Transposable Elements
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 (TEs), dynamic segments within plant genomes, have the unique ability to migrate within and across genomes of nearly all life forms. These elements are pivotal in fostering genomic diversity and play a significant role in variations in genome size, aside from the contributions of polyploidy events. The rapid and accurate identification, along with the annotation of TEs, is a crucial aspect of genomic sequence analysis. However, analyzing these elements presents significant hurdles due to their repetitive nature, structural polymorphisms, species-specific patterns alongside their conservation across different genera and families, and their rapid evolution even among closely related species. TEs are known for their ability to traverse genomes, induce mutations, and increase their own copy numbers.
TEs are broadly categorized based on their replication mechanisms into two main classes: Class I elements, or retrotransposons, which replicate through an RNA intermediate, and Class II elements, or DNA transposons, which move through a DNA intermediate. Plant genomes predominantly comprise transposons due to their replication strategies. Retrotransposons, in particular, are divided into four orders based on their structural traits and lifecycle: long terminal repeat retrotransposons (LTR-RTs), non-LTR retrotransposons, PLEs, and DIRSs.
The LTR-RTs are especially prevalent, making up to 80% of the genome in certain plants like wheat, barley, and rubber. This order includes two major superfamilies within plant genomes: Copia and Gypsy, distinguished by their coding domain organization. Each superfamily is further dissected into lineages and families through phylogenetic analysis, focusing on coding region similarities, particularly the reverse transcriptase enzymatic domain. The Copia superfamily encompasses lineages such as Ale (Retrofit), Alesia, Angela, and others, while the Gypsy superfamily includes Athila, Clamyvir, Galadriel, and additional groups, with Gypsy elements like Galadriel and Tekay (Del) classified into the Chromovirus branch based on chromodomain presence.
Identifying and annotating TEs within sequenced genomes can be approached through various methodologies, categorized into de novo, structure-based, comparative genomics, and homology-based strategies. Each method offers distinct advantages in specificity and sensitivity, though they commonly face challenges with high false-positive rates.
Our research zeroes in on the examination of transposable elements within plant, specifically coffee, genomes. We delve into the influence of TEs on genome evolution, species adaptation, and their direct impact on genome size variability. To this end, we are developing new bioinformatics tools tailored for the detection and annotation of LTR retrotransposons, aiming to illuminate the complex roles these genetic elements play in shaping the genomic landscapes of coffee and other plants.
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). https://doi.org/10.1038/s42003-023-05144-y
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 https://doi.org/10.1139/gen-2022-0083
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). https://doi.org/10.1007/s00705-023-05747-0
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.