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Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile.
Mar Genomics 2015; 24 Pt 3:397-404MG

Abstract

Posidonia oceanica is a monocotyledonous marine plant that plays a crucial role in maintaining the Mediterranean environment. Despite its ecological importance, basic knowledge of the functional and structural genomics of this species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive component of the genome of this seagrass using a low coverage of Illumina sequences and different assembly approaches. A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome, was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTR-retrotransposons were classified and their sequences analysed. Gypsy elements belong to three main lineages, while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have experienced amplification in more recent times compared to Copia ones.

Authors+Show Affiliations

Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy.Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy.Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy.Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy.Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy. Electronic address: andrea.cavallini@unipi.it.

Pub Type(s)

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

Language

eng

PubMed ID

26472701

Citation

Barghini, Elena, et al. "Analysis of the Repetitive Component and Retrotransposon Population in the Genome of a Marine Angiosperm, Posidonia Oceanica (L.) Delile." Marine Genomics, vol. 24 Pt 3, 2015, pp. 397-404.
Barghini E, Mascagni F, Natali L, et al. Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile. Mar Genomics. 2015;24 Pt 3:397-404.
Barghini, E., Mascagni, F., Natali, L., Giordani, T., & Cavallini, A. (2015). Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile. Marine Genomics, 24 Pt 3, pp. 397-404. doi:10.1016/j.margen.2015.10.002.
Barghini E, et al. Analysis of the Repetitive Component and Retrotransposon Population in the Genome of a Marine Angiosperm, Posidonia Oceanica (L.) Delile. Mar Genomics. 2015;24 Pt 3:397-404. PubMed PMID: 26472701.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile. AU - Barghini,Elena, AU - Mascagni,Flavia, AU - Natali,Lucia, AU - Giordani,Tommaso, AU - Cavallini,Andrea, Y1 - 2015/10/21/ PY - 2015/06/27/received PY - 2015/09/24/revised PY - 2015/10/08/accepted PY - 2015/10/17/entrez PY - 2015/10/17/pubmed PY - 2016/9/23/medline KW - Genome structure KW - LTR-retrotransposons KW - Low coverage illumina sequencing KW - Posidonia oceanica KW - Seagrasses SP - 397 EP - 404 JF - Marine genomics JO - Mar Genomics VL - 24 Pt 3 N2 - Posidonia oceanica is a monocotyledonous marine plant that plays a crucial role in maintaining the Mediterranean environment. Despite its ecological importance, basic knowledge of the functional and structural genomics of this species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive component of the genome of this seagrass using a low coverage of Illumina sequences and different assembly approaches. A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome, was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTR-retrotransposons were classified and their sequences analysed. Gypsy elements belong to three main lineages, while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have experienced amplification in more recent times compared to Copia ones. SN - 1876-7478 UR - https://www.unboundmedicine.com/medline/citation/26472701/Analysis_of_the_repetitive_component_and_retrotransposon_population_in_the_genome_of_a_marine_angiosperm_Posidonia_oceanica__L___Delile_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1874-7787(15)30035-0 DB - PRIME DP - Unbound Medicine ER -