Unknown

Dataset Information

0

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


ABSTRACT: 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).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%.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.

SUBMITTER: Martin G 

PROVIDER: S-EPMC4793746 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Martin Guillaume G   Baurens Franc-Christophe FC   Droc Gaëtan G   Rouard Mathieu M   Cenci Alberto A   Kilian Andrzej A   Hastie Alex A   Doležel Jaroslav J   Aury Jean-Marc JM   Alberti Adriana A   Carreel Françoise F   D'Hont Angélique A  

BMC genomics 20160316


<h4>Background</h4>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).<h4>Results</h4>We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. Th  ...[more]

Similar Datasets

2020-07-11 | GSE134166 | GEO
| S-EPMC8222437 | biostudies-literature
| S-EPMC5850475 | biostudies-literature
| S-EPMC6282646 | biostudies-literature
| S-EPMC7143517 | biostudies-literature
| S-EPMC2956553 | biostudies-literature
| S-EPMC5717134 | biostudies-literature
| S-EPMC3696114 | biostudies-literature
| S-EPMC7567712 | biostudies-literature
| S-EPMC6522570 | biostudies-literature