Rare transposable elements challenge the prevailing view of transposition dynamics in plants

Stritt, Christoph; Thieme, Michael; Roulin, Anne

doi:10.1002/ajb2.1709

Cited by 13 publications

(16 citation statements)

References 26 publications

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“…Most Alex1 and Alex3 insertion sites were localized in genic regions, consistent with the general characteristics of the Ale lineage (Wicker & Keller, 2007). Novel insertions of Alex1 and Alex3 were also positioned near genes, which possibly is one of the constituents of the adaptive mechanism allowing Ale elements to persist in low copy numbers, probably combined with self-regulation and the reduced length of internal repeats, as proposed by Stritt et al (2021). Active LTR-RTs usually represent stress-activated low-copy-number families, such as Tos17 (Hirochika et al, 1996a), Lullaby (Picault et al, 2009) and HUO in rice (Peng et al, 2019), ONSEN, ATPG and ATCOPIA93/Evade in Arabidopsis (Ito et al, 2011;Lee et al, 2020;Mirouze et al, 2009;Tsukahara et al, 2009), and Tnt1 and Tto1 in tobacco (Hirochika et al, 1996b;Pouteau et al, 1991).…”

Section: Ltr-trs Active In Carrot Callus Culturessupporting

confidence: 79%

“…Stritt et al. (2020, 2021) suggested that similar characteristics of Ale and Alesia lineages in other species indeed reflected their evolutionary strategy to persist at low copy numbers.…”

Section: Discussionmentioning

confidence: 99%

“…Taking into account the estimated age and number of copies, Wicker & Keller (2007) proposed three patterns of activity of Copia elements, reflecting: (i) short periods of intense activity; (ii) permanent activity over longer periods, but at a lower level; and (iii) moderate activity over long time periods, possibly spanning 1–2 Myr. However, the question of how LTR‐RTs evolved to adopt different strategies for their survival in the host genome and which strategy is more beneficial for both the TE and the host remains open (Stritt et al., 2021).…”

Section: Discussionmentioning

confidence: 99%

“…We speculate that they have been continuously active at a low level, preserving the survival of the lineage with a minimal impact on the integrity of the host genome. Stritt et al (2020Stritt et al ( , 2021 suggested that similar characteristics of Ale and Alesia lineages in other species indeed reflected their evolutionary strategy to persist at low copy numbers.…”

Section: Ltr-rt Landscape In the Carrot Genomementioning

confidence: 99%

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Diverse and mobile:eccDNA‐based identification of carrot low‐copy‐numberLTRretrotransposons active in callus cultures

et al. 2022

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Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copynumber subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.

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Section: Ltr-trs Active In Carrot Callus Culturessupporting

confidence: 79%

“…Stritt et al. (2020, 2021) suggested that similar characteristics of Ale and Alesia lineages in other species indeed reflected their evolutionary strategy to persist at low copy numbers.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Ltr-rt Landscape In the Carrot Genomementioning

confidence: 99%

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Diverse and mobile:eccDNA‐based identification of carrot low‐copy‐numberLTRretrotransposons active in callus cultures

et al. 2022

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“…It also raises several questions about how high TE copy number can be achieved without resulting in host population extinction. Dual survival, in our model, was predominantly characterized by low copy number, and, in natural populations, many TE families exhibit single or low copy numbers as well (Stitzer et al 2021; Stritt et al 2021). Extinction eliminates both the host population and the TE family.…”

Section: Discussionmentioning

confidence: 94%

Critical Role of Insertion Preference for Invasion Trajectory of Transposons

Munasinghe

Springer

Brandvain

2022

Preprint

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Transposable elements (TEs) are mobile DNA sequences that have been highly successful at invading eukaryotic genomes. It is unclear how TE families reach high copy number given the expectation that some novel insertions will be deleterious. It has been hypothesized that TE families may evolve to target and insert into specific DNA sequences to adjust the underlying distribution of fitness effects for new insertions. Preferentially inserting into neutral sites could minimize the cumulative deleterious load of a TE family, allowing the mean TE copy number to increase with less risk for host population extinction. To test this hypothesis, we constructed simulations to explore how the transposition probability and insertion preference of a TE family influence the evolution of mean TE copy number and host population size, allowing for extinction. We find that extinction is most common in our simulations under high transposition probabilities, but, as we reduce transposition rates, the risk of extinction persists while the preference for neutral insertion sites is high. In the absence of mechanisms that regulate TE transposition, a preference for neutral insertion sites is not protective and, in fact, actively accelerates both an increase in TE copy number and the time to population extinction.

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