Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

Abstract

BackgroundPolyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco) and parental genome donors, N. sylvesteris (S-Genome) and N. tomentosiformis (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant.ResultsA comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place.ConclusionsPolyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in Nicotiana tabacum suggesting it occurs at a low frequency in young polyploidy.

Homeologs of the Nicotiana benthamiana Antiviral ARGONAUTE1 Show Different Susceptibilities to microRNA168-Mediated Control

“…frequently contain so-called homeologs; these are duplicated genes in the same plant genome derived from different ancestors in polyploidy (Bombarely et al, 2012a). In this report, we show that N. benthamiana possesses two NbAGO1-like homeolog genes, NbAGO1-1H and NbAGO1-1L.…”

Time-calibrated phylogenetic trees establish a lag between polyploidisation and diversification in Nicotiana (Solanaceae)

“…Transcriptomic data from N. tabacum have shown that there is little evidence for positive selection on homeologs, and therefore, neofunctionalisation of genes seems unlikely due to the young age of this allotetraploid. However, gene silencing of some homeologs was evident, suggesting some degree of modification to gene expression in this young allotetraploid (Bombarely et al 2012). show that the three polyploids are similar to the sum of their progenitor genomes, but they have experienced small amounts of downsizing in the range of 2-5% below additivity (Leitch et al 2008).…”

“…A current focus is being given to the expression patterns of both young allopolyploids such as N. tabacum (Bombarely et al 2012) and older allopolyploids such as N. benthamiana of section Suaveolentes (Nakasugi et al 2013(Nakasugi et al , 2014. In the following section, we review aspects of diploidisation that have been documented for allopolyploids of different ages in Nicotiana.…”

The legacy of diploid progenitors in allopolyploid gene expression patterns

“…Another is quantitative SNP assays, such as the Sequenom MassARRAY, as used in Tragopogon [46,47] and Gossypium [48]. A third is high-throughput RNA sequencing, as used in Arabidopsis [49], Gossypium [50], Nicotiana [51], Glycine [52], Brassica [53,54] and Coffea [55] allopolyploids. These methods provide the most comprehensive data that we have so far on allopolyploid gene expression, though in general they measure gene expression relative to other genes rather than in an absolute sense (but see [56]), and post-transcriptional regulation can result in levels of protein expression that may not reflect RNA levels in the transcriptome [57,58].…”