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

BMC Genomics

Research Article

Flavia Mascagni¹  Matteo Buti¹  Elena Barghini¹  Andrea Cavallini¹  Rosa Maria Cossu¹  Tommaso Giordani¹  Lucia Natali¹  Michele Morgante²  Navdeep Gill³  Loren Rieseberg³  Nolan C Kane⁴ 

[1] Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy;Department of Crop and Environmental Sciences, University of Udine, Via delle Scienze, Udine, Italy;The Biodiversity Research Centre and Department of Botany, 3529–6270 University Blvd, University of British Columbia, V6T 1Z4, Vancouver, BC, Canada;The Biodiversity Research Centre and Department of Botany, 3529–6270 University Blvd, University of British Columbia, V6T 1Z4, Vancouver, BC, Canada;Ecology and Evolutionary Biology Department, UCB 334, University of Colorado, 80309, Boulder, CO, USA;

关键词: Genome structure;    Next Generation Sequencing;    Repetitive DNA;    Retrotransposon;    Sunflower;   

DOI  :  10.1186/1471-2164-14-686

 received in 2013-04-04, accepted in 2013-10-03,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundNext 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.ResultsBy 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Natali et al.; licensee BioMed Central Ltd. 2013