Title | Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods. |
Publication Type | Journal Article |
Year of Publication | 2016 |
Authors | Martin 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 |
Journal | BMC Genomics |
Volume | 17 |
Pagination | 243 |
Date Published | 2016 |
ISSN | 1471-2164 |
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> |
DOI | 10.1186/s12864-016-2579-4 |
Alternate Journal | BMC Genomics |
PubMed ID | 26984673 |
PubMed Central ID | PMC4793746 |
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