Genetic diversity of rbcL gene in Elymus trachycaulus complex and their phylogenetic relationships to several Triticeae species

Abstract

Elymus trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The phylogenetic relationships among the E. trachycaulus complex, and their systematic relation to other species in Triticeae remain unknown. Nucleotide diversity of ribulose-1,5 bisphosphate-carboxylase (rbcL) gene in E. trachycaulus complex species and several other Triticeae was first characterized and compared. A primary conclusion of the present study is that nucleotide diversity for rbcL gene in E. trachycaulus species was detected with the estimates of nucleotide diversity h = 0.00039 and p = 0.00043. The estimate of nucleotide diversity in rbcL gene for species with different genome constitution here ranged from 0.00099 (p) and 0.00099 (h) for the species with Ns genome to 0.00226 (p) and 0.00291 (h) for the species with St genome. The phylogenetic relationships of these species were assessed using these rbcL sequences. A total of 47 variable positions including 19 parsimony-informative sites were detected among 24 accessions of 18 species/subspecies. The species with St, H/I and Ns genomes well separated from each other, and formed a three distinct clades with higher bootstrap values support for both Parsimony and NJ analyses. The St genome containing species is sister group of H/I genome containing species. Our result confirms that Pseudoroegneria is the maternal genome donor to these Elymus species studied here, regardless of their distribution. Elymus trachycaulus complex are more related to each other than to E. glaucescens, E. patagonicus, and E. solandri. This study suggested that Elymus species with StH genomes may form from multiple closely related sets of donors.

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

“…The rate of intraspecific nucleotide variation in the study by was the highest within P. spicata and P. gracillima, which is consistent with studies on the genetic diversity of P. spicata (Fu & Thompson, 2006;Larson et al, 2000;Larson, Jones, & Jensen, 2004). The rate of divergence in the chloroplast (cpDNA) TrnD/T region, and that of the mitochondrial (mtDNA) CoxII gene was significantly lower than that of the nuclear (nDNA) genes studied, within similar sample sizes (Sun et al, 2007;Zeng et al, 2010). These large differences may be partially explained through the different evolutionary histories that occur between nuclear, chloroplast and mitochondrial genomes.…”

“…Low rates of nucleotide diversity in our study (Table 3) conformed well to our predictions, as these were closely related taxa and the rbcL gene is known to be highly conserved (Doebley et al, 1990;Gielly & Taberlet, 1994;Olmstead & Palmer, 1994;Sun, 2007). The inter-and intra-species genetic diversity from our study displayed many differences to a similar study by , who examined the nucleotide diversity using the TrnD/T chloroplast intergenic region, as well as two nuclear genes.…”

“…The large variety of biological and genetic mechanisms, including frequent hybridizations, introgression and rapid speciation that occur in the Triticeae make them a very useful group for studies in evolution, genetics and plant speciation (Petersen & Seberg, 1997;Sun, 2007).…”

“…This gene was chosen because it is present as a single copy in all land plants, and its highly conserved nature allows for simpler amplification among a wide variety of species and genera (Doebley et al, 1990). Several studies have indicated that the rbcL gene may be too conserved to be used at the intergenic or interspecies level (Doebley et al, 1990;Gielly & Taberlet, 1994), while more recent studies have indicated that the rbcL gene can be used at lower taxonomic levels depending on the methodology and the types of questions being asked (Sun, 2007). …”

Phylogenetic Relationships in the Festuca-Lolium Complex (Loliinae; Poaceae): New Insights from Chloroplast Sequences

“…The chloroplast has highly-conserved genes which are elementary to plants and are variable and informative regions over a long time scale. The use of cpDNA can also analyse the maternal source genome donor and has been applied successfully in the phylogenetic analysis of many taxa (Shaw et al, 2007;Sun, 2007;Nock et al, 2011).…”