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

Natali, L and Cossu, RM and Barghini, E and Giordani, T and Buti, M and Mascagni, F and Morgante, M and Gill, N and Kane, NC and Rieseberg, L and Cavallini, A (2013) The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads. BMC Genomics, 14 (686). pp. 1-14. ISSN 1471-2164

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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 Type: Article
Uncontrolled Keywords: 06 Biological Sciences, 11 Medical And Health Sciences, 08 Information And Computing Sciences
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Natural Sciences and Psychology
Publisher: BioMed Central
Related URLs:
Date Deposited: 14 Apr 2016 14:03
Last Modified: 14 Apr 2016 14:04
DOI or Identification number: 10.1186/1471-2164-14-686
URI: http://researchonline.ljmu.ac.uk/id/eprint/3428

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