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Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.
Genetica. 2017 Oct; 145(4-5):417-430.G

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.

Authors+Show Affiliations

CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina. rosaliapaz@gmail.com.Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina.Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina.Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, San Juan, Argentina.IBAM, Universidad Nacional de Cuyo, CONICET, FCA and FCEN, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28776161

Citation

Paz, Rosalía Cristina, et al. "Diversity, Distribution and Dynamics of Full-length Copia and Gypsy LTR Retroelements in Solanum Lycopersicum." Genetica, vol. 145, no. 4-5, 2017, pp. 417-430.
Paz RC, Kozaczek ME, Rosli HG, et al. Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum. Genetica. 2017;145(4-5):417-430.
Paz, R. C., Kozaczek, M. E., Rosli, H. G., Andino, N. P., & Sanchez-Puerta, M. V. (2017). Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum. Genetica, 145(4-5), 417-430. https://doi.org/10.1007/s10709-017-9977-7
Paz RC, et al. Diversity, Distribution and Dynamics of Full-length Copia and Gypsy LTR Retroelements in Solanum Lycopersicum. Genetica. 2017;145(4-5):417-430. PubMed PMID: 28776161.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum. AU - Paz,Rosalía Cristina, AU - Kozaczek,Melisa Eliana, AU - Rosli,Hernán Guillermo, AU - Andino,Natalia Pilar, AU - Sanchez-Puerta,Maria Virginia, Y1 - 2017/08/03/ PY - 2017/04/05/received PY - 2017/07/26/accepted PY - 2017/8/5/pubmed PY - 2018/3/2/medline PY - 2017/8/5/entrez KW - Expression KW - Family delimitation KW - Full length LTR retroelements KW - Insertion time KW - Phylogeny KW - Solanum lycopersicum SP - 417 EP - 430 JF - Genetica JO - Genetica VL - 145 IS - 4-5 N2 - 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. SN - 1573-6857 UR - https://www.unboundmedicine.com/medline/citation/28776161/Diversity_distribution_and_dynamics_of_full_length_Copia_and_Gypsy_LTR_retroelements_in_Solanum_lycopersicum_ L2 - https://doi.org/10.1007/s10709-017-9977-7 DB - PRIME DP - Unbound Medicine ER -