Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum

An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae)

Tragopogon miscellus and Tragopogon mirus are two rare examples of allopolyploids that have formed recently in nature. Molecular cytogenetic studies have revealed chromosome copy number variation and intergenomic translocations in both allotetraploids. Due to a lack of interstitial chromosome markers, there remained the possibility of additional karyotype restructuring in these neopolyploids, via intrachromosomal and intragenomic rearrangements. To address this issue, we searched for additional high-copy tandem repeats in genomic sequences of the diploid progenitor species-Tragopogon dubius, Tragopogon pratensis and Tragopogon porrifolius-for application to the chromosomes of the allotetraploids. Eight novel repeats were localised by fluorescence in situ hybridisation (FISH) in the diploids; one of these repeats, TTR3, provided interstitial coverage. TTR3 was included in a cocktail with other previously characterised probes, producing better-resolved karyotypes for the three diploids. The cocktail was then used to test a hypothesis of karyotype restructuring in the recent allotetraploid T. miscellus by comparing repeat distributions to its diploid progenitors, T. dubius and T. pratensis. Five individuals of T. miscellus were selected from across the range of karyotypic variation previously observed in natural populations. FISH signal distributions mostly matched those observed in the diploid progenitors, with the exception of several losses or gains of signal at chromosomal subtermini and previously noted intergenomic translocations. Thus, in T. miscellus, we find most changes restricted to the subterminal regions, and although some were recurrent, none of the changes were common to all individuals analysed. We consider these findings in relation to the gene loss reported previously for T. miscellus.

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

BACKGROUND

Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with more than a few hundred copies of the rDNA unit. Here we study rDNA complexity in species with arrays consisting of thousands of units.

METHODS

We examined homogeneity of genic (18S) and non-coding internally transcribed spacer (ITS1) regions of rDNA using Roche 454 and/or Illumina platforms in four angiosperm species, Nicotiana sylvestris, N. tomentosiformis, N. otophora and N. kawakamii. We compared the data with Southern blot hybridisation revealing the structure of intergenic spacer (IGS) sequences and with the number and distribution of rDNA loci.

RESULTS AND CONCLUSIONS

In all four species the intragenomic homogeneity of the 18S gene was high; a single ribotype makes up over 90% of the genes. However greater variation was observed in the ITS1 region, particularly in species with two or more rDNA loci, where >55% of rDNA units were a single ribotype, with the second most abundant variant accounted for >18% of units. IGS heterogeneity was high in all species. The increased number of ribotypes in ITS1 compared with 18S sequences may reflect rounds of incomplete homogenisation with strong selection for functional genic regions and relaxed selection on ITS1 variants. The relationship between the number of ITS1 ribotypes and the number of rDNA loci leads us to propose that rDNA evolution and complexity is influenced by locus number and/or amplification of orphaned rDNA units at new chromosomal locations.