Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species

Abstract

Molecular evolution of the second largest subunit of low copy nuclear RNA polymerase II (RPB2) in allotetrploid StH genomic species of Elymus is characterized here. Our study first reported a 39-bp MITE stowaway element insertion in the genic region of RPB2 gene for all tetraploid Elymus St genome and diploid Pseudoroegneria spicata and P. stipifolia St genome. The sequences on 3'-end are highly conserved, with AGTA in all sequences but H10339 (E. fibrosis), in which the AGTA was replaced with AGAA. All 12 Stowaway-containing sequences encompassed a 9 bp conserved TIRs (GAGGGAGTA). Interestingly, the 5'-end sequence of GGTA which was changed to AGTA or deleted resulted in Stowaway excision in the H genome of Elymus sepcies, in which Stowaway excision did not leave footprint. Another two large insertions in all St genome sequences are also transposable-like elements detected in the genic region of RPB2 gene. Our results indicated that these three transposable element indels have occurred prior to polyploidization, and shaped the homoeologous RPB2 loci in St and H genome of Eymus species. Nucleotide diversity analysis suggested that the RPB2 sequence may evolve faster in the polyploid species than in the diploids. Higher level of polymorphism and genome-specific amplicons generated by this gene indicated that RPB2 is an excellent tool for investigating the phylogeny and evolutionary dynamics of speciation, and the mode of polyploidy formation in Elymus species.

Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene

“…This sub-clade with P. spicata also contained the StH Elymus species, and E. solandri (StYW), which may indicate that P. spicata is the maternal genome donor for the StH Elymus species and E. solandri, while one or more of the other Pseudoroegneria species may be the maternal donor for the StY Elymus species. Several previous studies lend support to our findings as studies on the pep-C, ß-amylase, GBSSI, DMC1, EF-G, and RPB-2 nuclear genes have found P. spicata to be more closely related to the StH Elymus than any other Pseudoroegneria species (Mason-Gamer et al, 2010;Sun et al, 2007;Petersen et al, 2011;. In most cpDNA studies the relationship of P. spicata with the StH Elymus have not been observed, typically due to poor resolution of the trees, as was observed in Figure 5 ( Mason-Gamer et al, 2002;McMillan & Sun, 2004;Wang et al, 2011).…”

“…Thus, close association of polyploidy species with diploid species can be used to infer the maternal genome donor. As Thinopyrum and Dasyspyrum species were also found in the Pseudoroegneria paraphyly, we cannot rule out either as a possible maternal donor to Elymus (Figure 4 and 5), however, studies on nuclear genes and ITS data have indicated that Pseudoroegneria and either Hordeum, Agropyron, or Australopyrum (depending on the Elymus species) are the paternal genome donors to Elymus, while there does not appear to be any additional support for either Thinopyrum or Dasyspyrum as a genome donor to Elymus (Liu et al, 2006;MasonGamer, 2001;Mason-Gamer et al, 2010;Sun et al, 2007;.…”

Phylogenetic relationships of species in Pseudoroegneria (Poaceae: Triticeae) and related genera inferred from nuclear rDNA ITS (internal transcribed spacer) sequences

“…P. stipifolia have rough rachis densely covered by pricklets (Yen et al 2007). The molecular evidence based on nuclear RNA polymerase II (RPB2) reported a 39 bp MITE stowaway element insertion in the region of RPB2 gene for P. spicata and P. stipifolia, while P. tauri and P. libanotica did not have this insertion (Sun et al 2007). The Pseudoroegneria diploid species also have wide distribution.…”

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

“…Therefore, rpb2 is still phylogenetically informative even when duplication of the gene has occurred (Oxelman and Bremer 2000;Oxelman et al 2004;Luo et al 2007). Moreover, recent studies reported that the rpb2 gene was useful for exploring low-level phylogenetic relationships in the palm family (Loo et al 2006;Roncal et al 2005;Thomas et al 2006), in the genus Silene of the Caryophyllaceae family (Popp and Oxelman 2001), and in the genus Elymus of the Poaceae family (Sun et al 2007).…”