Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

Abstract

We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (<200,000 years old), with its diploid progenitors, Nicotiana sylvestris (maternal, S-genome donor), and Nicotiana tomentosiformis (paternal, T-genome donor). Analysis of 14,634 repetitive DNA sequences in the genomes of the progenitor species and N. tabacum reveal all major types of retroelements found in angiosperms (genome proportions range between 17-22.5% and 2.3-3.5% for Ty3-gypsy elements and Ty1-copia elements, respectively). The diploid N. sylvestris genome exhibits evidence of recent bursts of sequence amplification and/or homogenization, whereas the genome of N. tomentosiformis lacks this signature and has considerably fewer homogenous repeats. In the derived allotetraploid N. tabacum, there is evidence of genome downsizing and sequences loss across most repeat types. This is particularly evident amongst the Ty3-gypsy retroelements in which all families identified are underrepresented in N. tabacum, as is 35S ribosomal DNA. Analysis of all repetitive DNA sequences indicates the T-genome of N. tabacum has experienced greater sequence loss than the S-genome, revealing preferential loss of paternally derived repetitive DNAs at a genome-wide level. Thus, the three genomes of N. sylvestris, N. tomentosiformis, and N. tabacum have experienced different evolutionary trajectories, with genomes that are dynamic, stable, and downsized, respectively.

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

“…Subgenome dominance can also manifest itself in ways other than homoeolog expression bias. For instance, in Nicotiana, repeat abundances and rDNA levels exhibit subgenome-specific changes (Kovarik et al, 2008;Renny-Byfield et al, 2011), and in Brassica, expression bias of rRNA genes from a single parent in a hybrid or allopolyploid has been observed (Chen and Pikaard, 1997). In the future, exploring these questions in Mimulus may lead to a more comprehensive understanding of subgenome bias.…”

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

“…carrying chromosomal translocations, deletions and duplications; Lim et al, 2006;Gaeta et al, 2007). Even in synthetic polyploids, changing copy numbers of repeats can be observed (Petit et al, 2010;Renny-Byfield et al, 2011). From these variants, selection favours the most fertile individuals where chromosome pairing and segregation are regular.…”

Molecular Cytogenetics (FISH, GISH) of <b><i>Coccinia grandis</i></b>: A ca. 3 myr-Old Species of Cucurbitaceae with the Largest Y/Autosome Divergence in Flowering Plants

“…Nor is it clear in general how fast plant repetitive DNA is turned over [Renny-Byfield et al, 2011;Piednoel et al, 2012]. The only assembled Y chromosomes so far are those of Homo sapiens and chimpanzee [Skaletsky et al, 2003;Hughes et al, 2010].…”