Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa

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Authors

ŠTEFLOVÁ Pavlína TOKAN Viktor VOGEL Ivan LEXA Matej MACAS Jiří NOVAK Petr HOBZA Roman VYSKOT Boris KEJNOVSKÝ Eduard

Year of publication 2013
Type Article in Periodical
Magazine / Source GENOME BIOLOGY AND EVOLUTION
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://gbe.oxfordjournals.org/content/5/4/769.full.pdf+html
Doi http://dx.doi.org/10.1093/gbe/evt049
Field Genetics and molecular biology
Keywords sex chromosomes; sorrel (Rumex acetosa); transposable elements; satellites
Attached files
Description Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated.We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes,whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and otherswere depleted fromthe X chromosome. One group of CRM Gypsywas specifically localized to centromeres.Wealso found thatmajority of previously described satellites (RAYSI, RAYSII, RAYSIII, andRAE180) are accumulatedontheYchromosomeswherewe identifiedYchromosome-specific variant ofRAE180.Wediscovered two novel satellites-RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from IlluminaRNAsequencing showedthat the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa,where not only accumulation but also depletion of repetitiveDNAwas observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.
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