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Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae.
Mol Biol Evol 2012; 29(11):3601-11MB

Abstract

We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%-28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%-22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types.

Authors+Show Affiliations

Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany. piednoel@closun.snv.jussieu.frNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

22723303

Citation

Piednoël, Mathieu, et al. "Next-generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae." Molecular Biology and Evolution, vol. 29, no. 11, 2012, pp. 3601-11.
Piednoël M, Aberer AJ, Schneeweiss GM, et al. Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae. Mol Biol Evol. 2012;29(11):3601-11.
Piednoël, M., Aberer, A. J., Schneeweiss, G. M., Macas, J., Novak, P., Gundlach, H., ... Renner, S. S. (2012). Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae. Molecular Biology and Evolution, 29(11), pp. 3601-11. doi:10.1093/molbev/mss168.
Piednoël M, et al. Next-generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae. Mol Biol Evol. 2012;29(11):3601-11. PubMed PMID: 22723303.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae. AU - Piednoël,Mathieu, AU - Aberer,Andre J, AU - Schneeweiss,Gerald M, AU - Macas,Jiri, AU - Novak,Petr, AU - Gundlach,Heidrun, AU - Temsch,Eva M, AU - Renner,Susanne S, Y1 - 2012/06/21/ PY - 2012/6/23/entrez PY - 2012/6/23/pubmed PY - 2013/3/6/medline SP - 3601 EP - 11 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 29 IS - 11 N2 - We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%-28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%-22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/22723303/Next_generation_sequencing_reveals_the_impact_of_repetitive_DNA_across_phylogenetically_closely_related_genomes_of_Orobanchaceae_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mss168 DB - PRIME DP - Unbound Medicine ER -