Evolution and Expression of Homeologous Loci in Tragopogon miscellus (Asteraceae), a Recent and Reciprocally Formed Allopolyploid

Abstract

On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations of Tragopogon miscellus, an allotetraploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. pratensis. Using cDNA-AFLPs followed by genomic and cDNA cleaved amplified polymorphic sequence (CAPS) analyses, we found differences in the evolution and expression of homeologous loci in T. miscellus. Fragment variation within T. miscellus, possibly attributable to reciprocal formation, comprised 0.6% of the cDNA-AFLP bands. Genomic and cDNA CAPS analyses of 10 candidate genes revealed that only one ''transcript-derived fragment'' (TDF44) showed differential expression of parental homeologs in T. miscellus; the T. pratensis homeolog was preferentially expressed by most polyploids in both populations. Most of the cDNA-AFLP polymorphisms apparently resulted from loss of parental fragments in the polyploids. Importantly, changes at the genomic level have occurred stochastically among individuals within the independently formed populations. Synthetic F 1 hybrids between putative diploid progenitors are additive of their parental genomes, suggesting that polyploidization rather than hybridization induces genomic changes in Tragopogon. P OLYPLOIDY, or genome doubling, has been an important process in many eukaryotic lineages, particularly in flowering plants. Recent genome-level studies have revealed that even the model ''diploid'' plant Arabidopsis thaliana has undergone several rounds of whole-genome duplication (Vision et al. 2000;Blanc et al. 2003;Bowers et al. 2003;Blanc and Wolfe 2004b). Many polyploid plants are allopolyploids, having arisen through hybridization between genetically distinct entities (usually species) and chromosome doubling. This combination of divergent but compatible genomes in allopolyploids may provide a novel substrate for evolutionary processes (Stebbins 1950;Levin 1983;Grant 2002;Osborn et al. 2003). As all genes in allopolyploids are duplicated, a number of possibilities exist for the evolutionary fate of the homeologs (genes duplicated by polyploidy). Theory predicts three potential outcomes for these duplicated genes: (1) both copies are retained and remain functional, (2) one copy retains the original function while the other copy is lost or silenced, or (3) the two copies diverge such that each copy assumes only a part of the original gene function (subfunctionalization) or one copy acquires a new function (neofunctionalization) (Ohno 1970;Lynch and Conery 2000;Prince and Pickett 2002).In recent years, studies of genome evolution and gene expression have been in the foreground of polyploidy research (Leitch and Bennett 1997;Soltis and Soltis 1999;Wendel 2000;Liu and Wendel 2003). Much of this work has been conducted on Arabidopsis (Comai et al. 2000;Lee and Chen 2001), Brassica (Lukens et al. 2004Pires et al. 2004b), and crop plants, such as wheat (Feld...

Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

“…For thioredoxin, PCR products were digested with DdeI to identify parental homeologs, with a single cut site present in the T. dubius homeolog. For the three genes examined, we confirmed that the strongest amplification products matched the size that was documented previously (Tate et al, 2006;Koh et al, 2010).…”

“…Three genes that were previously found to be fixed in the parents, but show genetic non-additivity in some T. mirus, were PCR amplified: TDF36.3, a gene putatively encoding thioredoxin M-type I (Tate et al, 2006;Koh et al, 2010); TDF85, a gene putatively encoding β-fructosidase (Tate et al, 2006;Koh et al, 2010); and MHC, a gene putatively encoding myosin heavy chain . PCR primer sequences were THIOR_F1: 5′-AAT CAGAAGCATCCCGACTG-3′ and THIOR_R1 5′-CACAATCTTTTTGTGA AATGCAA-3′; BFRUCT4_F1: 5′-GGAAGACCTTGATTGATCGG-3′ and BFRUCT4_R1: 5′-AAGGATGTTGTGGTGGAAGC-3′; MHC_F1: 5′-CGAC ACGGAATATAGCATCC-3′ and MHC_R1: 5′-GGATAAAGTGATGCTC ATATGG-3′.…”

“…To generate a FISH probe for the β-fructosidase gene, we first searched assembled transcriptome sequence data from T. dubius (Buggs et al, 2010) using tBLASTx (Altschul et al, 1997) and querying with a partial β-fructosidase coding sequence (GenBank accession number: DQ267230; Tate et al, 2006). Primers were then designed as close as possible to the beginning and end of a tentative transcript that showed 99% similarity to the query (BFRUCT_1F: 5′-GAGGTTTCCGGTACACATCA-3′ and BFRUCT_2043R: 5′-AACGAC AATCATCATGCCACG-3′).…”

“…We use this approach in the present study to conduct a survey of chromosomal variation in T. mirus and compare the results with those obtained earlier for T. miscellus (Chester et al, 2012). We also make use of the karyotyped T. mirus individuals to examine the phenomenon of homeologous gene loss, where allotetraploids show non-additivity of homeologous progenitor genes (Tate et al, 2006;Buggs et al, 2009;Tate et al, 2009;Koh et al, 2010;Buggs et al, 2012). To assess whether parental gene non-additivity correlates with chromosome loss or non-reciprocal translocations, three pairs of homeologous genes are assayed via PCR for the T. mirus individuals that were karyotyped.…”

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

“…The amount of ITS1 transcript was normalised separately to each of three different reference genes: TDF46, GAPDH and Actin. TDF46 is a protein phosphatase 2C family protein constitutively expressed in Tragopogon (Tate et al, 2006). Primer sequences are available in Supplementary Table S1.…”