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LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions.
Planta. 2019 Nov; 250(5):1781-1787.P

Abstract

MAIN CONCLUSION

Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato. From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.

Authors+Show Affiliations

Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.Institut de Recherche pour le Développement, IRD DIADE, Université de Perpignan, Plant Genome and Development Laboratory, Perpignan, France.Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy. carputo@unina.it.Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy. raversan@unina.it.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31562541

Citation

Esposito, Salvatore, et al. "LTR-TEs Abundance, Timing and Mobility in Solanum Commersonii and S. Tuberosum Genomes Following Cold-stress Conditions." Planta, vol. 250, no. 5, 2019, pp. 1781-1787.
Esposito S, Barteri F, Casacuberta J, et al. LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions. Planta. 2019;250(5):1781-1787.
Esposito, S., Barteri, F., Casacuberta, J., Mirouze, M., Carputo, D., & Aversano, R. (2019). LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions. Planta, 250(5), 1781-1787. https://doi.org/10.1007/s00425-019-03283-3
Esposito S, et al. LTR-TEs Abundance, Timing and Mobility in Solanum Commersonii and S. Tuberosum Genomes Following Cold-stress Conditions. Planta. 2019;250(5):1781-1787. PubMed PMID: 31562541.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions. AU - Esposito,Salvatore, AU - Barteri,Fabio, AU - Casacuberta,Josep, AU - Mirouze,Marie, AU - Carputo,Domenico, AU - Aversano,Riccardo, Y1 - 2019/09/27/ PY - 2019/07/03/received PY - 2019/09/13/accepted PY - 2019/9/29/pubmed PY - 2020/2/11/medline PY - 2019/9/29/entrez KW - Extrachromosomal circular DNA KW - Insertion time KW - Mobilome KW - Potato KW - Wild species SP - 1781 EP - 1787 JF - Planta JO - Planta VL - 250 IS - 5 N2 - MAIN CONCLUSION: Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato. From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato. SN - 1432-2048 UR - https://www.unboundmedicine.com/medline/citation/31562541/LTR_TEs_abundance_timing_and_mobility_in_Solanum_commersonii_and_S__tuberosum_genomes_following_cold_stress_conditions_ L2 - https://dx.doi.org/10.1007/s00425-019-03283-3 DB - PRIME DP - Unbound Medicine ER -