Improvement of the banana Musa acuminata reference sequence using NGS data and semi-automated bioinformatics methods

Martin Guillaume, Baurens Franc-Christophe, Droc Gaëtan, Rouard Mathieu, Cenci Alberto, Kilian Andrzej, Hastie Alex, Dolezelova M., Aury Jean-Marc, Alberti Adriana, Carreel Françoise, D'Hont Angélique. 2016. Improvement of the banana Musa acuminata reference sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics, 17 (243), 12 p.

https://doi.org/10.1186/s12864-016-2579-4

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

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Version publiée - Anglais
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Musa_acuminata_V2_supp.pdf
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Url - jeu de données - Entrepôt autre : http://banana-genome.cirad.fr/ / Url - jeu de données - Entrepôt autre : http://www.ebi.ac.uk/ena/data/search?query=ERP013665

Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY

Note générale : Jeux de données : "Availability of supporting data Datasets (contigs, scaffold assembly, Pseudo-molecules, makers matrix and raw data of the genome map) are available through the banana genome hub (http://banana-genome.cirad.fr/) and the 5 kb library is deposited on the ENA read archive (ID number: ERP013665)"

Résumé : Background: Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). Results: We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. Conclusion: The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species.

Mots-clés Agrovoc : Musa acuminata, bioinformatique, génome, séquence nucléotidique, adn, carte génétique, génétique des populations, génie génétique, marqueur génétique

Mots-clés géographiques Agrovoc : Guadeloupe, France

Mots-clés complémentaires : Séquencage

Mots-clés libres : Musa acuminata, Genome assembly, Bioinformatics tool, Paired-end sequences, GBS, Genome map

Classification Agris : F30 - Génétique et amélioration des plantes
U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

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