Rui-Wu Yang

Phylogeny and evolutionary history of Leymus(Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

BackgroundSingle- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.ResultsTwo homoeologues of the Acc1 gene were isolated from nearly all the sampled Leymus species using allele-specific primer and were analyzed with those from 35 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) Leymus is closely related to Psathyrostachys, Agropyron, and Eremopyrum; (2) Psathyrostachys juncea is an ancestral Ns-genome donor of Leymus species; (3) the Xm genome in Leymus may be originated from an ancestral lineage of Agropyron and Eremopyrum triticeum; (4) the Acc1 sequences of Leymus species from the Qinghai-Tibetan plateau are evolutionarily distinct; (5) North America Leymus species might originate from colonization via the Bering land bridge; (6) Leymus originated about 11-12MYA in Eurasia, and adaptive radiation might have occurred in Leymus during the period of 3.7-4.3 MYA and 1.7-2.1 MYA.ConclusionLeymus species have allopolyploid origin. It is hypothesized that the adaptive radiation of Leymus species might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters in Leymus. Our results shed new light on our understanding of the origin of Xm genome, the polyploidization events and evolutionary history of Leymus that could account for the rich diversity and ecological adaptation of Leymus species.

Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences.

To estimate the phylogenetic relationship of polyploid Hystrix in Triticeae, two single-copy nuclear genes (Acc1 and DMC1) and chloroplast trnL-F sequences of six Hystrix taxa were analyzed with those of nine Leymus species (NsXm), four Elymus species (StH) and 13 diploid taxa from seven monogenomic genera. Phylogenetic analyses reveal that Hystrix taxa contain two distinct types of genome constitution, despite the overall morphological and ecological similarity among Hystrix taxa. One type of genome constitution is StH (Hy. patula) as Elymus, the other is NsXm (Hy. californica, Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata and Hy. komarovii) as Leymus. The St, H and Ns genomes in Hystrix are donated by Pseudoroegneria, Hordeum and Psathyrostachys, respectively. The donor of the Xm genome is closely related to Agropyron (P). The trnL-F data especially indicate that there has been a maternal haplotype polymorphism in Hystrix species. Based on these results, we suggest that Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. komarovii and Hy. californica should be included in the genus Leymus, and Hy. patula in the genus Elymus.

Phylogenetic Analysis of Leymus (Poaceae: Triticeae) Inferred from Nuclear rDNA ITS Sequences

To investigate the phylogenetic relationships of polyploid Leymus (Poaceae: Triticeae), sequences of the nuclear rDNA internal transcribed spacer region (ITS) were analyzed for 34 Leymus accessions representing 25 species, together with three Psathyrostachys species (Ns genome), two Pseudoroegneria (St genome) species, Lophopyrumxa0elongatum (Ee genome), and Thinopyrumbessarabicum (Eb genome). The phylogenetic analyses (maximum likelihood and Bayesian inference) supported two major clades, one including 21 Leymus species and three Psathyrostachys species, the other with nine Leymus species and four diploid species. The ITS RNA secondary structure of the Leymus species was compared with that of their putative diploid donor. It is suggested that (1) the species from the same areas or neighboring geographic regions are closely related to each other; (2) L.xa0coreanus, L.xa0duthiei, L.xa0duthiei var. longearistatus, and L.xa0komarovii are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix to Leymus; (3) the ITS sequences of Leymus are evolutionarily distinct; (4) the different Leymus species and different distribution of a species derived their Ns genome from different Psathyrostachys species; and (5) there is a close relationship among Leymus, Pseudoroegneria, Lophopyrum, and Thinopyrum, but it is difficult to presume that the St, Ee, and Eb genome may be the Xm genome donor of the Leymus species.

Relationships among Leymus species assessed by RAPD markers

The DNA genetic diversity of 40 accessions of genus Leymus was analyzed by random amplified polymorphic DNA (RAPD) markers. A total of 352 products were amplified by 34 10-mer arbitrary primers, among which 337 products (95.74 %) were found to be polymorphic. 5–14 polymorphic bands were amplified by each polymorphic primer, with an average of 9.91 bands. The data of 352 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. Great genetic diversity in genus Leymus was observed, the genetic diversity among the different species more abundant than that of the different accessions, and the different accessions in a species or the species from the same areas were clustered together.

Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequences

The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (E(b)) and Lophopyrum elongatum (E(e)) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix.

Phylogenetic analysis of Kengyilia species based on nuclear ribosomal DNA internal transcribed spacer sequences

Phylogenetic analysis was conducted based on sequences of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA in 17 species of Kengyilia, together with those of 18 species from Pseudoroegneria, Agropyron, Roegneria and Douglasdeweya by the maximum parsimony, maximum likelihood and neighbor-joining distance methods. The results indicate that species of Kengyilia had close affinities to species of Douglasdeweya and Agropyron. The species in Kengyilia was identified as two subgroups with regard to geographic distribution, indicating that species from the same distribution had a closer phylogenetic relationship. The genus Kengyilia was found as a ligament-group between Roegneria and Agropyron. The ITS sequence is a useful tool for studying the phylogeny of closely related species.

The Genetic Diversity Among Leymus Species Based on Random Amplified Microsatellite Polymorphism (RAMP)

The genetic diversity and similarities among 40 accessions of Leymus Hochst., distributed in 19 species and 1 subspecies, were analyzed by using random amplified microsatellite polymorphism (RAMP) markers. Of the 120 RAMP primer combinations tested, 24 (20%) produced polymorphic and clear bands. A total of 192 bands were amplified by 24 primer combinations, among which 179 (93.23%) bands were found to be polymorphic. Three to thirteen polymorphic bands were amplified by each primer combination, with an average of 7.64 bands. The data of 192 RAMP bands were used to generate Jaccards similarity coefficients and to construct a dendrogram by means of UPGMA in the NTSYS-pc computer program. The genetic similarity coefficients ranged from 0.10 to 0.73 with the mean of 0.34. The results showed as follows: (1) Distinct genetic differences were present among the different species; (2) The different accessions in a species were clustered together, respectively, which had larger genetic similarities and closer relations; (3) The species with similar morphological characters and the species from the same areas or neighboring geographical regions were clustered together; (4) RAMP results are basically comparable with those obtained from studies on morphology. It is a useful method for analysis of the genetic diversity and similarities in Leymus.

Genetic diversity and phylogeny in Hystrix (Poaceae, Triticeae) and related genera inferred from Giemsa C-banded karyotypes

The phylogenetic relationships of 15 taxa from Hystrix and the related genera Leymus (NsXm), Elymus (StH), Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), and Thinopyrum (E) were examined by using the Giemsa C-banded karyotype. The Hy. patula C-banding pattern was similar to those of Elymus species, whereas C-banding patterns of the other Hystrix species were similar to those of Leymus species. The results suggest high genetic diversity within Hystrix, and support treating Hy. patula as E. hystrix L., and transferring Hy. coreana, Hy. duthiei ssp. duthiei and Hy. duthiei ssp. longearistata to the genus Leymus. On comparing C-banding patterns of Elymus species with their diploid ancestors (Pseudoroegneria and Hordeum), there are indications that certain chromosomal re-arrangements had previously occurred in the St and H genomes. Furthermore, a comparison of the C-banding patterns of the Hystrix and Leymus species with the potential diploid progenitors (Psathyrostachys and Thinopyrum) suggests that Hy. coreana and some Leymus species are closely related to the Ns genome of Psathyrostachys, whereas Hy. duthiei ssp. duthiei, Hy. duthiei ssp. longearistata and some of the Leymus species have a close relationship with the E genome. The results suggest a multiple origin of the polyploid genera Hystrix and Leymus.

Nucleotide polymorphism pattern and multiple maternal origin in Thinopyrum intermedium inferred by trnH-psbA sequences

Thinopyrum intermedium is an important species with potential utilization value in breeding of wheat. In this study, the non-coding intergenic region of trnH-psbA was investigated to assess the genetic diversity and infer the maternal origin within T. intermedium accessions. Eleven haplotypes were distinguished among the thirty-five accessions of T. intermedium. They showed a relatively low nucleotide diversity (π) of 0.00473 ± 0.00037 and a moderately high haplotype diversity (Hd) of 0.733 ± 0.061. In the phylogenetic analysis, all accessions of T. intermedium were positioned into two clades, which corresponded to the different diploid donors. These results suggested that there were two phylogenetically divergent maternal donors in T. intermedium.

Karyomorphology of some taxa of Paris (Melanthiaceae) from Sichuan province, China

Abstract The karyomorphology of nine taxa of Paris from Sichuan province in China were reported. The primary lesions of P. undulatis were newly observed, the chromosome number and karyotype were reported for the first time. All of the materials were diploids. The chromosome numbers of all taxa studied were 2nu2009=u20092xu2009=u200910. The karyotypic asymmetry types of all taxa studied were 2A, except for P. polyphylla var. chinensis was 2B. Satellites were observed in four taxa, P. undulatis, P. polyphylla var. polyphylla, P. fargesii var. brevipetalata and P. polyphylla var. polyphylla. All of the investigated taxa were absent B chromosome except for P. polyphylla var. polyphylla and P. axialis. Karyotypic formula of nine Paris taxa were as follows: P. undulatis, 2nu2009=u20096mu2009+u20094t (2sat); P. polyphylla var. chinensis, 2nu2009=u20096mu2009+u20094t (2sat); P. polyphylla var. yunnanensis, 2nu2009=u20096mu2009+u20094t; P. cronquistii, 2nu2009=u20096mu2009+u20094t; P. polyphylla var. polyphylla, 2nu2009=u20096mu2009+u20092st (2sat)u2009+u20092t (2sat)u2009+u20092bs; P. axialis, 2nu2009=u20096mu2009+u20094tu2009+u20092bs; P. fargesii var. brevipetalata, 2nu2009=u20096mu2009+u20094t (2sat); P. mairei, 2nu2009=u20096mu2009+u20094t; P. marmorata, 2nu2009=u20096mu2009+u20091stu2009+u20093t. The variability of karyotypes occurred among taxa and phylogenetic positions of some taxa were investigated, and the infrageneric and the intergeneric relation ships of Paris were discussed.