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The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads Natali, Lucia; Cossu, Rosa M.; Barghini, Elena; Giordani, Tommaso; Buti, Matteo; Mascagni, Flavia; Morgante, Michele; Gill, Navdeep; Kane, Nolan C.; Rieseberg, Loren H.; et al.

Abstract

Background: Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries. Results By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified. Conclusions The results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.

Item Metadata

Title
The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads
Creator
Natali, Lucia; Cossu, Rosa M.; Barghini, Elena; Giordani, Tommaso; Buti, Matteo; Mascagni, Flavia; Morgante, Michele; Gill, Navdeep; Kane, Nolan C.; Rieseberg, Loren H.; Cavallini, Andrea
Contributor
University of British Columbia. Biodiversity Research Centre
Publisher
BioMed Central
Date Issued
2013-10-06
Description
Background: Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries. Results By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified. Conclusions The results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.
Subject
Genome structure; Next Generation Sequencing; Repetitive DNA; Retrotransposon; Sunflower
Genre
Article
Type
Text
Language
eng
Date Available
2015-11-10
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0215873
URI
http://hdl.handle.net/2429/55309
Affiliation
Botany, Department of; Non UBC; Science, Faculty of
Citation
BMC Genomics. 2013 Oct 06;14(1):686
Publisher DOI
10.1186/1471-2164-14-686
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
Natali et al.; licensee BioMed Central Ltd.
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)