Abstract
Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.
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Acknowledgements
This work was funded by Agencia Nacional de Promoción Científica y Tecnológica, Argentina (ANPCyT), D-TEC 0008/13 and PROJOVI 2015 (Universidad Nacional de San Juan). We thank C. Llorens for his valuable help with the Gypsy Database. This work was part of the undergraduate thesis of MEK.
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10709_2017_9977_MOESM1_ESM.pdf
Fig. S1. Criteria employed to define and annotate a retroelement as a full-length: A) Example of a retroelement containing both LTR sequences and all of their constitutive proteins based on a search of Conserved Domains (NCBI). B) Examples of incomplete, truncated or empty LTR retroelement that were not considered in this study (PDF 3268 KB)
10709_2017_9977_MOESM2_ESM.pdf
Fig. S2. Phylogenetic tree based on amino acid sequences of the retrotranscriptase of complete Gypsy LTR retroelements from tomato including reference sequences. Numbers above the branches represent bootstrap support values > 50% (PDF 511 KB)
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Fig. S3. Phylogenetic tree based on amino acid sequences of the retrotranscriptase of complete Copia LTR retroelements from tomato including reference sequences. Numbers above the branches represent bootstrap support values > 50%. (PDF 757 KB)
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Fig. S4. Phylogenetic tree based on amino acid sequences of the RNaseH of complete Gypsy LTR retroelements from tomato including reference sequences. Numbers above the branches represent bootstrap support values > 50% (PDF 612 KB)
10709_2017_9977_MOESM5_ESM.pdf
Fig. S5. Phylogenetic tree based on amino acid sequences of the RNaseH of complete Copia LTR retroelements from tomato including reference sequences. Numbers above the branches represent bootstrap support values > 50% (PDF 542 KB)
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Fig. S6. Distribution of insertion times of full-length retroelement copies of Copia (π) and Gypsy (λ) retroelements identified in tomato. Estimated insertion times were divided into bins of 100,000 yr. Frequency classes were limited each 0.5 Mya (JPG 106 KB)
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Paz, R.C., Kozaczek, M.E., Rosli, H.G. et al. Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum . Genetica 145, 417–430 (2017). https://doi.org/10.1007/s10709-017-9977-7
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DOI: https://doi.org/10.1007/s10709-017-9977-7