Biology Faculty Articles
Document Type
Article
Publication Date
10-6-2013
Publication Title
BMC Genomics
Keywords
Genome structure, Next Generation Sequencing, Repetitive DNA, Retrotransposon, Sunflower
ISSN
1471-2164
Volume
14
First Page
686
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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
NSUWorks Citation
Natali, Lucia; Rosa Maria Cossu; Elena Barghini; Tommaso Giordani; Matteo Buti; Flavia Mascagni; Michele Morgante; Navdeep Gill; Nolan Kane; Loren Rieseberg; and Andrea Cavallini. 2013. "The Repetitive Component of the Sunflower Genome as Shown by Different Procedures for Assembling Next Generation Sequencing Reads." BMC Genomics 14, (): 686. doi:https://doi.org/10.1186/1471-2164-14-686.
ORCID ID
orcid-logo http://orcid.org/0000-0003-3746-1866
DOI
https://doi.org/10.1186/1471-2164-14-686
Comments
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.