A novel web-based TinT application and the chronology of the Primate Alu retroposon activity

Churakov, Gennady; Grundmann, Norbert; Kuritzin, Andrej; Brosius, Jürgen; Makałowski, Wojciech; Schmitz, Jürgen

doi:10.1186/1471-2148-10-376

Cited by 47 publications

(57 citation statements)

References 26 publications

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“…Our analysis now provides overwhelming, conflict-free support at the genome-wide level for the haplorrhine hypothesis and a clear rejection of both the prosimian monophyly and tarsier-first hypotheses, as suggested by previous data7141516171819. The previous retroposon insertion data supporting the Haplorrhini hypothesis7 was likely biased by screening only human genome data and a clear rejection of the prosimian monophyly and tarsiers-first hypotheses were lacking; both of these limitations have now been overcome.…”

Section: Discussionmentioning

confidence: 52%

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Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

Hartig

Churakov

Warren³

et al. 2013

Sci Rep

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One of the most disputed issues in primate evolution and thus of our own primate roots, is the phylogenetic position of the Southeast Asian tarsier. While much molecular data indicate a basal place in the primate tree shared with strepsirrhines (prosimian monophyly hypothesis), data also exist supporting either an earlier divergence in primates (tarsier-first hypothesis) or a close relationship with anthropoid primates (Haplorrhini hypothesis). The use of retroposon insertions embedded in the Tarsius genome afforded us the unique opportunity to directly test all three hypotheses via three pairwise genome alignments. From millions of retroposons, we found 104 perfect orthologous insertions in both tarsiers and anthropoids to the exclusion of strepsirrhines, providing conflict-free evidence for the Haplorrhini hypothesis, and none supporting either of the other two positions. Thus, tarsiers are clearly the sister group to anthropoids in the clade Haplorrhini.

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Section: Discussionmentioning

confidence: 52%

“…Churakov et al19 found hundred thousand Alu Jb elements well distributed in the genomes of tarsiers and anthropoids but absent in strepsirrhines.…”

mentioning

confidence: 99%

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

Hartig

Churakov

Warren³

et al. 2013

Sci Rep

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“…For LTR retrotransposons, sequence divergence within individual element copies between the two LTRs has been proposed as an internal indicator of age, as these are usually identical to one another upon insertion (65, 109). In some organisms, one can also qualitatively corroborate relative ages of transposons by studying nested insertions, which are transposons inserted into preexisting transposons (20, 41). …”

Section: How Do We Know An Element Is Active?mentioning

confidence: 97%

Active Transposition in Genomes

2012

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Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes.

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“…Many such TE in TE insertions are found in present-day genomes. For example, Alu retroposon activity can be investigated using a computational algorithm called TinT [66]. Moreover, the BLAST search showed only sequences and amplicons with the inserted Alu 9.…”

Section: Alu Duplex Pcrsmentioning

confidence: 99%

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

Haß¹,

Hummel²,

Piskurek³

2017

Diversity

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Abstract:The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400-500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

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A novel web-based TinT application and the chronology of the Primate Alu retroposon activity

Cited by 47 publications

References 26 publications

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

Active Transposition in Genomes

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

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