The Impact of Transposable Elements in Genome Evolution and Genetic Instability and Their Implications in Various Diseases

Ayarpadikannan, Selvam; Kim, Heui‐Soo

doi:10.5808/gi.2014.12.3.98

Cited by 122 publications

(101 citation statements)

References 77 publications

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“…However, if lineage-specific rates of extinction would explain these results, lineages with high rates of extinction must have fewer TEs. This would be highly unexpected because bursts of TE activity most commonly cause genomic instabilities [71] and hence loss of fitness [72]. Thus, although more data within and across species would be necessary to rule out extinction as a contributor to the observed patterns, the results are consistent with the main prediction of the hypothesis that TE activity promotes speciation [9,10].…”

Section: Discussionsupporting

confidence: 79%

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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Section: Discussionsupporting

confidence: 79%

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

Feiner

2016

Proc. R. Soc. B.

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“…RIP may have also acted on some precise parts of the G + C/A + Tequilibrated regions as RIP indices were increasing concomitantly with an increase in A + T content notably in the promoter regions of the Bcbot4 gene. Even if most of the TEs detected in fungal genomes are inactive, they probably had a great impact on gene function and genome structure during genome evolution (Kazazian, 2004;Ayarpadikannan and Kim, 2014). As repeated sequences, they might allow genomic rearrangements by homologous recombination.…”

Section: The Bot Gene Cluster Is In a Genomic Locus With A Bipartite mentioning

confidence: 99%

The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)2Cys6 transcription factor BcBot6

Porquier¹,

Morgant²,

Moraga³

et al. 2016

Fungal Genetics and Biology

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a b s t r a c tBotrydial (BOT) is a non-host specific phytotoxin produced by the polyphagous phytopathogenic fungus Botrytis cinerea. The genomic region of the BOT biosynthetic gene cluster was investigated and revealed two additional genes named Bcbot6 and Bcbot7. Analysis revealed that the G + C/A + T-equilibrated regions that contain the Bcbot genes alternate with A + T-rich regions made of relics of transposable elements that have undergone repeat-induced point mutations (RIP). Furthermore, BcBot6, a Zn(II) 2 Cys 6 putative transcription factor was identified as a nuclear protein and the major positive regulator of BOT biosynthesis. In addition, the phenotype of the DBcbot6 mutant indicated that BcBot6 and therefore BOT are dispensable for the development, pathogenicity and response to abiotic stresses in the B. cinerea strain B05.10. Finally, our data revealed that B. pseudocinerea, that is also polyphagous and lives in sympatry with B. cinerea, lacks the ability to produce BOT. Identification of BcBot6 as the major regulator of BOT synthesis is the first step towards a comprehensive understanding of the complete regulation network of BOT synthesis and of its ecological role in the B. cinerea life cycle.

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“…Only a few TEs are currently active. However, TEs are thought to have greatly impacted gene function and genome structure during genome evolution (29,30). TEs can be broadly categorized into two major groups, retrotransposons and DNA transposons (31).…”

mentioning

confidence: 99%

A Novel Type Pathway-Specific Regulator and Dynamic Genome Environments of a Solanapyrone Biosynthesis Gene Cluster in the Fungus Ascochyta rabiei

et al. 2015

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c Secondary metabolite genes are often clustered together and situated in particular genomic regions, like the subtelomere, that can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full-genome sequencing of the ascomycete Ascochyta rabiei revealed a solanapyrone biosynthesis gene cluster embedded in an AT-rich region proximal to a telomere end and surrounded by Tc1/Mariner-type transposable elements. The highly AT-rich environment of the solanapyrone cluster is likely the product of repeat-induced point mutations. Several secondary metabolism-related genes were found in the flanking regions of the solanapyrone cluster. Although the solanapyrone cluster appears to be resistant to repeat-induced point mutations, a P450 monooxygenase gene adjacent to the cluster has been degraded by such mutations. Among the six solanapyrone cluster genes (sol1 to sol6), sol4 encodes a novel type of Zn(II)2Cys6 zinc cluster transcription factor. Deletion of sol4 resulted in the complete loss of solanapyrone production but did not compromise growth, sporulation, or virulence. Gene expression studies with the sol4 deletion and sol4-overexpressing mutants delimited the boundaries of the solanapyrone gene cluster and revealed that sol4 is likely a specific regulator of solanapyrone biosynthesis and appears to be necessary and sufficient for induction of the solanapyrone cluster genes. Despite the dynamic surrounding genomic regions, the solanapyrone gene cluster has maintained its integrity, suggesting important roles of solanapyrones in fungal biology.T he subtelomere, the region upstream of the telomere on a linear chromosome, is characterized by richness in repetitive sequences and frequent chromosomal rearrangement and lacks synteny among closely related species and even within the same species in fungi (1-4). Subtelomeric regions are also enriched with duplicate, translocated, and horizontally transferred genes and thought to be evolutionarily labile and important for niche adaptation (2, 5, 6). These plastic chromosomal regions often include contingency genes, such as genes involved in membrane transport (2, 6), nutrient assimilation (2, 7), anaerobiosis (8), and virulence (1, 9, 10). Secondary metabolite (SM) gene clusters also exhibit a subtelomeric bias (11)(12)(13)(14).In fungi, SMs play diverse roles in host and niche specialization, serving as virulence factors, antibiotics, and metal ionchelating agents (15, 16). Solanapyrones are polyketide-derived SMs that were originally found in the plant-pathogenic fungi Alternaria solani and Ascochyta rabiei (17, 18), as well as in some other ascomycetous fungi occupying different ecological niches (19-21). The fact that solanapyrones are produced by distantly related species like Nigrospora (Sordariomycetes) but not by closely related species of Ascochyta or Alternaria (Dothideomycetes) suggests the acquisition of the entire gene cluster by horizontal gene transfer (HGT) events. Recently, th...

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The Impact of Transposable Elements in Genome Evolution and Genetic Instability and Their Implications in Various Diseases

Cited by 122 publications

References 77 publications

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)2Cys6 transcription factor BcBot6

A Novel Type Pathway-Specific Regulator and Dynamic Genome Environments of a Solanapyrone Biosynthesis Gene Cluster in the Fungus Ascochyta rabiei

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