title: Phylogeny and differentiation of the St genome in Elymus L. sensu lato (Triticeae; Poaceae) based on one nuclear DNA and two chloroplast genes.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. DZZLL55@163.com.|Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. DZZLL55@163.com.
authors.forename: Zhen-Zhen
authors.initials: ZZ
authors.lastname: Dong
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. fanxing9988@163.com.
authors.forename: Xing
authors.initials: X
authors.lastname: Fan
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. rice_shazhi@163.com.
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Sha
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. wangy19823918@gmail.com.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Resources and Environment, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. zengjian777@126.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Zeng
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. xiaokang_69@126.com.
authors.forename: Hou-Yang
authors.initials: HY
authors.lastname: Kang
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. haiqinzhang@163.com.
authors.forename: Hai-Qin
authors.initials: HQ
authors.lastname: Zhang
authors.affiliation: College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China. wangxiaoli288@163.com.
authors.forename: Xiao-Li
authors.initials: XL
authors.lastname: Wang
authors.affiliation: College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China. zhang8434@sina.com.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China. dcb@sicau.edu.cn.
authors.forename: Chun-Bang
authors.initials: CB
authors.lastname: Ding
authors.affiliation: College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China. yrwu@sicau.edu.cn.
authors.forename: Rui-Wu
authors.initials: RW
authors.lastname: Yang
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. zhouyh@sicau.edu.cn.|Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China. zhouyh@sicau.edu.cn.
authors.forename: Yong-Hong
authors.initials: YH
authors.lastname: Zhou
mesh_terms: D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D060365:Chloroplast Proteins / Q000235:genetics / Q000378:metabolism; D018742:DNA, Chloroplast / Q000235:genetics / Q000378:metabolism; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D031749:Elymus / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D060365:Chloroplast Proteins; D018742:DNA, Chloroplast; D018744:DNA, Plant; D010940:Plant Proteins