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A computational comparative study of the repetitive DNA in the genus Quercus L

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Abstract

An overall picture comparing the repetitive components of the genomes of three Quercus species was obtained by genome skimming with Illumina sequence reads. Read sets of Q. lobata, Q. robur, and Q. suber species were subjected to hybrid clustering in order to assemble a repeatome of the Quercus genus and to annotate it. The repeatome was composed of 8573 clusters. The abundance of repeated sequences in the three species was assessed by mapping Illumina reads of each species onto the repeatome. The repetitive portion of the genome was similar among the three species. The most abundant repetitive sequences were long terminal repeat-retrotransposons. Copia elements were overrepresented when compared with Gypsy ones. The most abundant retrotransposon lineages were SIRE for the Copia superfamily and Ogre/TAT for the Gypsy superfamily. Some of the clusters belonging to these lineages showed different transpositional time profiles among the three species. Ribosomal DNAs accounted for 3.64–6.75% of the repetitive component. Satellite DNAs were much more abundant in Q. lobata (8.68% of the genome) than in the two other species. However, different satellite DNAs showed large variations in their abundances. Overall, the composition of the repetitive portion of the genome showed some differences among oak species, suggesting a possible role of repeats for Quercus species differentiation. In the cases of Q. lobata and Q. robur, both of which belong to the Quercus section of the Quercus genus, such differences may be related to the different geographical origins of the species.

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Data availability

All genomic DNA raw Illumina sequences used in this work are available at the NCBI Sequence Read Archive under the accession numbers SRR3244044 (Quercus lobata), ERR1824219 (Q. robur), and SRR5820934 (Q. suber). The fasta file of the repeatome of Quercus, containing 8497 clusters generated by RepeatExplorer, is available as Supplementary material no. 2. Computational resources for using RepeatExplorer were provided by the ELIXIR-CZ project (LM2015047), part of the international ELIXIR infrastructure.

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Funding

This research work was supported by Department of Agriculture, Food and Environment, University of Pisa, Italy, project Plantomics.

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  1. Flavia Mascagni and Alberto Vangelisti contributed equally to this work.

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  1. Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy

    Flavia Mascagni, Alberto Vangelisti, Tommaso Giordani, Andrea Cavallini & Lucia Natali

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  1. Flavia Mascagni
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  2. Alberto Vangelisti
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  4. Andrea Cavallini
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Correspondence to Lucia Natali.

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ESM 1

Perl scripts used in this study (DOC 24 kb)

ESM 2

Fasta file of the repeatome of Quercus, containing 8497 clusters generated by RepeatExplorer (version 2) (FASTA 6245 kb)

ESM 3

Annotation and number of mapped reads in the assembled Quercus repeatome (XLSX 2308 kb)

ESM 4

Satellite DNAs identified by RepeatExplorer/TAREAN. For each satellite, the corresponding graph, the consensus sequences, and the satellite probability according to RepeatExplorer/TAREAN are reported (PDF 120 kb)

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Mascagni, F., Vangelisti, A., Giordani, T. et al. A computational comparative study of the repetitive DNA in the genus Quercus L. Tree Genetics & Genomes 16, 11 (2020). https://doi.org/10.1007/s11295-019-1401-2

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