On the trail of tetu1: Genome-wide discovery of CACTA transposable elements in sunflower genome
| Autor: | Lucia Natali, Claudio Pugliesi, Alberto Vangelisti, Flavia Mascagni, Maria Ventimiglia, Tommaso Giordani, Andrea Cavallini, Gabriele Usai |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Transposable element DNA Plant Retroelements Transposases Retrotransposon Flowers Biology ENCODE Genes Plant 01 natural sciences Genome Class II transposons Catalysis Article CACTA CACTA classification Sunflower Inorganic Chemistry lcsh:Chemistry 03 medical and health sciences Helianthus annuus Coding region Physical and Theoretical Chemistry Molecular Biology Gene lcsh:QH301-705.5 Spectroscopy Transposase Conserved Sequence Plant Proteins Repetitive Sequences Nucleic Acid Genetics Organic Chemistry General Medicine Computer Science Applications 030104 developmental biology Phenotype lcsh:Biology (General) lcsh:QD1-999 DNA Transposable Elements Helianthus Genome Plant 010606 plant biology & botany |
| Zdroj: | International Journal of Molecular Sciences, Vol 21, Iss 6, p 2021 (2020) International Journal of Molecular Sciences Volume 21 Issue 6 |
| Popis: | Much has been said about sunflower (Helianthus annuus L.) retrotransposons, representing the majority of the sunflower’s repetitive component. By contrast, class II transposons remained poorly described within this species, as they present low sequence conservation and are mostly lacking coding domains, making the identification and characterization of these transposable elements difficult. The transposable element Tetu1, is a non-autonomous CACTA-like element that has been detected in the coding region of a CYCLOIDEA (CYC) gene of a sunflower mutant, tubular ray flower (turf). Based on our knowledge of Tetu1, the publicly available genome of sunflower was fully scanned. A combination of bioinformatics analyses led to the discovery of 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements. A detailed characterization of the identified elements allowed further classification into three subgroups of 347 elements on the base of their terminal repeat sequences. Only 39 encode a protein similar to known transposases (TPase), with 10 TPase sequences showing signals of activation. Finally, an analysis of the proximity of CACTA transposons to sunflower genes showed that the majority of CACTA elements are close to the nearest gene, whereas a relevant fraction resides within gene-encoding sequences, likely interfering with sunflower genome functionality and organization. |
| Databáze: | OpenAIRE |
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