The Transposons of the Sea Urchin Strongylocentrotus intermedius Agassiz, 1863: In Silico Versus In Vitro
| Autor: | A. L. Drozdov, D. I. Ostromyshenskii, A. S. Turenko, Olga I. Podgornaya, L. S. Adonin, Anna I. Solovyeva, E. E. Lebedev |
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| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Transposable element urogenital system 010604 marine biology & hydrobiology In silico Reading frame food and beverages 04 agricultural and veterinary sciences Computational biology Aquatic Science Biology Oceanography biology.organism_classification 01 natural sciences Genome Strongylocentrotus purpuratus Transcriptome stomatognathic diseases stomatognathic system biology.animal embryonic structures 040102 fisheries 0401 agriculture forestry and fisheries Primer (molecular biology) Sea urchin |
| Zdroj: | Russian Journal of Marine Biology. 45:418-424 |
| ISSN: | 1608-3377 1063-0740 |
| Popis: | The sequenced genome data from the sea urchin Strongylocentrotus purpuratus were used to identify transposons (TEs, transposable elements) and test for the presence of some of them in the genome of the sea urchin S. intermedius. The known TEs of S. purpuratus from the RepBase repeats database were used to calculate the primers and identify the corresponding TEs in the S. intermedius transcriptome. High-coverage TE sequences from the S. intermedius transcriptome were assembled based on comparison with the annotated TEs of the S. purpuratus genome. TEs with an insufficient number of reading frames in the transcriptome were beyond the analysis. The approach applied in the present study was successful: out of the 100 assembled TEs of S. intermedius, 92 corresponding TEs in the S. intermedius genome were identified using the calculated primer pairs. The TE sequences calculated by in silico methods are present in the S. intermedius genome and can be useful in further research. |
| Databáze: | OpenAIRE |
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