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The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes.

Permanyer J, Gonzàlez-Duarte R, Albalat R - Genome Biol. (2003)

Bottom Line: The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes.Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome.The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, E-08028 Barcelona, Spain.

ABSTRACT

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes.

Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families.

Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

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Phylogenetic tree of non-LTR elements based on the reverse transcriptase sequence. The elements identified in C. intestinalis are indicated with an asterisk. The number next to each node of the 14 clades indicates the bootstrap value as the percentage out of 1,000 replicates. The name of each non-LTR element and the species harboring it is listed to the right of the figure, shaded in light gray (protostomes) or dark gray (deuterostomes).
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Figure 3: Phylogenetic tree of non-LTR elements based on the reverse transcriptase sequence. The elements identified in C. intestinalis are indicated with an asterisk. The number next to each node of the 14 clades indicates the bootstrap value as the percentage out of 1,000 replicates. The name of each non-LTR element and the species harboring it is listed to the right of the figure, shaded in light gray (protostomes) or dark gray (deuterostomes).

Mentions: The reverse transcriptase domain of non-LTR elements was used to establish the phylogenetic relationships of the ascidian elements and the 14 reported non-LTR clades. In the neighbor-joining tree (Figure 3), all clades were supported with significant bootstrap values (≥70%), except clade I, with the lowest bootstrap value (67%) in agreement with previous analyses [11,12,14]. Therefore, ascidian sequences clustered within five distinct clades: I, L1, L2, LOA and R2 (bootstraps: 67%, 70%, 97%, 100% and 100%, respectively), as a result of which they were recorded as new members of such groups.


The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes.

Permanyer J, Gonzàlez-Duarte R, Albalat R - Genome Biol. (2003)

Phylogenetic tree of non-LTR elements based on the reverse transcriptase sequence. The elements identified in C. intestinalis are indicated with an asterisk. The number next to each node of the 14 clades indicates the bootstrap value as the percentage out of 1,000 replicates. The name of each non-LTR element and the species harboring it is listed to the right of the figure, shaded in light gray (protostomes) or dark gray (deuterostomes).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC329123&req=5

Figure 3: Phylogenetic tree of non-LTR elements based on the reverse transcriptase sequence. The elements identified in C. intestinalis are indicated with an asterisk. The number next to each node of the 14 clades indicates the bootstrap value as the percentage out of 1,000 replicates. The name of each non-LTR element and the species harboring it is listed to the right of the figure, shaded in light gray (protostomes) or dark gray (deuterostomes).
Mentions: The reverse transcriptase domain of non-LTR elements was used to establish the phylogenetic relationships of the ascidian elements and the 14 reported non-LTR clades. In the neighbor-joining tree (Figure 3), all clades were supported with significant bootstrap values (≥70%), except clade I, with the lowest bootstrap value (67%) in agreement with previous analyses [11,12,14]. Therefore, ascidian sequences clustered within five distinct clades: I, L1, L2, LOA and R2 (bootstraps: 67%, 70%, 97%, 100% and 100%, respectively), as a result of which they were recorded as new members of such groups.

Bottom Line: The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes.Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome.The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, E-08028 Barcelona, Spain.

ABSTRACT

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes.

Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families.

Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Show MeSH