Transposable Elements

picture ©Emmanuel couturon IRD

Wild coffea species db.

Hierarchical classification of Class I retrotransposon (Orozco-Arias et al., 2019)

Structure of non-autonomous and autonomous LTR retrotransposons in plants  (Orozco-Arias et al., 2019).

Transposable elements in plant genomes.

Transposable elements (TEs) are genomic units capable of moving within and between the genomes of virtually all organisms. They are primarily responsible for genomic diversity and variation in genome size, with the exception of polyploidy events. Rapid identification and reliable annotation of transgenic elements is an important issue in genomic sequence analysis. Analysis of these elements faces major obstacles and challenges, including their repetitive nature, structural polymorphism, species specificity and, conversely, conservation across genera and families, as well as their high rate of divergence, even between closely related species. They are capable of moving through genomes, generating mutations and, of course, amplifying their copy number. They are generally classified according to the coding regions involved in replication. Transgenic elements moving via an RNA molecule, known as retrotransposons, belong to class I, while elements moving via a DNA molecule, known as transposons, are classified in class II. Because of their mobility mechanisms, transposons account for the vast majority of transgenic elements present in plant genomes. Retrotransposons can be subdivided into four orders according to their structural characteristics and the element's life cycle: The long terminal repeat retrotransposon (LTR-RT), non-LTR retrotransposons, PLEs and DIRSs.

The LTR-RT order is the most common and can account for up to 80% of the plant genome size, as in the case of wheat, barley or rubber. The LTR-RT order comprises two plant superfamilies: Copia and Gypsy, based on the internal organization of the coding domain. Each Copia and Gypsy superfamily is further subdivided into lineages and families by phylogenetic analysis based on similarities in coding regions (often the enzymatic domain known as reverse transcriptase). For plant genomes, Ale (also known as Retrofit), Alesia, Angela, Bianca, Bryco, Lyco, Gymco, Ikeros (also known as Tork sto-4), Ivana (or Oryco), Osser, SIRE, Tar (also known as Tork), and Tork belong to the Copia superfamily, while Athila, Clamyvir, Galadriel, Selgy, Tcn1, Reina, Tekay (or Del), CRM (also known as centromeric retrotransposon), Phygy and TAT are grouped in the Gypsy superfamily. Phylogenetic studies have divided Gypsy into different groups based on the presence of a chromodomain. The Galadriel, Reina, Tekay (Del) and CRM lines have been grouped together in the Chromovirus branch. Several methods have been developed to identify and annotate transposable elements in sequenced genomes. They fall into four categories: de novo, structure-based, comparative genomics and homology-based. These approaches offer different specificities and sensitivities, and all suffer from a relatively high false-positive detection rate.

Our aim is to study transposable elements in plant genomes, and more specifically in coffee genomes. Our studies focus on the impact of transposable elements on genome evolution and species adaptation, as well as their direct contribution to genome size variation. To achieve these goals, new bioinformatics tools for the detection and annotation of LTR retrotransposons are being developed.

List of publications

Lozano-Arce, D., García, T., Gonzalez-Garcia, L.N. et al. Selection signatures and population dynamics of transposable elements in lima bean. Commun Biol 6, 803 (2023).

Rafael de Assis, Leandro Simões Azeredo Gonçalves, Romain Guyot, and André Luis Laforga Vanzela. 2023. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome. e-First

Camargo-Forero, N., Orozco-Arias, S., Perez Agudelo, J.M. et al. HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Arch Virol 168, 125 (2023).

Orozco-Arias, S.; Candamil, M.S.; Jaimes, P.A.; Cristancho, M.; Tabares-Soto, R.; Guyot, R. Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia vastatrix). Agronomy 2022, 12, 1665.

Leonardo Adabo Cintra, Thaíssa Boldieri de Souza, Letícia Maria Parteka, Lucas Mesquita Barreto, Luiz Filipe Protasio Pereira, Marcos Letaif Gaeta, Romain Guyot, and André Luís Laforga Vanzela. An 82 bp tandem repeat family typical of 3′ non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres. Genome. 65(3): 137-151.

Simon Orozco-Arias, Mathilde Dupeyron, David Gutiérrez-Duque, Reinel Tabares-Soto, Romain Guyot. High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes. bioRxiv 2022.02.23.481133; doi:

Pedro DLF, Amorim TS, Varani A et al. An Atlas of Plant Transposable Elements [version 1; peer review: 2 approved]. F1000Research 2021, 10:1194 (

Mr. Leonardo Adabo Cintra, Dr. Thaissa Boldieri de Souza, Mrs. Letícia Maria Parteka, Mr. Lucas Mesquita Barreto, Dr. Luiz Filipe Protasio Pereira, Dr. Marcos Letaif Gaeta, Dr. Romain Guyot, and Dr. André Luís Laforga Vanzela Sr.. An 82 bp tandem repeat family typical of 3' non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres. Genome. Just-IN

de Castro Nunes R, Orozco-Arias S, Crouzillat D, Mueller LA, Strickler SR, Descombes P, Fournier C, Moine D, de Kochko A, Yuyama PM, Vanzela ALL, Guyot R. Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions. Front Plant Sci. 2018 Feb 15;9:175. doi: 10.3389/fpls.2018.00175.

Liu J., Guyot R., Ming R. (2018) Transposable Elements in the Pineapple Genome. In: Ming R. (eds) Genetics and Genomics of Pineapple. Plant Genetics and Genomics: Crops and Models, vol 22. Springer, Cham.

Dupeyron M, de Souza RF, Hamon P, de Kochko A, Crouzillat D, Couturon E, Domingues DS, Guyot R. Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons. Mol Genet Genomics. 2017 Aug;292(4):741-754. doi: 10.1007/s00438-017-1308-2. 

Ming R, Wai CM, Guyot R. Pineapple Genome: A Reference for Monocots and CAM Photosynthesis. Trends Genet. 2016 Nov;32(11):690-696. doi: 10.1016/j.tig.2016.08.008. 

Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R. Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics. 2015 Oct 15;16:795. doi: 10.1186/s12864-015-2023-1.

Dias ES, Hatt C, Hamon S, Hamon P, Rigoreau M, Crouzillat D, Carareto CM, de Kochko A, Guyot R. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. Plant Mol Biol. 2015 Sep;89(1-2):83-97. doi: 10.1007/s11103-015-0352-8. 

Hamon, P., Duroy, PO., Dubreuil-Tranchant, C. et al. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genomics 285, 447–460 (2011).

Chaparro C, Guyot R, Zuccolo A, Piégu B, Panaud O. RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 2007 Jan;35(Database issue):D66-70. doi: 10.1093/nar/gkl780.

Piegu B, Guyot R, Picault N, Roulin A, Sanyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 2006 Oct;16(10):1262-9. doi: 10.1101/gr.5290206. Epub 2006 Sep 8. Erratum in: Genome Res. 2011 Jul;21(7):1201.