DrosophilaP transposons of the urochordata Ciona intestinalis

Kimbacher, Stefanie; Gerstl, Ingrid; Velimirov, Branko; Hagemann, Sylvia

doi:10.1007/s00438-009-0453-7

Cited by 9 publications

(9 citation statements)

References 36 publications

(40 reference statements)

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“…Several recent genome based phylogenies inferred from either nuclear or mitochondrial genome data have provided clear-cut evidence for the particularly high rates distinguishing tunicate evolution, as illustrated by the persisting long branches of the group in the reconstructed trees (Bourlat et al 2008;Delsuc et al 2008;Gissi et al 2008;Singh et al 2009). Similar conclusions have been drawn by studies focusing on individual genes such as 18S rRNA (Perez-Portela et al 2009;Yokobori et al 2006), cox1 (Turon and Lopez-Legentil 2004), Huntingtin (Gissi et al 2006), P transposase (Kimbacher et al 2009), or chordate gene families such as CYP 1 (Goldstone et al 2007) suggesting that tunicate sequence divergence may increase up to 30% between species of the same genus. Similarly, whole-genome sequence data analyses have also revealed high rates of molecular evolution at a within-species level, as indicated by the extremely high rates of structural (16.6 %) and single nucleotide polymorphism (4.5%) characterizing the Ciona savignyi genome (Small et al 2007a).…”

Section: Introductionmentioning

confidence: 72%

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

et al. 2010

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Phylogenomics has recently revealed that tunicates represent the sister-group of vertebrates in the newly defined clade Olfactores. However, phylogenomic and comparative genomic studies have also suggested that tunicates are characterized by an elevated rate of molecular evolution and a high degree of genomic divergence. Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only a few model species. In order to expand the available genomic data for the group, we used the high-throughput 454 technology to sequence the partial transcriptome of a previously unsampled tunicate, Microcosmus squamiger. This allowed us to get further insights into tunicate-accelerated evolution through a comparative analysis based on pertinent phylogenetic markers, i.e., a core of 35 housekeeping genes conserved across bilaterians. Our results showed that tunicates evolved on average about two times faster than the other chordates, yet the degree of this acceleration varied extensively upon genes and upon lineages. Appendicularia and Aplousobranchia were detected as the most divergent groups which were also characterized by highly heterogeneous substitution rates across genes. Finally, an estimation of the d (N)/d (S) ratio in three pairs of closely related taxa within Olfactores did not reveal strong differences between the tunicate and vertebrate lineages suggesting that for this set of housekeeping genes, the accelerated evolution of tunicates is plausibly due to an elevated mutation rate rather than to particular selective effects.

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Section: Introductionmentioning

confidence: 72%

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

et al. 2010

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“…2 and [27,28]). Further genome sequencing efforts over the past decade have led to the discovery of P elementrelated THAP9 genes or transposons in a variety of organisms in addition to humans, including other primates, zebrafish, Xenopus [29], Ciona [30], sea urchin, hydra [31] and the human pathogenic protozoan parasite, Trichomonas vaginalis [32]. Notably, the THAP9 gene is FIGURE 1 Features of the complete 2.9kb P element.…”

Section: P Transposable Elements Inmentioning

confidence: 99%

P Transposable Elements in Drosophila and other Eukaryotic Organisms

Majumdar

Rio

2015

Mobile DNA III

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P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3′ extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C 2 CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite Trichomonas vaginalis, the sea squirt Ciona, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the Drosophila P element transposon DNA in human and Drosophila cells, indicating that the THAP9 genes encode active P element "transposase" proteins.

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“…The mosquitoes Anopheles gambiae and Aedes aegypti have a high copy number of highly diversified P-like sequences in their genomes (Sarkar et al 2003;Carvalho et al 2004;Nene et al 2007). In vertebrates, P-like elements have been found in humans and chickens as a stationary, single-copy gene (Hagemann and Pinsker 2001;Hammer et al 2005); however, there are typical and putatively active P-elements in the fish Danio rerio and in the urochordate Ciona intestinalis (Kimbacher et al 2009). …”

Section: Introductionmentioning

confidence: 98%

New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies

et al. 2012

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Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.

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DrosophilaP transposons of the urochordata Ciona intestinalis

Cited by 9 publications

References 36 publications

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

P Transposable Elements in Drosophila and other Eukaryotic Organisms

New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies

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