Satellite repeats significantly contribute to chromosome divergence as a result of their high abundance and rapid evolution (Plohl et al., 2008). The diploid-like meiotic behaviour of allopolyploids is thought to result from the divergence between homeologous chromosomes, which may already exist and/or be accentuated at the onset of polyploid formation (Le Comber et al., 2010) and involve the rearrangement of large chromosome fragments, or from the activity of Pairing homeologous (Ph) genes (reviewed in (Jenczewski & Alix, 2004; Cifuentes et al., 2010). Indeed, many allopolyploids combining sufficiently similar genomes show intergenomic translocations at their early phase of evolution (Osborn et al., 2003; Lim et al., 2008), while allopolyploids combining divergent genomes appear to maintain intact parental chromosomes over a long evolutionary period of time (Kotseruba et al., 2003; Lim et al., 2005, 2007a,b). However, there is no strict consensus on the contribution of the phylogenetic divergence of parents to the successful formation of allopolyploid species (Buggs et al., 2008; Paun et al., 2009). Historically, Grant (1981) emphasized the role of chromosomal repatterning rather than phylogenetic distance per se. Here, we propose that structural divergence at the critical parts of chromosomes, such as the telomeres and centromeres, is important for stabilization of the allotetraploid nucleus, whereas the divergence of other parts of chromosomes may not play a role or may be less important. The following supports this hypothesis. In Nicotiana, three relatively recent allotetraploids exist, N. arentsii, N. rustica and N. tabacum, which are all believed to have originated < 200 000 yr ago (Clarkson et al., 2004). The phylogenetic distance between progenitor species decreases in the following order: N. tabacum > N. rustica > N. arentsii. Up to nine intergenomic translocations were identified in tobacco (Kenton et al., 1993; Moscone et al., 1996), whereas none were observed in N. rustica or N. arentsii (Lim et al., 2004), suggesting that tobacco has the least stable genome. The progenitors of N. arentsii and N. rustica evolved bulky subtelomeric satellites that were faithfully transmitted to the allotetraploids derived (this study; Lim et al., 2004). These megabase-sized subtelomeric clusters, which significantly differ in sequence or conformation, might contribute to the stabilization of parental chromosomes by preferential recognition of homologous chromosomes in allopolyploid meiosis. By contrast, the lack of subtelomeric satellites in one of the tobacco subgenomes (T), as evidenced by cytogenetic (Kenton et al., 1993), molecular (Horakova & Fajkus, 2000) and genomic (Renny-Byfield et al., 2011) studies, may stimulate homeologous pairing, possibly explaining the frequent intergenomic translocations in the tobacco genome. The second argument supporting a stabilizing role of subtelomeric satellites is based on the differential behaviour of subtelomeric satellites and rDNA repeats. It is known that rDNA, unlike satellite repeats, was largely homogenized in all natural Nicotiana allotetraploids, largely irrespective of age (Kovarik et al., 2004). Chromosome arms bearing active rDNA loci (NORs) at subtelomeric positions usually lack subtelomeric satellites (Lim et al., 2000). Thus, an absence of subtelometric satellites may render NOR-bearing chromosomes more vulnerable to genetic interaction (Kovarik et al., 2008).
We conclude that the positions of divergent (in primary structure or conformation) satellite repeats at critical chromosomal sites such as telomeres are likely to positively influence the survival time of parental chromosomes in the allopolyploid nucleus. Certainly, over longer evolutionary time periods (1 million yr), translocations of satellites to alien chromosomes can occur (Koukalova et al., 2010). In the future, it will be interesting to test this hypothesis in other natural and synthetic systems.