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Open Access Highly Accessed Research article

The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads

Lucia Natali1*, Rosa Maria Cossu1, Elena Barghini1, Tommaso Giordani1, Matteo Buti1, Flavia Mascagni1, Michele Morgante2, Navdeep Gill3, Nolan C Kane34, Loren Rieseberg3 and Andrea Cavallini1

Author Affiliations

1 Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy

2 Department of Crop and Environmental Sciences, University of Udine, Via delle Scienze, Udine, Italy

3 The Biodiversity Research Centre and Department of Botany, 3529–6270 University Blvd, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

4 Ecology and Evolutionary Biology Department, UCB 334, University of Colorado, Boulder, CO 80309, USA

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BMC Genomics 2013, 14:686  doi:10.1186/1471-2164-14-686

Published: 6 October 2013

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.

Keywords:
Genome structure; Next Generation Sequencing; Repetitive DNA; Retrotransposon; Sunflower