title: Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
abstract: 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%.
  
  
  CONCLUSIONS
  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.
authors.affiliation: CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Martin
authors.affiliation: CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
authors.forename: Franc-Christophe
authors.initials: FC
authors.lastname: Baurens
authors.affiliation: CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
authors.forename: Gaëtan
authors.initials: G
authors.lastname: Droc
authors.affiliation: Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Rouard
authors.affiliation: Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France.
authors.forename: Alberto
authors.initials: A
authors.lastname: Cenci
authors.affiliation: Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600, Australia.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.affiliation: BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Hastie
authors.affiliation: Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Carreel
authors.affiliation: CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France. dhont@cirad.fr.
authors.forename: Angélique
authors.initials: A
authors.lastname: D'Hont
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D005819:Genetic Markers; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D028521:Musa / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: Bioinformatics tool; GBS; Genome assembly; Genome map; Musa acuminata; Paired-end sequences