Tragopogon provides the unique opportunity to investigate the genetic and genomic changes that occur across an evolutionary series from F1 hybrids, synthetic allopolyploids, independently formed natural populations of T. mirus and T. miscellus that are 60-80 years post-formation, to older Eurasian polyploids that are dated by molecular clocks at several million years old, and finally to a putative ancient polyploidization thought to have occurred prior to or early in the history of the Asteraceae (40-43 mya).
Over the past several decades several different genomic approaches have been applied to the Tragopogon system. Our initial studies to examine nuclear gene loss and silencing employed a one gene at a time approach (e.g., Tate et al., 2006, 2009). As an initial genomics approach, we used Sequenom MassARRAY iPLEX genotyping; this methodology (Buggs et al. 2010) multiplexes locus assays and allows for the detection of losses of single alleles (of which each homeolog normally has two immediately after genome doubling. Using this methodology Buggs et al (2012) examined 139 putative SNPs across nearly 100 plants of T. miscellus representing polyploid populations of multiple origin as well as its diploid parents, T. dubius and T. pratensis. Buggs et al. (2012) found that genes were repeatedly retained or lost in clusters. Interestingly, the gene ontology categories of the missing genes in Tragopogon miscellus correspond to those lost after ancient polyploidy deep in time in the same family (Asteraceae)(Barker et al., 2008). These results of Buggs et al. (2012) provide more evidence that in fact the outcomes of polyploidy may be predictable, even in 40 generations. Also, Buggs et al. (2012) detected a high frequency of single-allele losses and a low frequency of changes fixed within populations—suggesting that they caught gene loss/silencing in the act in this young polyploid.
A subsequent series of studies (Boatwright et al., 2018, 2021; Shan et al. 2020) used transcriptomes to investigate gene loss and silencing in polyploid Tragopogon species. Boatwright et al. (2018) describe a novel analytical approach for assessing homeolog-specific expression in polyploids using transcriptome data. With this approach it was possible to examine a much larger gene set than in the earlier Sequenome studies. For example, Boatwright et al. (2018) isolated the overlapping orthologous pairs between T. dubius and T. porrifolius that did not exhibit mapping bias for parental reads resulting in 8,064 orthologous pairs with low read-mapping bias for their analysis of T. mirus and identified 7,202 orthologous pairs for their study of T. miscellus. With this method Boatwright et al. (2018) found that both Tragopogon allopolyploids exhibit relatively balanced homeolog expression with no strong parental bias.
Boatwright et al. (2021) used the same approach developed by Boatwright et al. (2018) to examine expression changes in the Old Word polyploid T. castellanus, a polyploid much older than T. mirus and T. miscellus (see section on Old World Polyploids). They found that expression changes are highly similar among independently formed polyploid populations of T. castellanus. They also compared results for T. castellanus with the two young New World Tragopogon allopolyploids. Homoeolog expression bias was balanced in all of three of these polyploids. However, the degree of additive expression was very different, with T. castellanus populations exhibiting more non-additive expression than the two young polyploids.
Over the past several years we have generated both short (illumina) and long-reads (Nanopore and Sequel) for all three diploid Tragopogon species with the goals of obtaining dense full-length gene coverage as well as complete genome assemblies. To date we have assembled most of gene space for these diploids. However, a complete genome assembly for the diploids has been extremely challenging perhaps due to the large content of rapidly evolving repeats.