in the evolution and rapid adaptation ofM. oryzae. However, there is still much to understand about how these elements behave in differentM. oryzaehost-specific lineages. In this study, we completed the annotation and phylogenetic classification of TEs in five lineages ofM. oryzae. We identified differences in TE content between these lineages, and showed that recent lineage-specific expansions of certain TEs have contributed to greater TE content in rice-infecting andSetaria-infecting lineages. We reconstructed the histories of LTR-retrotransposon expansions and found them to have experienced complex dynamics, where some were caused by the proliferation of one element, while others consisted of multiple elements from an older population of TEs that proliferated in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice and wheatM. oryzaelineages, and a region showing evidence of recombination between those lineages, which could have facilitated such a transfer. These results point towards key differences in TE dynamics, evolutionary history, and adaptive potential between the rice-and-Setaria-infecting and the wheat-Lolium-and-Eleusine-infecting lineage groups.

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Section: Effector Annotation and Analysismentioning

confidence: 99%

Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes

Nakamoto

Joubert

Krasileva

2022

Preprint

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“…At the whole-genome scale, Microbotryum lychnidis-dioicae carries long-terminal repeat (LTR) retroelements from the Copia and Ty3 (also known as Gypsy, but see Wei et al, 2022) superfamilies (Hood et al, 2005;Amselem et al, 2015) as well as, to a lesser extent, Helitron DNA transposons, i.e., rolling-circle replicating TEs (Kapitonov & Jurka, 2001). In the Microbotryum species parasitizing Dianthus carthusianorum, a burst of Ty3 retroelements has caused a massive accumulation of this element in a short period of time, in spite of RIP-like activity (Horns et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…At the whole-genome scale, Microbotryum lychnidis-dioicae carries long-terminal repeat (LTR) retroelements from the Copia and Ty3 (also known as Gypsy , but see Wei et al ., 2022) superfamilies (Hood et al ., 2005; Amselem et al ., 2015) as well as, to a lesser extent, Helitron DNA transposons, i.e. , rolling-circle replicating TEs (Kapitonov & Jurka, 2001).…”

Section: Introductionmentioning

confidence: 99%

Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi

Duhamel

Hood

Vega

et al. 2022

Preprint

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Background: Transposable element (TE) activity is generally deleterious to the host fitness, so that genomes often evolve TE control mechanisms, and TE copies are purged by recombination and selection. In the absence of recombination, the number of TE insertions usually increases, but the dynamics of such TE accumulations is unknown. Results: In this study, we investigated the tempo of TE accumulation in the non-recombining genomic regions of 15 Microbotryum species, leveraging on a unique dataset of 21 independent evolutionary strata of recombination cessation of different ages in closely related species. We show that TEs have rapidly accumulated following recombination suppression but that the TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 MY following recombination suppression. The same superfamilies repeatedly expanded in independently evolved non-recombining regions, and in particular Helitrons, despite being scarce before recombination suppression. TEs from the most abundant elements, i.e., Copia and Ty3/Gypsy retrotransposon superfamilies, have also expanded independently in the different non-recombining regions. Copia and Ty3 retrotransposons have accumulated through bursts affecting both the non-recombining regions of the mating-type chromosomes and autosomes at the same time, which supports the TE reservoir hypothesis, i.e., that the TEs accumulated in non-recombining regions have a genome-wide impact by transposing to recombining regions. Conclusion: This study sheds light on the genome-wide consequences of the accumulation of TEs in non-recombining regions, thus improving our knowledge on genome evolution.

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“…5E and S18). In particular, the DEG ~ Field:Population group was highly enriched for Ty3 (also known as Gypsy , Wei et al, 2022) retrotransposons in the J3 population ( P = 1.3 × 10 −6 , Fisher’s exact test). We also found that non-CG DMGs were TE insertion hotspots (Fig 5E), suggesting that many of the methylation changes may have arisen as a result of TE methylation spreading to genic regions.…”

Section: Resultsmentioning

confidence: 99%

Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential ofArabidopsis lyrata

Hämälä

Ning

Kuittinen

et al. 2022

Preprint

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Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environment-induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. The environmentally responsive genes evolve under strong selective constraint — the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to genetically variable environment-responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor and excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. In sum, although our results suggest that strong evolutionary constraint at environmentally responsive genes may limit the species' adaptive potential, plastic responses at TEs could rapidly create novel heritable variation that is primed towards environmental adaptation.

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Rethinking the “gypsy” retrotransposon: A roadmap for community-driven reconsideration of problematic gene names

Cited by 20 publications

References 0 publications

Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes

Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes

Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi

Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential ofArabidopsis lyrata

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