Long‐term genome diploidization in allopolyploidNicotianasectionRepandae(Solanaceae)

Abstract

Summary• Here, we analyze long-term evolution in Nicotiana allopolyploid section Repandae (the closest living diploids are N. sylvestris , the maternal parent, and N. obtusifolia , the paternal parent). We compare data with other more recently formed Nicotiana allopolyploids.• We investigated 35S and 5S nuclear ribosomal DNA (rDNA) chromosomal location and unit divergence. A molecular clock was applied to the Nicotiana phylogenetic tree to determine allopolyploid ages.• N. tabacum and species of Repandae were c . 0.2 and 4.5 Myr old, respectively. In all Repandae species, the numbers of both 35S and 5S rDNA loci were less than the sum of those of the diploid progenitors. Trees based on 5S rDNA spacer sequences indicated units of only the paternal parent.• In recent Nicotiana allopolyploids, the numbers of rDNA loci equal the sum of those of their progenitors. In the Repandae genomes, diploidization is associated with locus loss. Sequence analysis indicates that 35S and 5S units most closely resemble maternal and paternal progenitors, respectively. In Nicotiana , 4.5 Myr of allopolyploid evolution renders genomic in situ hybridization (GISH) unsuitable for the complete resolution of parental genomes.

Conservation of Plastid Sequences in the Plant Nuclear Genome for Millions of Years Facilitates Endosymbiotic Evolution

“…Using spontaneous mutation accumulation rate of the Arabidopsis nuclear genome (Ossowski et al, 2010), these nupt sequences were estimated to have been inserted into the nucleus between 1.06 and 5.81 Mya (Table II). These results are in accordance with molecular clock analyses that predicted that N. tomentosiformis and N. sylvestris diverged 4.5 to 11 Mya (Wikströ m et al, 2001;Clarkson et al, 2005). Similarly, we estimate that the two nupt sequences obtained from N. tabacum were transferred to the nucleus 0.033 and 4.86 Mya in an ancestor of N. tomentosiformis after the divergence of the N. tomentosiformis and N. sylvestris lineages.…”

“…These deletions observed in N. sylvestris were also present in the N. tabacum plastome. These two species contain the same deletions when compared with other Solanaceae since N. sylvestris was the maternal diploid parent of the allotetraploid N. tabacum, which was formed ,0.2 million years ago (Mya; Clarkson et al, 2005), and the plastomes of these two species only differ by nine nucleotides (Yukawa et al, 2006). Such comparisons revealed seven deletions that were unique to the plastome of N. tomentosiformis (five in the large single-copy [LSC] region and two in the inverted repeat [IR] region) and two that characterized the plastomes of N. sylvestris and N. tabacum (one in the LSC and one in the inverted repeat region; Fig.…”

“…1B). The presence of plastomic deletion events unique to N. sylvestris or to N. tomentosiformis indicates that they occurred after the divergence of these two species about 4.5 to 11 Mya (Wikström et al, 2001;Clarkson et al, 2005). We assumed that, prior to deletion, these regions could have been transferred from the chloroplast to the nucleus where they may still be found.…”

Dispersals of Hyoscyameae and Mandragoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia

“…Wikström et al (2001) dated the split between Nicotiana and Petunia at 23-25 mya in their chronogram of angiosperm. Clarkson et al (2005) dated the age of the split between Nicotiana and its sister, Symonanthus, at 15.3 mya by using ITS sequence data and one calibration point. The split between Nolana and Lycium inferred by our data is at 10.20 mya, which is very similar to the results of Dillon et al (2009), who dated it at 10.39 mya by using three plastid DNA regions and two fossil calibration points.…”

Unraveling the sequence dynamics of the formation of genus-specific satellite DNAs in the family solanaceae

“…Although some plants with large genomes are polyploid (Clarkson et al, 2005), most differences in size and composition arise from differences in the repetitive DNA complement of the species (Olmstead et al, 1999). Repetitive sequences exhibit diverse compositions in different genomes owing to a much faster evolutionary rate than that of coding sequences, and, therefore, changes in repetitive sequences may be particularly useful in understanding genome evolution.…”