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

0459912 - ÚEB 2017 RIV US eng J - Journal Article
Martin, G. - Baurens, F.C. - Droc, G. - Rouard, M. - Cenci, A. - Kilian, A. - Hastie, A. - Doležel, Jaroslav - Aury, J. M. - Alberti, A. - Carreel, F. - D'Hont, A.
Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
BMC Genomics. Roč. 17, MAR 16 (2016), s. 243. ISSN 1471-2164. E-ISSN 1471-2164
Institutional support: RVO:61389030
Keywords : Musa acuminata * Genome assembly * Bioinformatics tool
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 3.729, year: 2016

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 %.
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.
Permanent Link: http://hdl.handle.net/11104/0260068