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

BMC Genomics

Methodology Article

Alex Hastie¹  Alberto Cenci²  Mathieu Rouard²  Guillaume Martin³  Franc-Christophe Baurens³  Françoise Carreel³  Angélique D’Hont³  Gaëtan Droc³  Jean-Marc Aury⁴  Adriana Alberti⁴  Andrzej Kilian⁵  Jaroslav Doležel⁶ 

[1] BioNano Genomics, 9640 Towne Centre Drive, 92121, San Diego, CA, USA;Bioversity International, Parc Scientifique Agropolis II, 34397, Cedex 5, Montpellier, France;CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, cedex 5, Montpellier, France;Commissariat à l’Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France;Diversity Arrays Technology, 2600, Yarralumla, Australian Capital Territory, Australia;Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic;

关键词: Musa acuminata;    Genome assembly;    Bioinformatics tool;    Paired-end sequences;    GBS;    Genome map;   

DOI  :  10.1186/s12864-016-2579-4

 received in 2015-08-04, accepted in 2016-03-08,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundRecent 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).ResultsWe 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 %.ConclusionThe 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.

【 授权许可】

CC BY   
© Martin et al. 2016