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 able to move within and among the genomes of virtually all organisms. They are the main contributors to genomic diversity and genome size variation, with the exception of polyploidy events. An important issue in genome sequence analyses is to rapidly identify and to reliably annotate TEs. There are major obstacles and challenges in the analysis of these elements, including their repetitive nature, structural polymorphism, species specificity, and, conversely, their conservation across genera and families, as well as their high divergence rate, even across close relative species. They are able to move in the genomes, generate mutations, and obviously amplify the number of their copies. Usually they are classified according to their coding regions involved in the replication of the element. TEs moving via an RNA molecule called retrotransposons fall into Class I, while elements moving via a DNA molecule, called transposons, are classified into Class II. They represent the vast majority of TEs found in plant genomes due to their mobility mechanisms. Retrotransposons can be further subclassified into four orders according to their structural features and the element’s life cycle: Long Terminal Repeat retrotransposon (LTR-RT), non-LTR retrotransposons, PLEs, and DIRS.
LTR-RT is the most common order, and they can contribute up to 80% of the plant genome size, as in wheat, barley, or the rubber tree. The LTR-RT order is composed of two superfamilies in plants: Copia and Gypsy, based on the internal organization of the coding domain. Each Copia and Gypsy superfamily is further sub-classified into lineages and families through phylogenetic analysis based on coding region similarities (often of 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 lineages belong to the Copia superfamily, while Athila, Clamyvir, Galadriel, Selgy, Tcn1, Reina, Tekay (or Del), CRM (also named Centromeric Retrotransposon), Phygy, and TAT are grouped into the Gypsy superfamily. Phylogenetic studies have divided Gypsy into different groups according to the presence of a chromodomain. The Galadriel, Reina, Tekay (Del), and CRM lineages were grouped into the Chromovirus branch. Several methods were developed to identify and annotate transposable elements in sequenced genomes. These are classified into four categories: de novo, structure-based, comparative genomics, and homology-based. These approaches offer different specificities and sensibilities and all suffer from a relatively high rate of false positive detections.
Our objectives are to study transposable elements in the genomes of plants and more specifically in the genomes of coffee trees. Our studies focus on the impact of transposable elements on the genomes evolution and species adaptation as well as and their direct contribution to the genome size variations. To achieve these objectives, new bioinformatic tools for the detection and annotation of retrotransposons at LTR are under development.
List of publications
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. https://doi.org/10.3390/agronomy12071665
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. https://doi.org/10.1139/gen-2021-0045
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: https://doi.org/10.1101/2022.02.23.481133
Pedro DLF, Amorim TS, Varani A et al. An Atlas of Plant Transposable Elements [version 1; peer review: 2 approved]. F1000Research 2021, 10:1194 (https://doi.org/10.12688/f1000research.74524.1)
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 https://doi.org/10.1139/gen-2021-0045
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. https://doi.org/10.1007/978-3-030-00614-3_11
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). https://doi.org/10.1007/s00438-011-0617-0
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.