Biology 2018, 7(2), 32; https://doi.org/10.3390/biology7020032
Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics
Simon Orozco-Arias 1,†
, Juan Liu 2,†, Reinel Tabares-Soto 1, Diego Ceballos 3, Douglas Silva Domingues 4, Andréa Garavito 5, Ray Ming 2,6 and Romain Guyot 1,7,*
, Juan Liu 2,†, Reinel Tabares-Soto 1, Diego Ceballos 3, Douglas Silva Domingues 4, Andréa Garavito 5, Ray Ming 2,6 and Romain Guyot 1,7,*
1
Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170002, Colombia
2
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
3
Department of Systems and Informatics, Universidad de Caldas, Manizales 170002, Colombia
4
Department of Botany, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Rio Claro, SP 13506-900, Brazil
5
Department of Biological Sciences, Universidad de Caldas, Manizales 170002, Colombia
6
Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
7
Institut de Recherche pour le Développement (IRD), CIRAD, Université de Montpellier, Montpellier 34394, France
†
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 3 May 2018 / Revised: 16 May 2018 / Accepted: 22 May 2018 / Published: 25 May 2018
Abstract
One particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR retrotransposons is an essential step to precisely understand their effect at the genome level, but remains challenging in large-sized genomes, requiring the use of optimized bioinformatics tools that can take advantage of supercomputers. Here, we propose a new tool: Inpactor, a parallel and scalable pipeline designed to classify LTR retrotransposons, to identify autonomous and non-autonomous elements, to perform RT-based phylogenetic trees and to analyze their insertion times using High Performance Computing (HPC) techniques. Inpactor was tested on the classification and annotation of LTR retrotransposons in pineapple, a recently-sequenced genome. The pineapple genome assembly comprises 44% of transposable elements, of which 23% were classified as LTR retrotransposons. Exceptionally, 16.4% of the pineapple genome assembly corresponded to only one lineage of the Gypsy superfamily: Del, suggesting that this particular lineage has undergone a significant increase in its copy numbers. As demonstrated for the pineapple genome, Inpactor provides comprehensive data of LTR retrotransposons’ classification and dynamics, allowing a fine understanding of their contribution to genome structure and evolution. Inpactor is available at https://github.com/simonorozcoarias/Inpactor. View Full-TextKeywords:
Inpactor; transposable elements; LTR retrotransposons; parallel programming; pineapple; HPC
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Orozco-Arias, S.; Liu, J.; Tabares-Soto, R.; Ceballos, D.; Silva Domingues, D.; Garavito, A.; Ming, R.; Guyot, R. Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics. Biology 2018, 7, 32.
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