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LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome.

Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A - DNA Res. (2014)

Bottom Line: Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements.The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element.Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.

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Phylogenetic tree obtained from the neighbour-joining analysis of 93 Copia retrotranscriptase sequences. Different Copia families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates a Copia RE with an LTR/inter-LTR ratio of >10.
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DSU042F4: Phylogenetic tree obtained from the neighbour-joining analysis of 93 Copia retrotranscriptase sequences. Different Copia families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates a Copia RE with an LTR/inter-LTR ratio of >10.

Mentions: Phylogenetic analyses were performed by the neighbour-joining method to evaluate the relationship between isolated LTR-REs. Two phylogenetic trees were constructed based on the transcribed putative retrotranscriptase sequence of 93 Copia and 43 Gypsy REs (Figs 4 and 5). The bootstrap values suggest the occurrence of distinct families, indicated in the figures by different colours.Figure 4.


LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome.

Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A - DNA Res. (2014)

Phylogenetic tree obtained from the neighbour-joining analysis of 93 Copia retrotranscriptase sequences. Different Copia families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates a Copia RE with an LTR/inter-LTR ratio of >10.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379980&req=5

DSU042F4: Phylogenetic tree obtained from the neighbour-joining analysis of 93 Copia retrotranscriptase sequences. Different Copia families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates a Copia RE with an LTR/inter-LTR ratio of >10.
Mentions: Phylogenetic analyses were performed by the neighbour-joining method to evaluate the relationship between isolated LTR-REs. Two phylogenetic trees were constructed based on the transcribed putative retrotranscriptase sequence of 93 Copia and 43 Gypsy REs (Figs 4 and 5). The bootstrap values suggest the occurrence of distinct families, indicated in the figures by different colours.Figure 4.

Bottom Line: Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements.The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element.Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.

Show MeSH
Related in: MedlinePlus