Argout Xavier, Martin Guillaume, Droc Gaëtan, Fouet Olivier, Labadie Karine, Rivals Eric, Aury Jean-Marc, Lanaud Claire. 2017. The cacao Criollo genome v2.0: An improved version of the genome for genetic and functional genomic studies. BMC Genomics, 18:730, 9 p.
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Version publiée
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Url - jeu de données - Entrepôt autre : https://figshare.com/articles/figure/Additional_file_1_of_The_cacao_Criollo_genome_v2_0_an_improved_version_of_the_genome_for_genetic_and_functional_genomic_studies/5413564
Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY
Résumé : Background: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. Methods: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. Results: The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Conclusion: Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub (http://cocoa-genome-hub.southgreen.fr).
Mots-clés Agrovoc : Theobroma cacao, génome, variété
Mots-clés géographiques Agrovoc : Amazonie, Belize
Classification Agris : F30 - Génétique et amélioration des plantes
Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive
Auteurs et affiliations
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Argout Xavier, CIRAD-BIOS-UMR AGAP (COL)
ORCID: 0000-0002-0100-5511
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Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA)
ORCID: 0000-0002-1801-7500
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Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
ORCID: 0000-0003-1849-1269
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Fouet Olivier, CIRAD-BIOS-UMR AGAP (FRA)
ORCID: 0000-0001-8547-1474
- Labadie Karine, Institut de génomique (FRA)
- Rivals Eric, LIRMM (FRA)
- Aury Jean-Marc, CEA (FRA)
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Lanaud Claire, CIRAD-BIOS-UMR AGAP (FRA)
ORCID: 0000-0001-6411-7310
Source : Cirad-Agritrop (https://agritrop.cirad.fr/587579/)
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