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The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.
BMC Genomics 2013; 14:686BG

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.

Authors+Show Affiliations

Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy. lnatali@agr.unipi.it.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24093210

Citation

Natali, Lucia, et al. "The Repetitive Component of the Sunflower Genome as Shown By Different Procedures for Assembling Next Generation Sequencing Reads." BMC Genomics, vol. 14, 2013, p. 686.
Natali L, Cossu RM, Barghini E, et al. The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads. BMC Genomics. 2013;14:686.
Natali, L., Cossu, R. M., Barghini, E., Giordani, T., Buti, M., Mascagni, F., ... Cavallini, A. (2013). The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads. BMC Genomics, 14, p. 686. doi:10.1186/1471-2164-14-686.
Natali L, et al. The Repetitive Component of the Sunflower Genome as Shown By Different Procedures for Assembling Next Generation Sequencing Reads. BMC Genomics. 2013 Oct 6;14:686. PubMed PMID: 24093210.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads. AU - Natali,Lucia, AU - Cossu,Rosa Maria, AU - Barghini,Elena, AU - Giordani,Tommaso, AU - Buti,Matteo, AU - Mascagni,Flavia, AU - Morgante,Michele, AU - Gill,Navdeep, AU - Kane,Nolan C, AU - Rieseberg,Loren, AU - Cavallini,Andrea, Y1 - 2013/10/06/ PY - 2013/04/04/received PY - 2013/10/03/accepted PY - 2013/10/8/entrez PY - 2013/10/8/pubmed PY - 2014/7/1/medline SP - 686 EP - 686 JF - BMC genomics JO - BMC Genomics VL - 14 N2 - 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/24093210/The_repetitive_component_of_the_sunflower_genome_as_shown_by_different_procedures_for_assembling_next_generation_sequencing_reads_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-686 DB - PRIME DP - Unbound Medicine ER -