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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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Nucleotide diversity (the number of nucleotide substitutions per site) of six tandem repeat families, calculated aligning 100 “real” sequences per family (the 100 sequences most similar to the consensus). Histograms labeled with the same letter are not significantly different (P > 0.05).
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evu058-F7: Nucleotide diversity (the number of nucleotide substitutions per site) of six tandem repeat families, calculated aligning 100 “real” sequences per family (the 100 sequences most similar to the consensus). Histograms labeled with the same letter are not significantly different (P > 0.05).

Mentions: A distance tree was constructed using 100 sequences for each of the six repeat types, to evaluate the relationship among tandem repeat families (fig. 6). The tree shows that tandem repeat families are quite separated. For each tandem repeat family, nucleotide diversity (the number of nucleotide substitutions per site) was calculated. Figure 7 shows that Oe 218 is the most variable, followed Oe178, and Oe80; minor variations are observed within Oe179, Oe86, and Oe51.Fig. 6.—


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)

Nucleotide diversity (the number of nucleotide substitutions per site) of six tandem repeat families, calculated aligning 100 “real” sequences per family (the 100 sequences most similar to the consensus). Histograms labeled with the same letter are not significantly different (P > 0.05).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu058-F7: Nucleotide diversity (the number of nucleotide substitutions per site) of six tandem repeat families, calculated aligning 100 “real” sequences per family (the 100 sequences most similar to the consensus). Histograms labeled with the same letter are not significantly different (P > 0.05).
Mentions: A distance tree was constructed using 100 sequences for each of the six repeat types, to evaluate the relationship among tandem repeat families (fig. 6). The tree shows that tandem repeat families are quite separated. For each tandem repeat family, nucleotide diversity (the number of nucleotide substitutions per site) was calculated. Figure 7 shows that Oe 218 is the most variable, followed Oe178, and Oe80; minor variations are observed within Oe179, Oe86, and Oe51.Fig. 6.—

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