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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F16%3A00459912" target="_blank" >RIV/61389030:_____/16:00459912 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1186/s12864-016-2579-4" target="_blank" >http://dx.doi.org/10.1186/s12864-016-2579-4</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12864-016-2579-4" target="_blank" >10.1186/s12864-016-2579-4</a>

Result language

angličtina

Original language name

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

Original language description

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).nResults: 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 %. nConclusion: 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.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

EB - Genetics and molecular biology

OECD FORD branch

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Project

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Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

B M C Genomics

ISSN

1471-2164

e-ISSN

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Volume of the periodical

17

Issue of the periodical within the volume

MAR 16

Country of publishing house

US - UNITED STATES

Number of pages

12

Pages from-to

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UT code for WoS article

000372091000004

EID of the result in the Scopus database

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