The transposable element profile of the Anolis genome

Tollis, Marc; Boissinot, Stéphane

doi:10.4161/mge.1.2.17733

Cited by 26 publications

(23 citation statements)

References 45 publications

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“…nLTR-RTs have proliferated with great success in eukaryote genomes and they are the main drivers of genome size and structural variation among vertebrate lineages (Lander et al 2001; Furano et al 2004; Tollis and Boissinot 2011). A single type of nLTR-RT known as LINE-1 ( L ong I nterspersed N uclear E lement, L1 hereafter) dominates the human genome (Lander et al 2001), and ancient L1 fossils and their nonautonomous counterparts, including the Alu interspersed repeats, may account for over two-thirds of the human genome (de Koning et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

Tollis

Boissinot

2013

Genome Biology and Evolution

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Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila, applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard (Anolis carolinensis). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis. We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.

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Section: Introductionmentioning

confidence: 99%

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

Tollis

Boissinot

2013

Genome Biology and Evolution

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“…Their diversification into hundreds of species, through interspecific competition and natural selection, has been well documented across the Caribbean islands (Losos 2009). The genome sequence of Anolis carolinensis has in fact already suggested a strong evolutionary dynamism of transposons (Alföldi et al 2011; Tollis and Boissinot 2011). …”

Section: Discussionmentioning

confidence: 99%

Transposons, environmental changes, and heritable induced phenotypic variability

et al. 2014

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The mechanisms of biological evolution have always been, and still are, the subject of intense debate and modeling. One of the main problems is how the genetic variability is produced and maintained in order to make the organisms adaptable to environmental changes and therefore capable of evolving. In recent years, it has been reported that, in flies and plants, mutations in Hsp90 gene are capable to induce, with a low frequency, many different developmental abnormalities depending on the genetic backgrounds. This has suggested that the reduction of Hsp90 amount makes different development pathways more sensitive to hidden genetic variability. This suggestion revitalized a classical debate around the original Waddington hypothesis of canalization and genetic assimilation making Hsp90 the prototype of morphological capacitor. Other data have also suggested a different mechanism that revitalizes another classic debate about the response of genome to physiological and environmental stress put forward by Barbara McClintock. That data demonstrated that Hsp90 is involved in repression of transposon activity by playing a significant role in piwi-interacting RNA (piRNAs)-dependent RNA interference (RNAi) silencing. The important implication is that the fixed phenotypic abnormalities observed in Hsp90 mutants are probably related to de novo induced mutations by transposon activation. In this case, Hsp90 could be considered as a mutator. In the present theoretical paper, we discuss several possible implications about environmental stress, transposon, and evolution offering also a support to the concept of evolvability.

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“…However, this cannot solely explain the patterns of TE abundance within Anolis because it is unlikely that lineages with high rates of speciation also systematically experience more stressful environmental conditions. Although TE density across the genome in the green anole is high relative to many other vertebrates [27], Hox clusters appear to be particularly TE rich. This might be explained by biased TE insertion due to chromatin characteristics (facultative heterochromatin; [80]).…”

Section: Discussionmentioning

confidence: 99%

“…Recent evidence also points towards an important role for TEs in the evolution of the Anolis genome. Firstly, the genome of the green anole, Anolis carolinensis, contains a very high number of relatively young, active elements, in contrast with bird and mammalian genomes that are rich in remnants of old, extinct TEs [27,28]. Thus, proliferation of TEs may have contributed to genomic incompatibilities that enabled formation of distinct species during the adaptive radiation.…”

Section: Introductionmentioning

confidence: 99%

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

Feiner

2016

Proc. R. Soc. B.

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Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.

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The transposable element profile of the Anolis genome

Cited by 26 publications

References 45 publications

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

Transposons, environmental changes, and heritable induced phenotypic variability

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

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