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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...
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Context 1
... plant materials used in this study (Table 1) were grown from seed that were obtained from the USDA-ARS, Regional Plant Introduction Station, Pullman, Washington, USA, and the Swedish University of Agricultural Science. Seeds were germinated on absorbent paper in Petri dishes. ...
Citations
... Many Elymus species like E. sibiricus and E. nutans occur naturally in Eastern Mongolia, the Himalayas, and Western and Northern China [13]. Previous studies mainly focused on the classification between Elymus and their relatives, the origin determination of the ancestor species including St, H and Y genome, and the evolution relationships between basic genomes based on cytogenetics and molecular sequences [12,[14][15][16]. Information on molecular phylogeny and genetic structure among different Elymus species is limited, but necessary for germplasm collection, conservation and utilization. ...
Background
Elymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an important gene pool for improving cereal crops. However, a shortage of molecular marker limits the efficiency and accuracy of genetic breeding for Elymus species. High-throughput transcriptome sequencing data is essential for gene discovery and molecular marker development.
Results
We obtained the transcriptome dataset of E. sibiricus, the type species of the genus Elymus, and identified a total of 8871 putative EST-SSRs from 6685 unigenes. Trinucleotides were the dominant repeat motif (4760, 53.66%), followed by dinucleotides (1993, 22.47%) and mononucleotides (1876, 21.15%). The most dominant trinucleotide repeat motif was CCG/CGG (1119, 23.5%). Sequencing of PCR products showed that the sequenced alleles from different Elymus species were homologous to the original SSR locus from which the primer was designed. Different types of tri-repeats as abundant SSR motifs were observed in repeat regions. Two hundred EST-SSR primer pairs were designed and selected to amplify ten DNA samples of Elymus species. Eighty-seven pairs of primer (43.5%) generated clear and reproducible bands with expected size, and showed good transferability across different Elymus species. Finally, thirty primer pairs successfully amplified ninety-five accessions of seventeen Elymus species, and detected significant amounts of polymorphism. In general, hexaploid Elymus species with genomes StStHHYY had a relatively higher level of genetic diversity (H = 0.219, I = 0.330, %P = 63.7), while tetraploid Elymus species with genomes StStYY had low level of genetic diversity (H = 0.182, I = 0.272, %P = 50.4) in the study. The cluster analysis showed that all ninety-five accessions were clustered into three major clusters. The accessions were grouped mainly according to their genomic components and origins.
Conclusions
This study demonstrated that transcriptome sequencing is a fast and cost-effective approach to molecular marker development. These EST-SSR markers developed in this study are valuable tools for genetic diversity, evolutionary, and molecular breeding in E. sibiricus, and other Elymus species.
... 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). ...
The species within the Lolium/Festuca grass complex have dispersed and colonized large areas of temperate global grasslands both naturally and by human intervention. The species within this grass complex represent some of the most important grass species both for amenity and agricultural use worldwide. There has been renewed interest by grass breeders in producing hybrid combinations between these species and several countries now market Festulolium varieties as a combination of genes from both genera. The two genera have been differentiated by their inflorescence structure, but controversy has surrounded the taxonomic classification of the Lolium-Festuca complex species for several decades. In order to better understand the complexities within the Lolium/Festuca complex and their genetic background, the phylogeny of important examplers from the Lolium-Festuca complex were reconstructed. In total 40 taxa representing the Festuca and Lolium species with Vulpia myuros and Brachypodium distachyon as outgroups were sampled, using two non-coding intergenic spacers (trnQ-rps16, trnH-psbA) and one coding gene (rbcL). Maximum parsimony (MP), Bayesian inference (BI) analyses based on each partition and combined plastid DNA dataset, and median-jointing network analysis were employed. The outcomes strongly suggested that the subgen. Schedonorus has a close relationship to Lolium, and it is also proposed to move the sect. Leucopoa from subgen. Leucopoa to Subgen. Schedonorus and to separate sect. Breviaristatae from the subgen. Leucopoa. We found that F. californica could be a lineage of hybrid origin because of its intermediate placement between the “broad-leaved” and “fine-leaved” clade.
... It contains many important cereal grasses, such as barley (Hordeum vulgare), wheat (Triticum aestivum), and rye (Secale cereale), as well as many forage grasses (Hodge et al., 2010). The large variety of biological and genetic mechanisms that the Triticeae possess make them a very useful group for studying evolution, genetics and plant speciation (Sun, 2007). ...
... Low rates of nucleotide diversity in our study (Table 2) conformed well to our expectation, as these were closely related taxa and the rbcL gene is known to be highly conserved (Doebley et al., 1990;Sun, 2007). The nucleotide diversity from our study is differences to the study of Yan and Sun (2011), who examined the nucleotide diversity using the TrnD/T chloroplast intergenic region, as well as two nuclear genes, in which they found that the species with the highest nucleotide diversity was The N is the number of sequences used, n is the number of sites, s is the number of segregating/polymorphic sites, Tajima's p is the average pairwise diversity, Watterson q is the diversity based on s, Fu and Li's D and Tajima's D are tests of neutral evolution, which are indicated in red if significant (p < 0.05). ...
The Pseudoroegneria species are perennial grasses in the Triticeae tribe, whose St genome has been linked to several important polyploid species. Due to frequent hybridization and complex genetic mechanism, the relationships within Pseudoroegneria, and within the Triticeae have been heavily disputed. Using the chloroplast rbcL gene we estimated the nucleotide diversity of 8 Pseudoroegneria species. We also examined the phylogenetic relationships within Pseudoroegneria and of Pseudoroegneria within the Triticeae. The estimates of nucleotide diversity indicated that Pseudoroegneria tauri and Pseudoroegneria spicata species had the highest diversity, while Pseudoroegneria gracillima had the lowest diversity. The phylogenetic analysis of Pseudoroegneria placed all P. spicata species into a clade separate from the other Pseudoroegneria species, while the relationship of the other Pseudoroegneria species could not be determined. Due to the groupings of Pseudoroegneria with the polyploid Elymus, our results strongly supported Pseudoroegneria as the maternal genome donor to Elymus. There was also weak support that P. spicata may be the maternal donor to the StH Elymus species.
... The molecular data also shows differentiation in Pseudoroegneria. Sun et al. [63] reported a 39 bp MITE stowaway element insertion in the region of nuclear RNA polymerase II (RPB2) gene for Pse. spicata and Pse. ...
Hybridization and polyploidization can be major mechanisms for plant evolution and speciation. Thus, the process of polyploidization and evolutionary history of polyploids is of widespread interest. The species in Elymus L. sensu lato are allopolyploids that share a common St genome from Pseudoroegneria in different combinations with H, Y, P, and W genomes. But how the St genome evolved in the Elymus s. l. during the hybridization and polyploidization events remains unclear. We used nuclear and chloroplast DNA-based phylogenetic analyses to shed some light on this process.
The Maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) data showed that the Pseudoroegneria, Hordeum and Agropyron species served as the St, H and P genome diploid ancestors, respectively, for the Elymus s. l. polyploids. The ML tree for the chloroplast genes (matK and the intergenic region of trnH-psbA) suggests that the Pseudoroegneria served as the maternal donor of the St genome for Elymus s. l. Furthermore, it suggested that Pseudoroegneria species from Central Asia and Europe were more ancient than those from North America. The molecular evolution in the St genome appeared to be non-random following the polyploidy event with a departure from the equilibrium neutral model due to a genetic bottleneck caused by recent polyploidization.
Our results suggest the ancient common maternal ancestral genome in Elymus s. l. is the St genome from Pseudoroegneria. The evolutionary differentiation of the St genome in Elymus s. l. after rise of this group may have multiple causes, including hybridization and polyploidization. They also suggest that E. tangutorum should be treated as C. dahurica var. tangutorum, and E. breviaristatus should be transferred into Campeiostachys. We hypothesized that the Elymus s. l. species origined in Central Asia and Europe, then spread to North America. Further study of intraspecific variation may help us evaluate our phylogenetic results in greater detail and with more certainty.
... Previous studies using cpDNA sequences have confirmed that the diploid St genome species, Pseudoroegneria, is the maternal donor of E. trachycaulus [41,[54][55][56]. At present study, the phylogenetic analysis of TrnL/F data placed all sequences from E. trachycaulus with the sequences from Pseudoroegneria (St), Thinopyrum (E b , E e ), Dasypyrum (V), Agropyron (P), Eremopyrum (F) and Australopyrum (W) (Fig 4). ...
... In contrast to the chloroplast TrnL/F data, phylogenies of two nuclear gene sequences (Rpb2 and Pepc) placed the E. trachycaulus into Pseudoroegneria and Hordeum clades, and clearly separated from the Thinopyrum, Dasypyrum and other diploid species analyzed here (Figs 1 and 3). Thus, Pseudoroegneria as a maternal donor to E. trachycaulus is consistent with nuclear data in this study and previous chloroplast data [41,[54][55][56], as well as genomepairing data [13]. Two distinct copies of Rpb2 sequences each from 9 out of thirteen accessions of E. trachycaulus were obtained, and were separated into St and H clades by phylogenetic analysis, indicating that the StH genome constitution of these nine accessions (PI387895, PI440098, PI440101, H10665A, H3526, H10140, PI232150, H4228, H3995) of E. trachycaulus. ...
... The Rpb2 sequence data indicated the presence of StHH, while Pepc data indicated the presence of H1H1H2 sequences in this accession. Chloroplast data well separated the sequences of E. trachycaulus from H-genome species, indicating non-Hordeum species as maternal donor to E. trachycaulus, and presence of one copy of non-Hordeum genome in nuclear of tetraploid E. trachycaulus, most likely St genome as discussed above and suggested previously [41,[54][55][56]. ...
To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL-trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus.
... Before accepting either of these possibilities, this study re-examined the history of polyploid Triticeae, as well as the evolution of the 3-phosphoglycerate kinase encoding nuclear pgk1 gene within the tribe. This analysis was performed with a larger data set and represented a comprehensive analysis of all of major genomes in the tribe, contrary to many previous studies focusing specifically within a common genus or group of genera (Huang et al., 2001(Huang et al., , 2002aHsiao et al., 1995;Fan et al., 2012;Kilian et al., 2007;Mason-Gamer et al., 2002;Sun, 2007). ...
Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A(u), B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π=0.03343 and θ=0.03536 for polyploid Ns genome sequences and π=0.03886 and θ=0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π=0.0011 and θ=0.0011. Nucleotide variation of diploid Aegilops speltoides (π=0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π=0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A(u), and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A(u), B, and D genomes were linked to Triticum urartu, Aegilops speltoides, and Aegilops tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.
... For example, it has been shown that tetraploid Elymus species are the products of multiple and independent hybridization as well as polyploidization events. There have been multiple contributions from both Pseudoroegneria species as well as Hordeum species to tetraploid Elymus species (Sun, 2007;Mason-Gamer, 2008). These studies have also shown that Eurasian and American Elymus tetraploids have independent origins involving different St and H genome progenitors. ...
Understanding species evolution and improvement requires information of their genome origin and differentiation. Among the
species in the family Gramineae, genome identities of Agropyron-Elytrigia-Leymus group are still ambiguous. In order to delineate the genome relationship, nucleotide sequence analysis in the rDNA ITS regions
was carried out among the species in the genera Elytrigia, Agropyron, Psathyrostachys, Leymus, and Psacopyrum containing E, St, P, Ns, and Xm genomes. The ITS-1 and ITS-2 showed a narrow range of variation in length except for the
presence of a pentanucleotide, TGGGG, in/del in some haplotypes, whereas higher numbers of nucleotide substitutions were observed
in most genera. There were 187 variable sites in the ITS-1, 5.8S, and ITS-2 regions, in which a few genome specific mutations
were observed. While the level of variation was similar between ITS-1 and ITS-2, the rate of transition mutation versus transversion
mutations was different among the ITS-1, 5.8S, and ITS-2 segments. GC contents of the ITS regions ranged between 55–65% between
genomes and the haplotypes of P and H genomes were slightly higher than others. In phylogenetic analysis, the ITS haplotypes
were classified into two groups; one containing H, Ns, NsXm genomes, and another containing P, St, and E genomes, which are
congruous to the genome affinities from other studies. Among the four genomes in Pascopyrum smithii (2n=8x=56, StStNsNsHHXmXm), the haplotypes of H and St genomes were identified with the reference diploid species, but the haplotypes
having Ns and Xm genomes were not found in the present analysis.
Keywords
Agropyron-Elytrigia-Leymus
-Genome-rDNA-ITS-Haplotypes
... Nucleotide diversity with the trnH-psbA was slightly greater than that observed for the trnS-trnG region, even though the former was estimated from a set of more closely related taxa, indicating the rapidly evolution of the trnH-psbA region (Aldrich et al., 1988;Hamilton et al., 2003). In contrast with the low level of nucleotide diversity found in rbcL intergenic region for E. trachycaulus species (q ¼ 0.00039; p ¼ 0.00043) (Sun, 2007), nucleotide diversity found here in Asp(GUC)-Thr(GGU) (trnD-trnT) region for E. trachycaulus species was approximately as twenty times high (q ¼ 0.01003; p ¼ 0.00722) as those observed in other intergenic regions (Xu and Ban, 2004;Liu et al., 2006). The estimates of nucleotide diversity in several Elymus species are very close to the values reported for the same region in Cunninghamia (nucleotide diversity ¼ 0.01018) (Lu et al., 2001). ...
Nucleotide variation in chloroplast Asp(GUC)–Thr(GGU) intergenic region and genetic relationships among this group were examined among Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus. The estimates of nucleotide diversity (π) ranged from 0.00111 for Elymus virescens to 0.03086 for E. caninus. Highest nucleotide diversity was found for E. caninus among the taxa analyzed here and followed by Elymus hyperarcticus. E. virescens accessions are genetically very uniform. Phylogenetic analysis suggested that E. caninus is paraphyletic. Elymus violaceus is genetically distinct from both E. alaskanus and E. trachycaulus. Our result indicates that Asp (GUC)–Thr (GGU) intergenic region has a high rate of evolutionary in Elymus species. Large indels detected in this region appear to have a highly rate of evolution and are thus more prone to homoplasy. We also first reported a minisatellite discovered in Asp (GUC)–Thr (GGU) region in Elymus species. The minisatellite identified here is an excellent candidate marker for studying population structures of Elymus species.
Elymus sensu stricto includes tetraploid species in the tribe Triticeae with a StH genome combination derived from Hordeum (H) and Pseudoroegneria (St). The group is related to many important cereals and forage grasses and is considered an important wild genetic resource for crop breeding. The relationships within Elymus s.s. have been difficult to resolve due to the large number of widely distributed species, a high degree of morphological diversity, introgression between species, and potential multiple origins. Using genome-wide DArTseqLD data from 57 taxa, including the StH group and associated species, it is possible to gain representative information about the genetic structure of the genus. SplitsTree, STRUCTURE and principal component analysis (PCoA) show that Elymus s.s. is divided into two major clades highly correlating with geographical origin separating American species from Eurasians. These findings, together with the contribution of different Pseudoroegneria and Hordeum species to the two clades, support the conclusion that Elymus s.s. has at least two independent origins. The Eurasian and American clades are further divided into three and two subclades, respectively. The results show that Elymus species have migrated multiple times from North to South America and between America and Eurasia. The new findings could be used to develop a new classification of Elymus s.s. with sections based on phylogenetic data.
Elymus nutans is an important forage and ecological restoration herbage in the Qinghai-Tibet Plateau, which is an allohexaploid species with the StStYYHH genomes. Previous studies suggested that Pseudoroegneria is the maternal genome donor to E. nutans, but exactly which Pseudoroegneria species is still unknown. Here, we report the complete chloroplast (cp) genome sequence of two E. nutans from the Qinghai-Tibet and five Pseudoroegneria species. The cp genomes of the seven samples ranged narrowly from 134,924 bp to 135,142 bp in size, comprising inverted repeats of 20,808–20,814 bp, single-copy regions of 80,536–80,754 bp (LSC) and 12,762–12,772 bp (SSC). It encoded 111 total genes, of which 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. A comparative cp genome analysis and characteristic junctions of St-containing species revealed that the gene content and organization were conserved, but differences were still found in sequence variation and border regions. Further, the Bayesian inference (BI) phylogenetic tree using the whole chloroplast genome sequence demonstrated that P. cognata might be the most likely St genome donor of E. nutans in the Qinghai-Tibet Plateau, followed by P. strigosa. However, whether E. nutans has other maternal genomes still needs further research.
