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The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.
Genome Biol Evol 2014; 6(4):776-91GB

Abstract

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

Authors+Show Affiliations

Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Italy.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 available

Pub Type(s)

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

Language

eng

PubMed ID

24671744

Citation

Barghini, Elena, et al. "The Peculiar Landscape of Repetitive Sequences in the Olive (Olea Europaea L.) Genome." Genome Biology and Evolution, vol. 6, no. 4, 2014, pp. 776-91.
Barghini E, Natali L, Cossu RM, et al. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. Genome Biol Evol. 2014;6(4):776-91.
Barghini, E., Natali, L., Cossu, R. M., Giordani, T., Pindo, M., Cattonaro, F., ... Cavallini, A. (2014). The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. Genome Biology and Evolution, 6(4), pp. 776-91. doi:10.1093/gbe/evu058.
Barghini E, et al. The Peculiar Landscape of Repetitive Sequences in the Olive (Olea Europaea L.) Genome. Genome Biol Evol. 2014;6(4):776-91. PubMed PMID: 24671744.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. AU - Barghini,Elena, AU - Natali,Lucia, AU - Cossu,Rosa Maria, AU - Giordani,Tommaso, AU - Pindo,Massimo, AU - Cattonaro,Federica, AU - Scalabrin,Simone, AU - Velasco,Riccardo, AU - Morgante,Michele, AU - Cavallini,Andrea, PY - 2014/3/28/entrez PY - 2014/3/29/pubmed PY - 2015/2/13/medline KW - Olea europaea KW - assembly of NGS reads KW - genome landscape KW - repetitive DNA KW - retrotransposons KW - tandem repeats SP - 776 EP - 91 JF - Genome biology and evolution JO - Genome Biol Evol VL - 6 IS - 4 N2 - Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/24671744/The_peculiar_landscape_of_repetitive_sequences_in_the_olive__Olea_europaea_L___genome_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evu058 DB - PRIME DP - Unbound Medicine ER -