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Review

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

1
IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
2
Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), Université d’Evry Val d’Essonne, Université Paris-Saclay, UMR CNRS 8071, ENSIIE, USC INRAE, 23 bvd de France, CEDEX, 91037 Evry Paris, France
3
Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(9), 1046; https://doi.org/10.3390/genes11091046
Received: 30 July 2020 / Revised: 1 September 2020 / Accepted: 2 September 2020 / Published: 4 September 2020
(This article belongs to the Special Issue A Tale of Genes and Genomes)
Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question. View Full-Text
Keywords: gene duplication; bioinformatic tools; paralogous genes; genome evolution; synteny gene duplication; bioinformatic tools; paralogous genes; genome evolution; synteny
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MDPI and ACS Style

Lallemand, T.; Leduc, M.; Landès, C.; Rizzon, C.; Lerat, E. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. Genes 2020, 11, 1046. https://doi.org/10.3390/genes11091046

AMA Style

Lallemand T, Leduc M, Landès C, Rizzon C, Lerat E. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. Genes. 2020; 11(9):1046. https://doi.org/10.3390/genes11091046

Chicago/Turabian Style

Lallemand, Tanguy, Martin Leduc, Claudine Landès, Carène Rizzon, and Emmanuelle Lerat. 2020. "An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice" Genes 11, no. 9: 1046. https://doi.org/10.3390/genes11091046

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