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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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Sequence composition of the OLEAREP database (HR and MR sequences).
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evu058-F4: Sequence composition of the OLEAREP database (HR and MR sequences).

Mentions: The frequency distribution of different sequence types in OLEAREP is reported in figure 4, in which RCs were further subdivided into two fractions, according to their average coverage, highly repeated (HR, 5,744 contigs), and medium repeated (MR, 80,727 contigs).Fig. 4.—


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)

Sequence composition of the OLEAREP database (HR and MR sequences).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu058-F4: Sequence composition of the OLEAREP database (HR and MR sequences).
Mentions: The frequency distribution of different sequence types in OLEAREP is reported in figure 4, in which RCs were further subdivided into two fractions, according to their average coverage, highly repeated (HR, 5,744 contigs), and medium repeated (MR, 80,727 contigs).Fig. 4.—

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