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

TitleImprovement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
Publication TypeJournal Article
Year of Publication2016
AuthorsMartin G, Baurens F-C, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury J-M, Alberti A, Carreel F, D'Hont A
JournalBMC Genomics
Volume17
Pagination243
Date Published2016
ISSN1471-2164
Abstract

<p><b>BACKGROUND: </b>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).</p><p><b>RESULTS: </b>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%.</p><p><b>CONCLUSION: </b>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.</p>

DOI10.1186/s12864-016-2579-4
Alternate JournalBMC Genomics
PubMed ID26984673
PubMed Central IDPMC4793746
Showing 2 of 2 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Pahang ITC0609 acuminata subsp. malaccensis Unknown ITC
CIRAD 930
ITC1511 acuminata subsp. malaccensis Guadeloupe ITC