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

0394950 - BFÚ 2014 RIV GB eng J - Journal Article
Šteflová, Pavlína - Tokan, Viktor - Vogel, Ivan - Lexa, M. - Macas, Jiří - Novák, Petr - Hobza, Roman - Vyskot, Boris - Kejnovský, Eduard
Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa.
Genome Biology and Evolution. Roč. 5, č. 4 (2013), s. 769-782. ISSN 1759-6653. E-ISSN 1759-6653
R&D Projects: GA ČR(CZ) GAP305/10/0930; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP501/12/2220
Grant - others:GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707 ; RVO:60077344
Keywords : Y-CHROMOSOME * REPETITIVE SEQUENCES * SILENE-LATIFOLIA
Subject RIV: BO - Biophysics; EB - Genetics ; Molecular Biology (BC-A)
Impact factor: 4.532, year: 2013

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 Y-1 and Y-2 chromosomes, whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y-1 and Y-2 chromosomes, and others were depleted from the X chromosome. One group of CRM Gypsy was specifically localized to centromeres. We also found that majority of previously described satellites (RAYSI, RAYSII, RAYSIII, and RAE180) are accumulated on the Y chromosomes where we identified Y chromosome-specific variant of RAE180.
Permanent Link: http://hdl.handle.net/11104/0223208