Next-generation sequencing reveals the impact of repetitive DNA in phylogenetically closely related genomes of Orobanchaceae

Piednoël, Mathieu; Aberer, Andre J.; Schneeweiss, Gerald M.; Macas, Jiri; Novak, Petr; Gundlach, Heidrun; Temsch, Eva M. and Renner, Susanne S. (2012): Next-generation sequencing reveals the impact of repetitive DNA in phylogenetically closely related genomes of Orobanchaceae. In: Molecular biology and evolution, Vol. 29, No. 11: pp. 3601-3611

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.

• Item Type: Journal article
• Form of publication: Postprint
• Keywords: next-generation sequencing, polyploidy, genome size, genome downsizing, transposable elements, LTR retrotransposons, Ty3/Gypsy, Orobanche, Phelipanche, Orobanchaceae
• Faculties: Biology
• Subjects: 500 Science > 570 Life sciences; biology
• ISSN: 0737-4038
• Language: English