CAULIFINDER: A pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes

Vassilieff Héléna, Haddad Sana, Jamilloux Véronique, Choisne Nathalie, Sharma Vikas, Giraud Delphine, Wan Mariène, Serfraz Saad, Geering Andrew D., Teycheney Pierre-Yves, Maumus Florian. 2022. CAULIFINDER: A pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mobile DNA, 13:31, 12 p.

https://doi.org/10.1186/s13100-022-00288-w

Article de revue ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total

Prévisualisation

Version publiée - Anglais
Sous licence

.
Vassilieff et al.pdf
Télécharger (2MB) | Prévisualisation

Url - jeu de données - Entrepôt autre : https://figshare.com/projects/Caulifinder/143532

Résumé : Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.

Mots-clés Agrovoc : Caulimovirus, Adenoviridae, virus associé à l'adénome, génome, technique analytique, analyse de séquence

Mots-clés libres : Endogenous viral elements, Plant genomes, Paleovirology, Caulimoviridae, Repetitive elements, Bioinformatics, Genome annotation

Classification Agris : H20 - Maladies des plantes
F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Regional Development Fund

Agences de financement hors UE : Agence Nationale de la Recherche

Projets sur financement : (FRA) Séquences virales endogènes: rôle dans l'évolution des virus et fonctions chez les plantes

Auteurs et affiliations