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

Renny-Byfield S, Kovařík A, Chester M, Nichols RA, Macas J, Novák P, Leitch AR - PLoS ONE (2012)

Bottom Line: Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations.We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor).Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum.

View Article: PubMed Central - PubMed

Affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

ABSTRACT
Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations. We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor). Using next generation sequencing, a recently developed graph-based repeat identification pipeline, Southern blot and fluorescence in situ hybridisation (FISH) we characterise two highly repetitive DNA sequences (NicCL3 and NicCL7/30). Analysis of two independent high-throughput DNA sequencing datasets indicates NicCL3 forms 1.6-1.9% of the genome in N. tomentosiformis, sequences that occur in multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum. Surprisingly elimination of NicCL3 is repeated in some synthetic lines of N. tabacum in their forth generation. The retroelement NicCL7/30, which occurs interspersed with NicCL3, is also under-represented but to a much lesser degree, revealing targeted elimination of the latter. Analysis of paired-end sequencing data indicates the tandem component of NicCL3 has been preferentially removed in natural N. tabacum, increasing the proportion of the dispersed component. This occurs across multiple blocks of discontinuous repeats and based on the distribution of nucleotide similarity among NicCL3 units, was concurrent with rounds of sequence homogenisation.

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Sequence similarity of NicCL3.Histogram of sequence similarity of NicCL3 derived reads in N. tomentosiformis (a) and N. tabacum (b). Kernel density estimations are also shown (black line). Note that both species have evidence of sequence amplification and/or homogenisation (peak at sequence similarity of one). There are 6 peaks in N. tabacum, perhaps indicative of several independent rounds of ancient amplification and or homogenisation. There are a relatively high proportion of low similarity sequences in N. tabacum compared to N. tomentosiformis.
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pone-0036963-g005: Sequence similarity of NicCL3.Histogram of sequence similarity of NicCL3 derived reads in N. tomentosiformis (a) and N. tabacum (b). Kernel density estimations are also shown (black line). Note that both species have evidence of sequence amplification and/or homogenisation (peak at sequence similarity of one). There are 6 peaks in N. tabacum, perhaps indicative of several independent rounds of ancient amplification and or homogenisation. There are a relatively high proportion of low similarity sequences in N. tabacum compared to N. tomentosiformis.

Mentions: In order to detect evidence for rounds of amplification and/or homogenisation of NicCL3, we compared sequence similarity of NicCL3 derived 454 reads in N. tomentosiformis, N. tabacum and N. sylvestris. Reads deriving from N. tomentosiformis and N. tabacum were analysed separately. In addition, we analysed a dataset consisting of reads from N. sylvestris and N. tomentosiformis (representing parental additivity). However because there were so few reads from N. sylvestris the output was nearly identical to that from N. tomentosiformis alone (data not shown). Pair-wise similarity scores for NicCL3 sequences from N. tabacum and N. tomentosiformis were plotted as frequency distributions and kernel density estimates (Fig. 5). This analysis revealed a peak of identical sequences in both N. tomentosiformis and separately in N. tabacum. In addition a major peak of reads with sequence similarity close to 0.95 is evident in N. tomentosiformis. In N. tabacum six separate peaks are visible and the N. tabacum genome contains proportionally more reads with lower sequence similarity compared with N. tomentosiformis (Fig. S1). A two-sample Wilcoxon test revealed a significant difference (p<0.00001) between mean sequence similarity of NicCL3 derived-sequences in N. tomentosiformis (0.93) and N. tabacum (0.90). We also examined the proportion of sequence reads from N. tabacum or N. tomentosiformis matching the consensus (NicCL3, contig 8) for each nucleotide along its length (Figure S1 A). We plotted the average proportion of bases identical to the consensus over consecutive 20 bp windows (Figure S1 B). The data indicate that a similar proportion of bases match along the length of the consensus in both species, with the exception of a region towards the end of NicCL3, where the reads are more divergent.


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

Renny-Byfield S, Kovařík A, Chester M, Nichols RA, Macas J, Novák P, Leitch AR - PLoS ONE (2012)

Sequence similarity of NicCL3.Histogram of sequence similarity of NicCL3 derived reads in N. tomentosiformis (a) and N. tabacum (b). Kernel density estimations are also shown (black line). Note that both species have evidence of sequence amplification and/or homogenisation (peak at sequence similarity of one). There are 6 peaks in N. tabacum, perhaps indicative of several independent rounds of ancient amplification and or homogenisation. There are a relatively high proportion of low similarity sequences in N. tabacum compared to N. tomentosiformis.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3351487&req=5

pone-0036963-g005: Sequence similarity of NicCL3.Histogram of sequence similarity of NicCL3 derived reads in N. tomentosiformis (a) and N. tabacum (b). Kernel density estimations are also shown (black line). Note that both species have evidence of sequence amplification and/or homogenisation (peak at sequence similarity of one). There are 6 peaks in N. tabacum, perhaps indicative of several independent rounds of ancient amplification and or homogenisation. There are a relatively high proportion of low similarity sequences in N. tabacum compared to N. tomentosiformis.
Mentions: In order to detect evidence for rounds of amplification and/or homogenisation of NicCL3, we compared sequence similarity of NicCL3 derived 454 reads in N. tomentosiformis, N. tabacum and N. sylvestris. Reads deriving from N. tomentosiformis and N. tabacum were analysed separately. In addition, we analysed a dataset consisting of reads from N. sylvestris and N. tomentosiformis (representing parental additivity). However because there were so few reads from N. sylvestris the output was nearly identical to that from N. tomentosiformis alone (data not shown). Pair-wise similarity scores for NicCL3 sequences from N. tabacum and N. tomentosiformis were plotted as frequency distributions and kernel density estimates (Fig. 5). This analysis revealed a peak of identical sequences in both N. tomentosiformis and separately in N. tabacum. In addition a major peak of reads with sequence similarity close to 0.95 is evident in N. tomentosiformis. In N. tabacum six separate peaks are visible and the N. tabacum genome contains proportionally more reads with lower sequence similarity compared with N. tomentosiformis (Fig. S1). A two-sample Wilcoxon test revealed a significant difference (p<0.00001) between mean sequence similarity of NicCL3 derived-sequences in N. tomentosiformis (0.93) and N. tabacum (0.90). We also examined the proportion of sequence reads from N. tabacum or N. tomentosiformis matching the consensus (NicCL3, contig 8) for each nucleotide along its length (Figure S1 A). We plotted the average proportion of bases identical to the consensus over consecutive 20 bp windows (Figure S1 B). The data indicate that a similar proportion of bases match along the length of the consensus in both species, with the exception of a region towards the end of NicCL3, where the reads are more divergent.

Bottom Line: Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations.We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor).Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum.

View Article: PubMed Central - PubMed

Affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

ABSTRACT
Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations. We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor). Using next generation sequencing, a recently developed graph-based repeat identification pipeline, Southern blot and fluorescence in situ hybridisation (FISH) we characterise two highly repetitive DNA sequences (NicCL3 and NicCL7/30). Analysis of two independent high-throughput DNA sequencing datasets indicates NicCL3 forms 1.6-1.9% of the genome in N. tomentosiformis, sequences that occur in multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum. Surprisingly elimination of NicCL3 is repeated in some synthetic lines of N. tabacum in their forth generation. The retroelement NicCL7/30, which occurs interspersed with NicCL3, is also under-represented but to a much lesser degree, revealing targeted elimination of the latter. Analysis of paired-end sequencing data indicates the tandem component of NicCL3 has been preferentially removed in natural N. tabacum, increasing the proportion of the dispersed component. This occurs across multiple blocks of discontinuous repeats and based on the distribution of nucleotide similarity among NicCL3 units, was concurrent with rounds of sequence homogenisation.

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