Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years

Koukalová, B.; Moraes, Ana Paula; Renny‐Byfield, Simon; Matyášek, Roman; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.1111/j.1469-8137.2009.03101.x

Cited by 74 publications

(75 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The lower the copy number of a satellite, the less homogenization takes place which inhibits the formation of a species-specific satellite family [Hemleben et al, 2007] as can be seen in B. lomatogona , B. nana and C. quinoa . However, when the copy number strongly increases, fast homogenization might occur, and a speciesspecific and homogenized satellite family may evolve [Koukalova et al, 2010]. Because pEV is highly abundant in species of the sections Beta and Procumbentes , the species-specific pEV subfamilies contain highly similar and homogenized pEV copies which might have been generated by rolling circle amplification [Cohen et al, 2008[Cohen et al, , 2010Navrátilová et al, 2008;Cohen and Segal, 2009].…”

Section: Discussionmentioning

confidence: 99%

Cytosine Methylation of an Ancient Satellite Family in the Wild Beet Beta procumbens

Schmidt

Hense

Minoche³

et al. 2014

Cytogenet Genome Res

View full text Add to dashboard Cite

DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.

show abstract

Section: Discussionmentioning

confidence: 99%

Cytosine Methylation of an Ancient Satellite Family in the Wild Beet Beta procumbens

Schmidt

Hense

Minoche³

et al. 2014

Cytogenet Genome Res

View full text Add to dashboard Cite

show abstract

“…Southern blotting followed the protocol described by Koukalova et al (2010) using rDNA probes labeled with [α-32 P]dCTP (Izotop, Hungary) in a random-primed reaction (DekaPrime kit, Fermentas, Lithuania). For gene ratio estimation, the probe was a cloned ITS1 subregion obtained by amplification of B. napus DNA with the 18Sfor and 5.8Srev primers ).…”

Section: Southern Blot Analysis Of 35s Rdnamentioning

confidence: 99%

Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus

Książczyk

Kovařı́k

Eber³

et al. 2011

Chromosoma

Self Cite

View full text Add to dashboard Cite

The dynamics of genome modification that occurred from the initial hybridization event to the stabilization of allopolyploid species remains largely unexplored. Here, we studied inheritance and expression of rDNA loci in the initial generations of Brassica napus allotetraploids (2n = 38, AACC) resynthesized from Brassica oleracea (2n = 18, CC) and B. rapa (2n = 20, AA) and compared the patterns to natural forms. Starting already from F1 generation, there was a strong uniparental silencing of B. oleracea genes. The epigenetic reprogramming was accompanied with immediate condensation of C-genome nucleolar organizer region (NOR) and progressive transgeneration hypermethylation of polymerase I promoters, mainly at CG sites. No such changes were observed in the A-genome NORs. Locus loss and gains affecting mainly non-NOR loci after the first allotetraploid meiosis did not influence established functional status of NORs. Collectively, epigenetic and genetic modifications in synthetic lines resemble events that accompanied formation of natural allopolyploid species.

show abstract

“…By examining the changes in the duplicated regions (homoeologous) in soybean following polyploidy, Innes et al (2008) demonstrated that the largest contributor to genome expansion was retroelement content, with homoeolog 2 having expanded to threefold the size of homoeolog 1, suggesting that retrotransposon accumulation contributed to the genome expansion. A recent report suggested that amplifications of dispersed microsatellite repeats may play a role in genome size evolution in polyploids (Koukalova et al 2010).…”

Section: Evolutionary Genomicsmentioning

confidence: 99%

Genomic aspects of research involving polyploid plants

Yang

Cheng

et al. 2010

Plant Cell Tiss Organ Cult

View full text Add to dashboard Cite

Almost all extant plant species have doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been developed during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomic diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. Polyploids will be a focus of genomic research in the future as rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

show abstract

Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years

Cited by 74 publications

References 68 publications

Cytosine Methylation of an Ancient Satellite Family in the Wild Beet <b><i>Beta procumbens</i></b>

Cytosine Methylation of an Ancient Satellite Family in the Wild Beet <b><i>Beta procumbens</i></b>

Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus

Genomic aspects of research involving polyploid plants

Contact Info

Product

Resources

About