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The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

Barghini E, Natali L, Cossu RM, Giordani T, Pindo M, Cattonaro F, Scalabrin S, Velasco R, Morgante M, Cavallini A - Genome Biol Evol (2014)

Bottom Line: The genome data set was subdivided into highly and medium redundant and nonredundant contigs.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.

View Article: PubMed Central - PubMed

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

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.

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Composition of the tandem repeat class in the olive genome, based on the number of Illumina reads that map to the OLEAREP database.
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evu058-F5: Composition of the tandem repeat class in the olive genome, based on the number of Illumina reads that map to the OLEAREP database.

Mentions: Olive tandem repeats belong to six major families, defined according to their sequence and length (table 7 and fig. 5). The first three families (Oe80, Oe178, and Oe86) correspond to the OeTaq80, OeTaq178, and OeGEM86 families described by Bitonti et al. (1999) and Minelli et al. (2000) and account for ∼72% of tandem repeats. The fourth family (Oe179) was for the first time identified in this survey: it represents 12.6% of the tandem repeats and the most common repeat unit is 179-bp long; within this family, a number of repeats resulted truncated, with a variable length. In some cases, truncated elements were also arranged in repeat arrays, suggesting that the truncation has occurred while Oe179 was still replicating, with the truncated units that have continued their amplification.Fig. 5.—


The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

Barghini E, Natali L, Cossu RM, Giordani T, Pindo M, Cattonaro F, Scalabrin S, Velasco R, Morgante M, Cavallini A - Genome Biol Evol (2014)

Composition of the tandem repeat class in the olive genome, based on the number of Illumina reads that map to the OLEAREP database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4007544&req=5

evu058-F5: Composition of the tandem repeat class in the olive genome, based on the number of Illumina reads that map to the OLEAREP database.
Mentions: Olive tandem repeats belong to six major families, defined according to their sequence and length (table 7 and fig. 5). The first three families (Oe80, Oe178, and Oe86) correspond to the OeTaq80, OeTaq178, and OeGEM86 families described by Bitonti et al. (1999) and Minelli et al. (2000) and account for ∼72% of tandem repeats. The fourth family (Oe179) was for the first time identified in this survey: it represents 12.6% of the tandem repeats and the most common repeat unit is 179-bp long; within this family, a number of repeats resulted truncated, with a variable length. In some cases, truncated elements were also arranged in repeat arrays, suggesting that the truncation has occurred while Oe179 was still replicating, with the truncated units that have continued their amplification.Fig. 5.—

Bottom Line: The genome data set was subdivided into highly and medium redundant and nonredundant contigs.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.

View Article: PubMed Central - PubMed

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

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.

Show MeSH