Figures
Abstract
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.
Citation: Zuo H, Wu P, Wu D, Sun G (2015) Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae). PLoS ONE 10(5): e0125417. https://doi.org/10.1371/journal.pone.0125417
Academic Editor: Wujun Ma, Murdoch University, AUSTRALIA
Received: February 13, 2015; Accepted: March 23, 2015; Published: May 6, 2015
Copyright: © 2015 Zuo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Data Availability: All relevant data are within the paper.
Funding: This project was supported in part by an internal grant from Anhui Agricultural University, a discovery grant (RGPIN-2014-05249) from the Natural Sciences and Engineering Research Council of Canada, and a Senate Research Grant at Saint Mary’s University, Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: This manuscript or substantial parts of it, submitted to the journal has not be under consideration by any other journal. No material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party. All authors have approved the manuscript. The authors have declared that no competing interests exist.
Introduction
Interspecific or intergeneric hybridization and polyploidization are two widespread and evolutionarily important phenomena in plants, which play important roles in the formation of new allopolyploid species [1–3]. Numerous studies have indicated that many intra- and inter-genomic changes that accompanied allopolyploid formation such as rapid elimination and recombination of low-copy sequence fragment, DNA methylation pattern changes, retrotransposon activation, intergenomic conversion and epigenetic changes, might have produced a more harmonious behavior and activity of the different constituent genomes. More importantly, those genomic alterations exhibited different evolutionary dynamics which might lead to genetic asymmetry evolution resulting in conformity and convergent effects [4–9].
The tribe Triticeae combines a wide variety of biological mechanisms and genetic systems, and is an excellent group for studying evolutionary dynamics and speciation in plants [10]. Within this tribe, Elymus L. is the largest genus composed exclusively of allopolyploids with approximately 150 species [11]. Five basic genomes (St, H, Y, P, and W) have been cytologically assigned to the species in this genus (Genome symbols follow [12]). The St genome found in all Elymus species was supposedly donated by Pseudoroegneria (Nevski) Á. Löve. The H, P, and W genomes were derived from Hordeum L., Agropyron Gaertn., and Australopyrum (Tzvelev) Á. Löve, respectively, while the origin of Y genome is unknown [13–21].
Elymus trachycaulus (Link) (2n = 4x = 28) is a short-lived perennial, self-pollinating allotetraploid species. The distribution range of E. trachycaulus extends from Alaska to Newfoundland and all the way down south to Mexico, and usually grows in open forests and along roadsides [22]. The number of infraspecific taxa in the E. trachycaulus complex that are currently recognized varies from three to six, but considerably more have been recognized in the past [23]. The delimitation of taxa within E. trachycaulus complex is controversial and difficult, since the morphological characters used to distinguish infraspecific taxa (for instance, length and density of the spike), are at least partially under environmental control. Adding to this difficulty are some relatively distinct entities linked by morphologically intermediate plants derived from hybridization [23]. Previous studies have shown that E. trachycaulus complex is the most morphologically and geographically diverse species of Elymus in North America [24], and have showed considerable diversity [24–33]. Like most North American species of Elymus, E. trachycaulus is a tetraploid that combines the genomes of a Pseudoroegneria species (St genome) and a wild Hordeum species (H genome) [34–37], but little more is known about its origin and evolutionary dynamics.
In this study, we used two single copy nuclear genes: the second largest subunit of RNA polymerase II (Rpb2) and the phosphoenolpyruvate carboxylase (Pepc), along with chloroplast DNA trnL–trnF region (spacer between the tRNA-Leu (UAA) gene and the tRNA-Phe (GAA) gene) to explore genome evolutionary dynamics and the origin of tetraploid E. trachycaulus.
Materials and Methods
Plant materials and DNA extraction
Thirteen accessions of E. trachycaulus species were analyzed. DNA was extracted from fresh young leaf using the method of [38]. Two low copy nuclear gene (Rpb2 and Pepc) and chloroplast TrnL/F sequences from different accessions of E. trachycaulus were amplified and sequenced. Rpb2, Pepc and TrnL/F sequences for some diploid Triticeae species representing the St, H, I, Xa, Xu, W, P, E and V genomes were obtained from the published data [39–41], and included in the analyses. Plant materials with accession number, genomic constitution, geographical origin, and GenBank identification number are presented in Table 1.
DNA amplification and sequencing
The sequences of Rpb2, Pepc and cpDNA TrnL/F were amplified by polymerase chain reaction (PCR) using the primers P6F and P6FR [42], PEPC-F and PEPC-R [40], and TrnL and TrnF [41], respectively. DNA was amplified in a 20 μl reaction containing 20 ng template DNA, 0.25 mM of each deoxynucleotide (dATP, dCTP, dGTP and dTTP), 2.0 mM MgCl2, 2.0 U Taq polymerase (TransGen, Beijing, China), 0.25 μM of each primer. Amplification was performed in a DNA Thermo-cycler (iCycler, Bio-Rad). The amplification profile for the Rpb2 gene was: an initial denaturation at 94°C for 4 min; 35–40 cycles of 94 C for 40 s, 60°C for 50 s, 72°C for 2 min, and a final cycle of 72°C for 10 min. The PCR profile for amplifying Pepc gene was: an initial denaturation at 94°C for 4 min; 38 cycles of 94°C for 40 s, 65°C for 50 s, 72°C for 2 min, and a final cycle of 72°C for 10 min. The PCR condition for TrnL/F was: 5 min at 95°C, 40 cycles of 30 s at 94°C, 1 min at 61°C, 2 min at 72°C, followed by 10 min at 72°C. PCR products were purified using the EasyPure Quick Gel Extraction Kit (TransGen, Beijing, China) according to manufacturer’s instructions. The PCR products of the nuclear genes amplified from E. trachycaulus were cloned into the pGEM-easy T vector (Promega Corporation, Madison, Wis., USA) according to the manufacturer’s instructions, and transformed into E. coli competent cell DH5α (TransGen, Beijing, China). 12–24 clones from each accession were sequenced. The PCR product amplified by cpDNA primer TrnL/F was purified and directly sequenced. Both the PCR products and positive colonies were commercially sequenced by the Shanghai Sangon Biological Engineering & Technology Service Ltd (Shanghai, China). To enhance the sequence quality, both forward and reverse strands were sequenced independently. To avoid any error which would be induced by Taq DNA polymerase during PCR amplification, each PCR product amplified by cpDNA primer TrnL/F was independently amplified twice and sequenced, since Taq errors that cause substitutions are mainly random and it is unlikely that any two sequences would share identical Taq errors to create a false synapomorphy.
Data analysis
The chromatographs of automated sequence results were visually checked. Multiple sequence alignments were made using Clustal X with default parameters and additional manual editing to minimize gaps [43]. Maximum-parsimony (MP) analysis was performed using the computer program PAUP ver. 4 beta 10 [44]. All characters were specified as unweighted and unordered, and gaps were excluded in the analysis. Most-parsimonious trees were obtained by performing a heuristic search using the Tree Bisection-Reconnection (TBR) option with MulTrees on, and ten replications of random addition sequences with the stepwise addition option. Multiple parsimonious trees were used to generate a strict consensus tree. Overall character congruence was estimated by the consistency index (CI), and the retention index (RI). In order to infer the robustness of clades, bootstrap values with 1000 replications [45] were calculated. In addition to MP analysis, Bayesian analyses analysis was also performed. Eight evolution models of sequence were tested using PhyML 3.0 [46]. For each data set, the general time-reversible (GTR) [47] model led to a largest ML score compared to the other 7 substitution models: JC69 [48], K80 [49], F81 [50], F84 [51], HKY85 [52], TN93 [53] and custom (data not shown). As the result, the GTR model was used in the Bayesian analysis using MrBayes 3.1 [54]. MrBayes 3.1 was run with the program’s standard setting of two analyses in parallel, each with four chains, and estimates convergence of results by calculating standard deviation of split frequencies between analyses. In order to make the standard deviation of split frequencies fall below 0.01 so that the occurrence of convergence could be certain, 1,159,000 generations for Rpb2 data, 1,037,000 generations for Pepc, and 4,110,000 generations for TrnL/F were run. Samples were taken every 1000 generations under the GTR model with gamma-distributed rate variation across sites and a proportion of invariable sites. For all analyses, the first 25% of samples from each run were discarded as burn-in to ensure the stationarity of the chains. Bayesian posterior probability (PP) values were obtained from a majority rule consensus tree generated from the remaining sampled trees.
Results
Rpb2 analysis
Maximum parsimony analysis of 58 Rpb2 sequences was conducted using B. inermis and B. catharticus as outgroup (125 parsimony informative characters, 316 equally most parsimonious trees, CI = 0.791; RI = 0.932).
The separated Bayesian analyses using GTR model resulted in identical trees with mean log-likelihood values -3928.47 and -3973.80 (data not shown). The tree topology generated by Bayesian analyses using the GTR model is similar to those generated by maximum parsimony. One of the most parsimonious trees with Bayesian PP and maximum parsimony bootstrap (1000 replicates) value is shown (Fig 1).
Numbers above and below branches are bootstrap values from MP and Bayesian posterior probability (PP) values, respectively. Bromus inermis was used as an outgroup. Consistency index (CI) = 0.791, retention index (RI) = 0.932.
Two distinct copies of sequences were recovered from each nine accessions of E. trachycaulus (PI387895, PI440098, PI440101, H10665A, H3526, H10140, PI232150, H4228, H3995). Phylogenetic analysis clearly separated the two copies of sequences from each accession into two distinct groups, one copy with St genome diploid species, and another copy associated with H genome diploid species. Two copies of sequences from accession PI 236685 were recovered, but both were grouped into H clade in 99% bootsrtap support and 0.99 PP (Fig 1). Three distinct copies of sequences were found from accession PI232147, one was grouped into the St and two were placed into the H genome clade. Only one copy of sequence from accession PI232151 was recovered, and was placed into the St clade. The three H genome species (H. roshevitzii, H. stenostachys, H. brevisubulatum) were grouped together with a 95% bootstrap support in MP, and 0.99 PP in Bayesian analysis, and was sister to the H-like copy sequences from nine accessions of E. trachycaulus which were grouped together in a 86% bootstrap support and 0.98 PP. The H-like sequence from EF596764 and H3526 formed a group, and was sister to the H genome diploids.
Pepc analysis
Pepc gene from 13 accessions of E. trachycaulus were cloned and sequenced. At least 10 clones from each cloned PCR product were screened and sequenced. Two distinct copies of sequences were recovered from each 9 accessions of E. trachycaulus. The relative large insertion/deletion was observed between the two copies sequences from each accession, and shown in Fig 2. Three copies of sequences were recovered from accession PI232147, and relative large insertion/deletion among the three copies of sequences was also observed (Fig 2). Only one copy of sequence was recovered each from accession H10140, PI 232150 and PI 440101.
Phylogenetic analysis of the 54 Pepc sequences was performed using B. tectorum as an outgroup. The data matrix contained 958 characters, of which 600 were constant, 154 were parsimony uninformative, and 204 were parsimony informative. Heuristic searches resulted in 570 most parsimonious trees with a CI = 0.735 (excluding uninformative characters), and RI = 0.906. The Bayesian analyses using GTR model resulted in identical trees with mean log-likelihood values -5561.85 and -5701.88 (data not shown). The tree topologies generated by MP and Bayesian analyses were similar to each other. One of the most parsimonious trees with BS and PP values is shown in Fig 3.
Numbers above and below branches are bootstrap values from MP and Bayesian posterior probability (PP) values, respectively. Bromus tectorum was used as an outgroup. Consistency index (CI) = 0.735, retention index (RI) = 0.906.
Phylogenetic analysis separated two copies sequences each from accession PI 387895, H10665a and H3526 into two distinct clades, one in H genome and another in St genome clade (Fig 3). However, the two different copies of sequences each from accession PI 232151, PI 372644, PI 236685, PI H3995, PI 440098 and H4228 were placed in the H clade with diploid Hordeum species together with a 96% bootstrap support and 0.99 PP. Within the H clade, two well separated subclades were observed. One contained 4 sequences from E. trachycaulus and the sequences from H. roshevitzii, H. muticum and H. pusillum in 100% BS and 1.00 PP support. Another contained 17 E. trachycaulus sequences and one H. bodganii sequence in 100% BS and 1.00PP support. Two different copies of sequences each from accession PI 372644, PI232151 and PI 236685 were separated into two H subclades, whereas two different copies of sequences each from accession PI 440098, H3995 and H4228 were placed into the same subclade (H2). Three different copies of sequences from accession PI 232147 were placed into the H1, H2 and St clade, respectively.
TrnL/F analysis
Phylogenetic analysis of 67 TrnL/F sequences was performed using B. tectorum as an outgroup. The data matrix contained 793 characters, of which 684 were constant, and 36 were parsimony informative. Heuristic searches resulted in 134 most parsimonious trees with a CI = 0.903 (excluding uninformative characters) and RI = 0.941. The separated Bayesian analyses using GTR model resulted in identical trees with mean log-likelihood values -2494.43 and -2590.54 (data not shown). One of the most parsimonious trees with BS values from MP and PP value from Bayesian analysis is shown in Fig 4.
Numbers above branches are MP bootstrap values and Bayesian posterior probability (PP) values, respectively. Bromus tectorum was used as an outgroup. Consistency index (CI) = 0.903, retention index (RI) = 0.941.
Phylogenetic analyses divided the 67 sequences into two clades. All sequences from Hordeum species were placed into one clade with 69% bootstrap support. All sequences from E. trachycaulus were grouped with the St genome, Eb, Ee, V, W, P and F in a 51% bootstrap value and 0.68 PP. Within this clade, the sequence from accession PI232147of E. trachycaulus formed a subclade with P. strigosa subsp. aegilopoides (St) in 60% SB and 0.76 PP support. The sequences from F, P and W genomic species formed a subclade in 82% BS and 0.98 PP support.
Discussion
Multiple origins of E. trachycaulus
Previous studies using cpDNA sequences have confirmed that the diploid St genome species, Pseudoroegneria, is the maternal donor of E. trachycaulus [41, 54–56]. At present study, the phylogenetic analysis of TrnL/F data placed all sequences from E. trachycaulus with the sequences from Pseudoroegneria (St), Thinopyrum (Eb, Ee), Dasypyrum (V), Agropyron (P), Eremopyrum (F) and Australopyrum (W) (Fig 4). It is difficult to rule out Thinopyrum, Dasypyrum, Agropyron, Eremopyrum and Australopyrum as potential maternal donors to E. trachycaulus. Our result is consistent with a study based on combined cpDNA restriction sites, rpoA sequences, and tRNA spacer sequences, in which the several North American Elymus species including E. trachycaulus were also grouped with Pseudoroegneria, Thinopyrum and Dasypyrum [41]. 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, 54–56], as well as genome-pairing 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 Pepc sequence data confirmed the presence of StH genome in PI 387895, H10665A and H3526 (Fig 3). Sequence alignment revealed two distinct copies from each accession PI440098, H4228, PI 236685 and H3995. However, phylogenetic analysis grouped the two copies sequences each from accession PI440098, H4228, and H3995 into the H2 group, while the two copies of sequences from accession PI236685 were separated into H1 and H2 groups (Fig 3). Only one copy of Pepc sequence each was recovered from accession PI 440101, H10140 and PI 232150, and grouped into H2 group. Both Rpb2 and Pepc data suggested that accession PI 236685 contained two different copies of H genome (Figs 1 and 3). Only one copy Rpb2 sequence was obtained from accession PI 232151 and PI 372644, but two copies of Pepc sequences each from these accessions were obtained, and were phylogenetically grouped into H1 and H2. Three copies of Rpb2 and Pepc sequences were recovered from the accession PI 232147. 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, 54–56].
In a study of tetraploid Elymus canius with StH genomes by [57], the Rpb2 data also indicated presence of either St1 or St2 together with H genome in E. caninus. The GBSSI data indicated the presence of Pseudoroegneria (St), Hordeum (H) and an “unknown” Pseudoroegneria-like genome in Elymus repens [58]. Our Rpb2 data here indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus were contributed by multiple sources (Figs 1 and 3), whether due to multiple origins or to subsequent hybridization.
Genome diversity and evolution
Allopolyploidization, brought about by inter-specific or inter-generic hybridization followed by chromosome doubling, contributes to the evolution of new functions in duplicated genes [59–61]. During or after the process of allopolyploidization, rapid sequence elimination and rearrangement, cytosine methylation, as well as transposable element activation and epigenetic gene silencing in allopolyploids might have been occurred [3– 6]. Rapid elimination of low-copy DNA gene from one genome is a general phenomenon in newly synthesized allopolyploids after hybridization or after chromosome doubling [7, 9]. The genome asymmetry caused by the lost of one parental gene copy was not restricted in Triticum or Elymus [8, 62], it was also evident in allotetraploid soybean [63–67].
It has cytological been confirmed that E. trachycaulus is allotetraploid [20, 21]. Two distinct copies of sequences for each single copy of nuclear gene are expected to be recovered from allotetraploid E. trachycaulus. However, two distinct copies were not recovered from all accessions for either Rpb2 or Pepc gene. Only one copy Rpb2 sequence was obtained from accession PI 232151 and PI372644, and one copy of Pepc sequence each was recovered from accession PI 440101, H10140 and PI 232150 even though more than ten clones were screened from each accession. Assuming no bias in cloning or PCR amplification, this gives a 99.9% chance of obtaining at least one copy of each of the two ancestral allelic types for the allotetraploid [68]. This might be due to mutation in the primers region causing failure of amplification of the “missing” gene copy. Another possibility might be genome convergent evolution in allopolyploids, partly because the St genome in Elymus species acquired this part of the sequence by the inter-genome introgression of sequence segments from the H genome to the St genome and abundant genome-wide recombination following the fusion of St and H gametes, accompanying the process of polyploidization. Genome-wide recombination between the St and H genomes could result in the two genome sequences at this location being identical to the extent that we could not distinguish one from the other in this specific DNA fragment [57]. There were growing evidences that homoeologous rearrangements in Brassica napus [69–73], and exchange among homoeologous chromosomes [74] might lead to genetic asymmetry expression and promote convergent evolution of the two parental genomes and phenotypic variation in newly formed polyploids.
Surprisingly, the Pepc phylogenetic tree showed that St copies were recovered from only 3 accessions (PI 387895, H10665A, and H3526), and other accessions had 2 to 3 different H copies except PI232150 and H10140, from which only one copy of H genome sequence was recovered (Figs 2 and 3). One scenario is that St copy might been missed and not be found, but this situation is less likely because most accessions did not show the St copy even though at least 10 clones screened, and it is less likely that the St copy from about 10 accessions missed at the same time.
Sequence alignment (Fig 2) revealed deletions and insertions between/among the different copies of H sequences from the same accession (Fig 2). It has been reported instability of the Pepc sequences within Hordeum as revealed by numerous insertions and deletions, with some of them involving gain or loss of Stowaway-like transposable elements [75]. The two copies of Pepc sequences each from accession H4228, PI 440098, and H3995 and PI 232147 which were phylogenetically grouped into the same clade might be caused by instability of Pepc sequences in H- genome. The two/three H-like sequences from accession PI 372644, PI 232151, PI 232147, PI 236685 were clearly separated into H1 and H2 clades in the phylogenetic analysis. The two distinct sequences each isolated from those accessions might be less likely explained by Pepc instabilities in Hordeum since phylogenetic analysis excluded the insertion/deletions. The two phylogenetic distinct copies of H sequences in these accessions might be caused by gene introgression from Hordeum into E. trachycaulus following polyploidization. Incomplete concerted evolution cannot be excluded which incompletely homogenized St copy of Pepc toward second H copy of Pepc. Concerted evolution appears to be a common feature of highly repetitive nuclear sequences, however, low-copy nuclear genes are also not free from concerted evolution [76, 77].
Author Contributions
Conceived and designed the experiments: GS DW. Performed the experiments: HZ PW. Analyzed the data: GS HZ. Contributed reagents/materials/analysis tools: GS. Wrote the paper: GS HZ DW.
References
- 1.
Stace CA (1975) Hybridization and the Flora of the British Isles. 626 S., 10 Abb. Academic Press, London, New York, San Francisco.
- 2.
Rieseberg LH, Wendel JF (1993) Introgression and its consequences in plants. In: Harrison RG ed. Hybrid Zones and Evolutionary Process. New York: Oxford University Press. pp. 70–109.
- 3. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, et al (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16: 738–749. pmid:16702410
- 4. Comai L, Tyaqi AP, Winter K, Holmes-Davis R, Reynolds SH (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12: 1551–1567. pmid:11006331
- 5. Lee HS, Chen ZJ (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98: 6753–6758. pmid:11371624
- 6. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM (1998) Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes. Genetics 147: 1381–7.
- 7. Ozkan H, Levy AA, Feldman M (2002) Rapid differentiation of homoeologous chromosomes in newly formed allopolyploid wheat. Isr J Plant Sci 50: 65–76.
- 8. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749–1759. pmid:11487690
- 9. Feldman M, Levy AA, Fahima T, Korol A (2012) Genomic asymmetry in allopolyploid plants: wheat as a model. J Exp Bot 63: 5045–5059. pmid:22859676
- 10.
Bothmer von R, Salomon B (1994) Triticeae: a tribe for food, feed and fun. In: Wang RRC, Jensen KB, Jaussi C, eds. Proceedings of the 2nd international Triticeae symposium. Utah: Logan Press. pp. 1–12.
- 11. Löve A (1984) Conspectus of the Triticeae. Feddes Report 95: 425–521.
- 12.
Wang RR–C, von Bothmer R, Dvorak J, Fedak G, Linde-Laursen I, Muramatsu M (1994) Genome symbols in the Triticeae. In: Wang RRC, Jensen KB, Jaussi C, eds. Proceeding of the 2nd International Triticeae Symposium. Utah: Logan Press. pp. 29–34.
- 13.
Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. In: Gustafson JP, ed. Gene manipulation in Plant Improvement. New York: Columbia University Press. pp. 209–280.
- 14. Jensen KB (1990) Cytology, fertility, and morphology of Elymus kengii (Keng) Tzvelev and E. grandiglumis (Keng) Á. Löve (Triticeae: Poaceae). Genome 33: 563–570.
- 15. Torabinejad J, Mueller RJ (1993) Genome Constitution of the Australian hexaploid grass Elymus scabrus (Poaceae: Triticeae). Genome 36: 147–151. pmid:18469977
- 16. Jensen KB, Salomon B (1995) Cytogenetics and morphology of Elymus panormitanus var. heterophyllus (Keng) Á. Löve and its relationship to Elymus panormitanus (Poaceae: Triticeae). Int J Plant Sci 156:31–739.
- 17. Liu Q, Ge S, Tang H, Zhang X, Zhu G, Lu BR (2006) Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences. New Phytol 170: 411–420. pmid:16608465
- 18. Sun GL, Salomon B (2009) Molecular evolution and origin of tetraploid Elymus species. Breed Sci 59: 487–491.
- 19. Yan C, Hu QN, Sun GL (2014) Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus. Genome 57: 97–109. pmid:24702067
- 20. Dewey DR (1968) Synthetic hybrids among Hordeum brachyantherum, Agropyron scribneri, and Agropyron latiglume. Bull Torrey Bot Club 95: 454–464.
- 21. Dewey DR (1975) Introgression between Agropyron dasystachyum and A. trachycaulum. Bot Gaz 136: 122–128.
- 22.
Hitchcock AS (1951) Manual of grasses of the United States. Ed. 2, rev. by A. Chase. USDA Misc Publ 200.
- 23.
Barkworth M (1994) The Elymus trachycaulus complex in North America: more question than answer. In: Wang RRC, Jensen LB, Jaussi C, eds. Proceedings of the 2nd international Triticeae symposium. Utah: Logan Press. pp. 189–198.
- 24.
Dewey DR (1982) Genomic and phylogenetic relationships among North American perennial Triticeae. In: Estes JR, Tyrl RJ, Brunken JN, eds. Grasses and grasslands. Norman: University of Oklahoma Press. pp. 51–88.
- 25. Jaaska V (1992) Isoenzyme variation in the grass genus Elymus (Poaceae). Hereditas 117: 11–22.
- 26. Knapp EE, Rice KJ (1996) Genetic structure and gene flow in Elymus glaucus (blue wild rye): implications for native grassland restoration. Restorat Ecol 4: 1–10.
- 27. Sun GL, Salomon B, Bothmer von B (1998) Characterization of microsatellite loci from Elymus alaskanus and length polymorphism in several Elymus species (Triticeae: Poaceae). Genome 41: 455–463. pmid:9729781
- 28. Sun GL, Díaz O, Salomon B, Bothmer von R (1998) Microsatellite variation and its comparison with allozyme and RAPD variation in Elymus fibrosis (Schrenk) Tzvel. (Poaceae). Hereditas 129: 275–282.
- 29. Sun GL, Díaz O, Salomon B, Bothmer von R (2001) Genetic diversity and structure in a natural Elymus caninus population from Denmark based on microsatellite and isozyme analysis. Plant Syst Evol 227: 235–244.
- 30. Díaz O, Sun GL, Salomon B, Bothmer von R (2000) Level and distribution of allozyme and RAPD variation in populations of Elymus fibrosus (Poaceae). Genet Resour Crop Evol 47: 11–24.
- 31. Wilson BL, Kitzmiller J, Rolle W, Hipkins VD (2001) Isozyme variation and its environmental correlates in Elymus glaucus from the California Floristic Province. Canad J Bot 79: 139–153.
- 32. Gaudett M, Salomon B, Sun GL (2005) Molecular variation and population structure in Elymus trachycaulus and comparison with its morphologically similar E.alaskanus. Plant Syst Evol 250: 81–91.
- 33. Sun GL, Li WB (2006) Molecular diversity of Elymus trachycaulus complex species and their relationships to non-North American taxa. Plant Syst Evol 256: 179–191.
- 34. Dewey DR (1968) Synthetic Agropyron-Elymus hybrids: III. Elymus canadensis x Agropyron caninum, A. trachycaulum, and A. striatum. Am J Bot 55: 1133–1139.
- 35. Dewey DR (1976) The genome constitution and phylogeny of Elymus ambiguous. Am J Bot 63: 626–634.
- 36. Bowden WM (1965) Cytotaxonomy of the species and interspecific hybrids of genus Agropyron in Canada an neihgbouring areas. Can J Bot 43: 1421–1448.
- 37. Murry LE, Tai W (1980) Genome relations of Agropyron sericeum, Hordeum jubatum and their hybrids. Amer J Bot 67: 1374–1379.
- 38. Junghans H, Metzlaff M (1990) A simple and rapid method for the preparation of total plant DNA. Biotechnique 8: 176. pmid:2317373
- 39. Sun GL, Ni Y, Daley T (2008) Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation of H genome, and the relationship of the Y genome to other genomes in Elymus species. Mol Phylogenet Evol 46: 897–907. pmid:18262439
- 40. Helfgott DM, Mason-Gamer RJ (2004) The evolution of North American Elymus (Triticeae, Poaceae) allotetraploids: evidence from phosphoenolpyruvate carboxylase gene sequences. Syst Bot 29: 850–861.
- 41. Mason-Gamer RJ, Orme NL, Anderson CM (2002) Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets. Genome 45: 991–1002. pmid:12502243
- 42. Sun GL, Daley T, Ni Y (2007) Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species. Plant Mol Biol 64: 645–665. pmid:17551673
- 43. Thompson JD, Gibson TJ, Plewniak F, Jeanmouguin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25: 4876–4882. pmid:9396791
- 44.
Swofford DL (2003) PAUP. Phylogenetic Analysis using Parsimony, version 4. Sunderland, MA, USA: Sinaeur Associates.
- 45. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
- 46. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696–704. pmid:14530136
- 47. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86–93. pmid:6429346
- 48.
Jukes T, Cantor C (1969) Evolution of protein molecules. In: Munro H, ed. Mammalian protein metabolism. New York: Academic Press. pp. 21–132.
- 49. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120. pmid:7463489
- 50. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376. pmid:7288891
- 51.
Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.6a2. Seattle: Department of Genetics, University of Washington.
- 52. Hasegawa M, Kishino H, Yano T (1985) Dating of the Human–Ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160–174. pmid:3934395
- 53. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512–526. pmid:8336541
- 54. Redinbaugh MG, Jones TA, Zhang Y (2000) Ubiquity of the St-containing chloroplast genome in St-containing Triticeae polyploids. Genome 43: 846–852. pmid:11081975
- 55. McMillan E, Sun GL (2004) Genetic relationships of tetraploid Elymus species and their genomic donor species inferred from polymerase chain reaction—restriction length polymorphism analysis of chloroplast gene regions. Theor Appl Genet 108: 535–542. pmid:14513222
- 56. Sun GL (2007) Genetic diversity of rbcL gene in Elymus trachycaulus complex and their phylogenetic relationships to several Triticeae species. Genet Resour Crop Evol 54: 1737–1746.
- 57. Yan C, Sun GL (2012) Multiple origins of allopolyploid wheatgrass Elymus caninus revealed by RPB2, PepC and TrnD/T genes. Mol Phylogenet Evol 64: 441–451. pmid:22617317
- 58. Mahelka V, Kopecky D (2010) Gene capture from across the grass family in the allohexaploid Elymus repens (L.) Gould (Poaceae, Triticeae) as evidenced by ITS, GBSSI, and molecular cytogenetics. Mol Biol Evol 27: 1370–1390. pmid:20106909
- 59.
Ohno S (1970) Evolution by Gene Duplication. New York: Springer-Verlag.
- 60. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nature Rev Genet 2: 333–41. pmid:11331899
- 61. Liu B, Wendel JF (2002) Non-mendelian phenomena in allopolyploid genome evolution. Curr Genomics 3: 489–505.
- 62. Yan C, Sun GL, Sun DF (2011) Distinct Origin of the Y and St Genome in Elymus Species: Evidence from the Analysis of a Large Sample of St Genome Species Using Two Nuclear Genes. PloS One 6: e26853. pmid:22046383
- 63. Tate JA, Ni Z, Scheen AC, Koh J, Gilbert CA, Lefkowitz D, et al (2006) Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173: 1599–1611. pmid:16648586
- 64. Tate JA, Joshi P, Soltis KA, Soltis PS, Soltis DE (2009) On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). BMC Plant Biol 9: 80. pmid:19558696
- 65. Buggs RJA, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, et al (2009) Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103: 73–81. pmid:19277058
- 66. Buggs RJA, Chamala S, Wu W, Gao L, May GD, Schnable PS, et al (2010a) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol Ecol 19: 132–146. pmid:20331776
- 67. Koh J, Soltis PS, Soltis DE (2010) Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics 11: 97. pmid:20141639
- 68. Jakobsson M, Hagenblad J, Tavaré S, Säll T, Halldén C, Lind-Halldén C, et al (2006) A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol Biol Evol 23: 1217–1231. pmid:16549398
- 69. Pires JC, Zhao JW, Schranz ME, Leon EJ, Quijada PA, Lukens LN, et al (2004) Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc Lond 82: 675–688.
- 70. Udall JA, Quijada PA, Osborn TC (2005) Detection of chromosomal rearrangements derived from homoeologous recombination in four mapping populations of Brassica napus L. Genetics 169: 967–979. pmid:15520255
- 71. Leflon M, Eber F, Letanneur JC, Chelysheva L, Coriton O, Huteau V, et al (2006) Pairing and recombination at meiosis of Brassica rapa (AA) x Brassica napus (AACC) hybrids. Theor Appl Genet 113: 1467–1480. pmid:16983552
- 72. Liu ZQ, Adamczyk K, Manzanares-Dauleux M, Eber F, Lucas MO, Delourme R, et al (2006) Mapping PrBn and other quantitative trait loci responsible for the control of homoeologous chromosome pairing in oilseed rape (Brassica napus L.) haploids. Genetics 174: 1583–1596. pmid:16951054
- 73. Nicolas SD, et al (2007) Homoeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics 175: 487–503. pmid:17151256
- 74. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19: 3403–3417. pmid:18024568
- 75. Mason-Gamer RJ (2008) Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae). Mol Phylogen Evol 47: 598–611. pmid:18372193
- 76. Clegg MT, Cummings MP, Durbin ML (1997) The evolution of plant nuclear genes. Proc Natl Acad Sci USA 94: 7791–7798. pmid:9223265
- 77. Small RL, Cronn RC, Wendel JF (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot 17: 145–170.