LTR-retrotransposons contribute substantially to the structural diversity of plant genomes. Recent models of genome evolution suggest that retrotransposon amplification is offset by removal of retrotransposon sequences, leading to a turnover of retrotransposon populations. While bursts of amplification have been documented, it is not known whether removal of retrotransposon sequences occurs continuously, or is triggered by specific stimuli over short evolutionary periods. In this work, we have characterized the evolutionary dynamics of four populations of copia-type retrotransposons in allotetraploid tobacco (Nicotiana tabacum) and its two diploid progenitors Nicotiana sylvestris and Nicotiana tomentosiformis. We have used SSAP (Sequence-Specific Amplification Polymorphism) to evaluate the contribution retrotransposons have made to the diversity of tobacco and its diploid progenitor species, to quantify the contribution each diploid progenitor has made to tobacco's retrotransposon populations, and to estimate losses or amplifications of retrotransposon sequences subsequent to tobacco's formation. Our results show that the tobacco genome derives from a turnover of retrotransposon sequences with removals concomitant with new insertions. We have detected unique behaviour specific to each retrotransposon population, with differences likely reflecting distinct evolutionary histories and activities of particular elements. Our results indicate that the retrotransposon content of a given plant species is strongly influenced by the host evolutionary history, with periods of rapid turnover of retrotransposon sequences stimulated by allopolyploidy.
"It is thought that the maternal ancestor of common tobacco was Nicotiana sylvestris.   It is also thought that its paternal ancestor was derived from either N. tomentosiformis,      N. otophora or from introgressive hybridization of N. otophora and N. tomentosiformis within the subgenus of common tobacco.  It has been shown that N. rustica originated from a natural chromosome duplication event after ancestral hybridization of N. paniculata and N. undulate. "
[Show abstract][Hide abstract] ABSTRACT: A pair of primers was designed to amplify the propylene alcohol dehydrogenase gene sequence based on the cDNA sequence of the tobacco allyl-alcohol dehydrogenase gene. All introns were sequenced using traditional polymerase chain reaction (PCR) methods and T-A cloning. The sequences from common tobacco (Nicotiana tabaccum L.) and rustica tobacco (Nicotiana rustica L.) were analysed between the third intron and the fourth intron of the propylene alcohol dehydrogenase gene. The results showed that the alcohol dehydrogenase gene is a low-copy nuclear gene. The intron sequences have a combination of single nucleotide polymorphisms and length polymorphisms between common tobacco and rustica tobacco, which are suitable to identify the different germplasms. Furthermore, there are some single nucleotide polymorphism sites in the target sequence within common tobacco that can be used to distinguish intraspecific varieties.
"s directional [ Skalická et al . , 2005 ; Renny - Byfield et al . , 2012 ; Kovarik et al . , 2012 ] . Se - lected families of copia LTR - retrotransposons diversified subsequent to allopolyploidization , with retroelement losses being more frequent from the paternal T - genome and novel insertions targeting preferentially the maternal S - genome [ Petit et al . , 2007 , 2010 ] . However , spreading of genome - specific transposons to the other parental ge - nome has also been found in cotton [ Zhao et al . , 1998 ] . Genome downsizing in tobacco [ Leitch et al . , 2008 ] can be attributed to extensive losses across most repeat types ( NicCL3 ; A1 / A2 repeats ; NsEPRV , Ty3 / gypsy LTR ele - ments , "
[Show abstract][Hide abstract] ABSTRACT: Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
Cytogenetic and Genome Research 06/2013; 140(2-4). DOI:10.1159/000351727 · 1.56 Impact Factor
"Further, the N. sylvestris genome was reported to have a higher content of Tnt1 transposons and a more uniform distribution of the elements than the N. tomentosiformis genome [42,43]. A more detailed analysis showed that the relative copy numbers of four retrotransposons (Tnt1-OL13, Tnt1-OL16, Tnt2d and Tto1-1R) were higher in N. sylvestris than in N. tomentosiformis . Conversely, Renny-Byfield et al.  found that a highly repetitive DNA sequence (NicCL3) made up to 2% of the N. tomentosiformis genome but was almost absent in the N. sylvestris genome. "
[Show abstract][Hide abstract] ABSTRACT: Background
Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species.
Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis.
The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution.
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