Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

Matyášek, Roman; Renny‐Byfield, Simon; Fulneček, Jaroslav; Macas, Jiří; Grandbastien, Marie–Angèle; Nichols, Richard A.; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.1186/1471-2164-13-722

Cited by 51 publications

(49 citation statements)

References 81 publications

(99 reference statements)

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“…The reads were mapped to the 256 bp of ITS1 ( B. oleracea and B. rapa ) and sorted into clusters according to the procedures described by Matyasek et al (2012). The cut off for scoring SNPs was set to ≥ 10 % reads.…”

Section: Methodsmentioning

confidence: 99%

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

Sochorová

Coriton

Kuderová

et al. 2016

Ann Bot

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Background and aims Brassica napus (AACC, 2n = 38, oilseed rape) is a relatively recent allotetraploid species derived from the putative progenitor diploid species Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18). To determine the influence of intensive breeding conditions on the evolution of its genome, we analysed structure and copy number of rDNA in 21 cultivars of B. napus, representative of genetic diversity.Methods We used next-generation sequencing genomic approaches, Southern blot hybridization, expression analysis and fluorescence in situ hybridization (FISH). Subgenome-specific sequences derived from rDNA intergenic spacers (IGS) were used as probes for identification of loci composition on chromosomes.Key Results Most B. napus cultivars (18/21, 86 %) had more A-genome than C-genome rDNA copies. Three cultivars analysed by FISH (‘Darmor’, ‘Yudal’ and ‘Asparagus kale’) harboured the same number (12 per diploid set) of loci. In B. napus ‘Darmor’, the A-genome-specific rDNA probe hybridized to all 12 rDNA loci (eight on the A-genome and four on the C-genome) while the C-genome-specific probe showed weak signals on the C-genome loci only. Deep sequencing revealed high homogeneity of arrays suggesting that the C-genome genes were largely overwritten by the A-genome variants in B. napus ‘Darmor’. In contrast, B. napus ‘Yudal’ showed a lack of gene conversion evidenced by additive inheritance of progenitor rDNA variants and highly localized hybridization signals of subgenome-specific probes on chromosomes. Brassica napus ‘Asparagus kale’ showed an intermediate pattern to ‘Darmor’ and ‘Yudal’. At the expression level, most cultivars (95 %) exhibited stable A-genome nucleolar dominance while one cultivar (‘Norin 9’) showed co-dominance.Conclusions The B. napus cultivars differ in the degree and direction of rDNA homogenization. The prevalent direction of gene conversion (towards the A-genome) correlates with the direction of expression dominance indicating that gene activity may be needed for interlocus gene conversion.

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Section: Methodsmentioning

confidence: 99%

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

Sochorová

Coriton

Kuderová

et al. 2016

Ann Bot

Self Cite

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“…To eliminate production of chimeric products, templates for 454 sequencing were amplified by emulsion PCR described in Matyasek et al (2012). The reads obtained from genomic and cDNA samples were sorted according to sequencing primers into two groups comprising 18S sequences (primers A) and ITS1 sequences (primer B).…”

Section: Sequencing and Cluster Analysismentioning

confidence: 99%

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

et al. 2014

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To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n = 24), formed from the diploid progenitors T. dubius (2n = 12, D-genome donor) and T. porrifolius (2n = 12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely different rRNA gene dosages. Plant 33B had~400 rRNA genes at the D-genome locus, which is typical for T. mirus, accounting for~25% of total rDNA. We observed characteristic expression dominance of T. dubius-origin genes in all organs. Its sister plant 33A harboured a homozygous macrodeletion that reduced the number of T. dubius-origin genes to about 70 copies (~4% of total rDNA). It showed biparental rDNA expression in root, flower and callus, but not in leaf where D-genome rDNA dominance was maintained. There was upregulation of minor rDNA variants in some tissues. The RNA polymerase I promoters of reactivated T. porrifolius-origin rRNA genes showed reduced DNA methylation, mainly at symmetrical CG and CHG nucleotide motifs. We hypothesise that active, decondensed rDNA units are most likely to be deleted via recombination. The silenced homeologs could be used as a 'first reserve' to ameliorate mutational damage and contribute to evolutionary success of polyploids. Deletion and reactivation cycles may lead to bidirectional homogenisation of rRNA arrays in the long term.

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“…This also implies that an asymmetric meiosis is not a prerequisite for the persistence of multiple ITS ribotypes. Instead, intragenomic polymorphisms may be related to distribution of rDNA between different loci [Matyasek et al, 2012], since intralocus homogenization is weaker than that of interlocus [Schlötterer and Tautz, 1994]. Karyotypes with multiple loci may arise from complex reticulation, incomplete lineage sorting, and chromosome rearrangements.…”

Section: Cytogenetic and Molecular Characterization Of Rdna Loci In Tmentioning

confidence: 99%

High Penetrance of a Pan-Canina Type rDNA Family in Intersection Rosa Hybrids Suggests Strong Selection of Bivalent Chromosomes in the Section Caninae

Khaitová

Werlemark²,

Kovaříková³

et al. 2014

Cytogenet Genome Res

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All dogroses (Rosa sect. Caninae) are characterized by the peculiar canina meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-canina rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) Rosa rubiginosa as female parent (producing 4x egg cells due to the unique asymmetrical canina meiosis) and the tetraploid (2n = 4x = 28) garden rose R. hybrida ‘André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that R. rubiginosa and ‘André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In R. rubiginosa and ‘André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to R. rubiginosa. In these individuals, the pan-canina beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in Caninae polyploids.

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Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

Cited by 51 publications

References 81 publications

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

High Penetrance of a Pan-<b><i>Canina</i></b> Type rDNA Family in Intersection <b><i>Rosa</i></b> Hybrids Suggests Strong Selection of Bivalent Chromosomes in the Section <b><i>Caninae</i></b>

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