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Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods
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SYSNO ASEP 0459912 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods Tvůrce(i) Martin, G. (FR)
Baurens, F.C. (FR)
Droc, G. (FR)
Rouard, M. (FR)
Cenci, A. (FR)
Kilian, A. (AU)
Hastie, A. (US)
Doležel, Jaroslav (UEB-Q) RID, ORCID
Aury, J. M. (FR)
Alberti, A. (FR)
Carreel, F. (FR)
D'Hont, A. (FR)Zdroj.dok. BMC Genomics. - : BioMed Central - ISSN 1471-2164
Roč. 17, MAR 16 (2016), s. 243Poč.str. 12 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova Musa acuminata ; Genome assembly ; Bioinformatics tool Vědní obor RIV EB - Genetika a molekulární biologie Institucionální podpora UEB-Q - RVO:61389030 UT WOS 000372091000004 DOI https://doi.org/10.1186/s12864-016-2579-4 Anotace 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.Pracoviště Ústav experimentální botaniky Kontakt David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Rok sběru 2017
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