Abstract
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. 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. 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.
Highlights
Non-long terminal repeat retrotransposons have contributed to shaping the structure and function of genomes
TBLASTX comparisons showed that the ascidian elements belonged to the I, LINE1, LINE2, LOA and R2 clades (E-values: 4e-69 with Biomphalaria glabrata BGR, 2e-89 with Nycticebus coucang L1, 2e-50 with Danio rerio CR1Dr2, e-146 with Aedes aegypti Lian, and e-106 with Drosophila melanogaster R2, respectively)
The apurinic/apyrimidic endonuclease (APE) region was clearly identified in CiI, CiL1, CiL2 and CiLOA (Figure 2a) on the basis of the reported domains I to VII [17]
Summary
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. The ascidian Ciona intestinalis has joined the select group of fully sequenced genomes [1]. Current information about ascidian transposable elements is limited to only 1 Mb of genomic sequences [3]. These elements are, R73.2 Genome Biology 2003, Volume 4, Issue 11, Article R73 Permanyer et al
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