Phylogeny and maternal donors of the tetraploid species with St genome (Poaceae: Triticeae) inferred from CoxII and ITS sequences

Mitochondrial CoxII and ITS sequences of 29 tetraploid species with St genome were compared with their related genera and species of Pseudoroegneria (Nevski) Á. Löve (St), Hordeum L. (H), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (E^b), Lophopyrum elongatum (Host) Á. Löve (E^e), Agropyron Gaertner (P), Australopyrum (Tzvelev) Löve (W) and Psathyrostachys Nevski (Ns). The results indicate that: (1) the maternal donors of North American and Eurasian StStHH tetraploid species may have acquired their St genome from distinct Pseudoroegneria gene pools, with Pse. spicata (Pursh) Á. Löve potentially the maternal donor of North American species; (2) Lophopyrum is the maternal donor of StStE^eE^e tetraploid species, hence, Pse. geniculata ssp. scythica (Nevski) Á. Löve, Elytrigia caespitosa (K. Koch) Nevski and El. caespitosa ssp. nodosa (Nevski) Tzvelev should be identified as species of Trichopyrum Á. Löve; (3) tetraploid species with the same maternal donors were more closely related to each other than those with different maternal donors.     

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.     

基于质体基因组学方法研究广义玄参科的系统发育

该研究利用GenBank数据库已公开发表的玄参科及相关类群的107属129个物种的质体基因组数据对广义玄参科的系统发育关系进行了分析。该文利用蛋白质编码基因构建了矩阵，并采用最大似然法及贝叶斯推断重建系统发育树。基于两种分析方法获得的系统发育树的拓扑结构完全一致且分辨率及支持率较高。在ML树中，总分支数为129个，其中支持率≥70%的分支数目为123个。结果表明：(1)广义玄参科不是一个单系类群，隶属于广义玄参科的51个物种(37属)分散于列当科、泡桐科、美丽桐科、通泉草科、母草科、狭义玄参科和车前科。(2)狭义玄参科为单系类群，除原隶属于广义玄参科的Bontia、Calamphoreus、Diocirea、Eremophila、Glycocystis、Leucophyllum、玄参属和毛蕊花属外，还包括了原隶属于马钱科的醉鱼草属和原隶属于苦槛蓝科的苦槛蓝属。(3)唇形目为一个单系，目下共形成了14个支持率高的单系分支，对应于14个科(其中美丽桐科和胡麻科仅包括一个物种，不包括在内),科间关系得到较好的解决，木犀科为最早分化出来的类群，其余的类群共同组成核心唇形目。在核心唇形目中，类群...     

Phylogeny and molecular evolution of the Acc1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy gene encoding plastid acetyl-CoA carboxylase (Acc1) within the StH genome species, two Acc1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from 35 diploid taxa representing 19 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) the StH genome species from the same areas or neighboring geographic regions are closely related to each other; (2) the Acc1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) Dasypyrum has contributed to the nuclear genome of Elymus repens and Elymus mutabilis; (4) the StH genome polyploids have higher levels of sequence diversity in the H genome homoeolog than the St genome homoeolog; and (5) the Acc1 sequence may evolve faster in the polyploid species than in the diploids. Our result provides some insight on evolutionary dynamics of duplicate Acc1 gene, the polyploidy speciation and phylogeny of the StH genome species.     

A molecular genetic linkage map identifying the St and H subgenomes of Elymus (Poaceae: Triticeae) wheatgrass

Elymus L. is the largest and most complex genus in the Triticeae tribe of grasses with approximately 150 polyploid perennial species occurring worldwide. We report here the first genetic linkage map for Elymus. Backcross mapping populations were created by crossing caespitose Elymus wawawaiensis (EW) (Snake River wheatgrass) and rhizomatous Elymus lanceolatus (EL) (thickspike wheatgrass) to produce F(1) interspecific hybrids that were then backcrossed to the same EL male to generate progeny with segregating phenotypes. EW and EL are both allotetraploid species (n = 14) containing the St (Pseudoroegneria) and H (Hordeum) genomes. A total of 387 backcross progeny from four populations were genotyped using 399 AFLP and 116 EST-based SSR and STS markers. The resulting consensus map was 2574 cM in length apportioned among the expected number of 14 linkage groups. EST-based SSR and STS markers with homology to rice genome sequences were used to identify Elymus linkage groups homoeologous to chromosomes 1-7 of wheat. The frequency of St-derived genome markers on each linkage group was used to assign genome designations to all linkage groups, resulting in the identification of the seven St and seven H linkage groups of Elymus. This map also confirms the alloploidy and disomic chromosome pairing and segregation of Elymus and will be useful in identifying QTLs controlling perennial grass traits in this genus.     

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

The level and pattern of nucleotide variation in duplicate genes provide important information on the evolutionary history of polyploids and divergent processes between homoeologous loci within lineages. Leymus, a group of allopolyploid species with the NsXm genomes, is a perennial genus with a diverse array of morphology, ecology, and distribution in Triticeae. To estimate the phylogeny and molecular evolution of a single-copy DMC1 gene in Leymus and its diploid relatives,DMC1 homoeologous sequences were isolated from the sampled Leymus species and were analyzed with those from 30 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that: (i) different Leymus species might derive their Ns genome from different Psathyrostachys species; (ii) Pseudoroegneria has contributed to the nuclear genome of some Leymus species, which might result from recurrent hybridization or incomplete lineage sorting; (iii) the Xm genome origin of Leymus could differ among species; (iv) rapid radiation and multiple origin might account for the rich diversity, numbers of species, and wide ecological adaptation of Leymus species; and (v) the DMC1 sequence diversity of the Ns genome in Leymus species was lower than that in the Psathyrostachys diploids, while the level of DMC1 sequence diversity in Leymus was higher than that in diploid Pseudoroegneria. Our results provide new insight on the evolutionary dynamics of duplicate DMC1 genes, polyploid speciation, and the phylogeny of Leymus species.     

10个四倍体披碱草属物种的核型（简报）

本文报道了来自北美和亚洲10个四倍体披碱草属物种Elymus(StStHH)的核型.其核型属于1A或2A型,核型公式如下:24m+4sm(2sat)(加拿大披碱草E. canadensis);20m+8sm(4sat)(E. elymoides);20m+8sm(4sat)(E. glaucus);22m+6sm(4sat)(E.lanceolatus);22m+6sm(2sat)(E. mutabilis);22m+6sm(2sat)(老芒麦.E.sibiricus);24m+4sm(E.trachycaulus);22m+4sm+2st(2sat)(E.trachycaulus ssp.subsecundus);24m+4sm(4sat)(E.virginicus);20m+8sm(4sat)(E.wawawaiensis).     

Phylogeny and Classification of Prunus sensu lato （Rosaceae）

The classification of the economically important genus Prunus L. sensu lato （s.L） is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.I. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions （atpB- rbcL, matK, ndhF, psbA-trnH, rbcL, rpL 16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycfl） and three nuclear genes （ITS, s6pdh and Sbel） to explore their infrageneric used to develop a new, phylogeny-based classification relationships. The results of these analyses were of Prunus s.I. Our phylogenetic reconstructions resolved three main clades of Prunus s.I. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades： subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae （T. T. yu ＆ L. T. Lu） S. L. Zhou and one new species name, Prunus tianshanica （Pojarkov） S. Shi, were proposed.     

The genome constitution ofRoegneria grandis (Poaceae, Triticeae)

Roegneria grandis was hybridized withR. ciliaris var.japonensis (2n = 28, SSYY),Elymus caninus (2n = 28, SSHH), andPseudoroegneria spicata (2n = 28, SSSS). Chromosome pairing was studied in parents and hybrids. It is concluded from this study that: (i)R. grandis is an allotetraploid species and contains the basic genomes S and Y: (ii) a certain degree of homoeology exists between the S and Y genomes of the species studied.     

Genome constitution of Elymus tangutorum (Poaceae: Triticeae) inferred from meiotic pairing behavior and genomic in situ hybridization

Elymus tangutorum (Nevski) Hand.-Mazz (2n = 6x = 42) is a perennial species in the tribe Triticeae, which distributes in Nepal and north and northwest China. However, the genome constitution of E. tangutorum is controversial and its taxonomic status is not clear. Hybridizations of E. tangutorum were carried out with E. wawawaiensis J. R. Carlson & Barkworth (StH), Roegneria grandis Keng (StY), and E. dahuricus Turcz. ex Griseb. (StYH). Meiotic pairing in the hybrids E. tangutorum × E. wawawaiensis (StH), E. tangutorum × R. grandis (StY), and E. tangutorum × E. dahuricus (StYH) averaged 10.48, 11.12, and 20.92 bivalents per cell, respectively. The results suggested that E. tangutorum is an allohexaploid and contains the StYH genomes. Results of genomic in situ hybridization analysis strongly supported the chromosome pairing data. Therefore, E. tangutorum should be treated as Campeiostachys dahurica var. tangutorum (Nevski) B. R. Baum, J. L. Yang & C. Yen. Intergenomic rearrangements of E. tangutorum may be affected by environmental factors.     

Genomic constitution and taxonomy of the Chinese hexaploids Elymus cylindricus and E. breviaristatus (Poaceae: Triticeae)

Elymus cylindricus (2n = 6x = 42) and E. breviaristatus (2n = 6x = 42) are distributed in grasslands and deserts of northern and north‐western China. Their genomic constitution and taxonomic status are unclear. Elymus cylindricus was crossed with E. wawawaiensis J.R.Carlson & Barkworth ( StH ), Roegneria grandis Keng ( StY ) and Campeiostachys dahurica (Turcz. ex Griseb.) B.R.Baum, J.L. Y ang & C. Y en var. dahurica ( StYH ). Meiotic pairing in the hybrids E. cylindricus × E. wawawaiensis ( StH ), E. cylindricus × R. grandis ( StY ) and E. cylindricus × C. dahurica var. dahurica ( StYH ) showed on average 10.00, 11.30 and 20.92 bivalents per cell, respectively. Elymus breviaristatus was crossed with C. dahurica var. dahurica ( StYH ) and E. cylindricus. Chromosome pairing in the hybrids of E. breviaristatus × C. dahurica var. dahurica and E. breviaristatus × E. cylindricus showed on average 19.60 and 19.27 bivalents, respectively. Genomic in situ hybridization (GI SH ) revealed the presence of St , Y and H genomes in E. cylindricus and E. breviaristatus. An intergenomic rearrangement was observed in E. cylindricus using GI SH . Meiotic pairing data and GI SH indicated that both E. cylindricus and E. breviaristatus are allohexaploids containing the StYH genomes. Elymus cylindricus and E. breviaristatus should be treated as Campeiostachys dahurica var. cylindrica and Campeiostachys breviaristata, respectively.     

Characterization and analysis of microsatellite loci in Elymus caninus (Triticeae: Poaceae)

 Microsatellites are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. The potential of microsatellite markers for use in a genetic diversity study in Elymus species was evaluated. Genomic libraries of Elymus caninus were constructed. The libraries were screened with two dinucleotide, (GA)n and (GT)n, and two trinucleotide repeats, (TCT)n and (CAC)n. A total of 19 positive clones were found for the two dinucleotide repeats; no positive clone was found for the trinucleotide repeats. Positive clones were sequenced to confirm the presence of microsatellites and to generate polymerase chain reaction (PCR) primers based on the sequences flanking the microsatellite. All sequenced (GA)n clones have repeats of n>10; over half of the (GT)n microsatellites have n<10 repeats. Primer pairs were designed and evaluated for 8 selected microsatellites. PCR products were amplified from 15 Elymus caninus accessions. The number of alleles found for the eight loci varied from 1 for ECGA89 and ECGT35 to 13 for ECGA22, as determined by non-denaturing polyacrylamide electrophoresis. Six microsatellite loci were found to be polymorphic in E. caninus. The eight primer pairs were tested on three other species; seven were successful in amplifying DNA from Elymus alaskanus and E. mutabilis, and four amplified DNA from E. caucasicus. Based on these results, microsatellites appear to be useful markers in detecting variation in E. caninus. Received: 8 September 1997/Accepted: 6 October 1997     

Biosystematic studies of the Elymus hispidus (Poaceae: Triticeae) group in Iran

Biosystematic studies on the Elymus hispidus group included investigations on morphological characters and variability in cultivation, crossing experiments, hybrid fertility and meiotic configuration in hybrids. Elymus gentry! is a distinct species with a different altitudinal distribution from that of E. hispidus. Morphological characters which have been used to split E. hispidus into distinct species or subspecies are not constant in cultivation. The majority of the cultivated plants were morphologically similar to the maternal individuals from which seed was collected in the field. However, in some accessions the offspring represented different morphological variants when cultivated. Hybrids between different variants were fertile and showed regular meiosis. Different variants within the E. hispidus group tend to grow in different habitats and as characters to some extent show constancy in cultivation, three varieties, var. hispidus , var. podperae and var. villosus are recognized for E. hispidus in Iran.     

Genomic relationships between species of theElymus semicostatus group andElymus sensu lato (Poaceae)

Meiotic pairing behaviour in 19 interspecificElymus hybrids is reported and discussed. The hybrids were made between four species belonging to theE. semicostatus group of sect.Goulardia, viz.,E. semicostatus, E. abolinii, E. fedtschenkoi, andE. panormitanus (all 2n = 28), andElymus species of seven different sections, viz., sect.Clinelymiopsis:E. caucasicus (2n = 28); sect.Elymus:E. sibiricus (2n = 28); sect.Goulardia:E. caninus (2n = 28),E. trachycaulus (2n = 28), andE. tsukushiensis (2n = 42); sect.Hyalolepis:E. batalinii (2n = 42); sect.Hystrix:E. hystrix (2n = 28); sect.Macrolepis:E. canadensis (2n = 28); and sect.Turczaninovia:E. dahuricus (2n = 42). Chromosomal pairing at meiotic metaphase I indicated that the species of theE. semicostatus group are genomically closer to the tetraploidE. caucasicus and the hexaploid species, regardless of sectional origin, than to the other tetraploid species of sectionGoulardia. Highest meiotic pairing was found in hybrids involvingE. caucasicus, E. tsukushiensis, andE. dahuricus. The presence of pairing regulating genes inE. abolinii is suspected.     

Molecular phylogeny of RNA polymerase II gene reveals the relationships of tetraploid species with St genome (Triticeae: Poaceae)

To evaluate phylogeny of tetraploid with St genome, phylogenetic analyses of RNA polymerase II (RPB2), a member of the nuclear gene family encoding the second largest subunit, were performed. Our results showed that: (1) Roegneria magnicaespes and Roegneria alashanica are related to Pseudoroegneria. (2) Roegneria elytrigioides has StStStSt genomes and should therefore be classified as Pseudoroegneria elytrigioides. (3) Pseudoroegneria tauri and Pseudoroegneria deweyi which have StStPP genomes should be transferred to Douglasdeweya and be renamed as Douglasdeweya wangii and Douglasdeweya deweyi, respectively. (4) Pseudoroegneria geniculata ssp. scythica is related to Pseudoroegneria and Lophyrum, and hence should be identified as a species of Trichopyrum. (5) Pseudoroegneria libanotica might be a parental donor for Elytrigia caespitosa rather than Elytrigia caespitosa ssp. nodosa. It is unreasonable to recognize El. caespitosa ssp. nodosa as a subspecies of El. caespitosa. (6) Interspecific and intergeneric variations are detected in St genome of these tetraploid species.     

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae)

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.     

Synopsis of Leymus Hochst. (Triticeae: Poaceae)

Leymus is a genus in the Triticeae tribe, Poaceae. The taxa of this genus are allopolyploid species which possess the Ns and Xm genomes. According to cytological, cytogenetic and molecular genetic analyses, some species of Hystrix and Elymus ought to be transferred to this genus. A world revision of the genus Leymus is needed. In this paper we summarize experimental results, provide a key to sections, species and varieties, and list all the taxa we recognize in Leymus with their synonyms. This synopsis is a new taxonomic system to be used for the revision of Leymus.     

A molecular phylogeny and classification of Leptochloa (Poaceae: Chloridoideae: Chlorideae) sensu lato and related genera

Background and Aims

Leptochloa (including Diplachne) sensu lato (s.l.) comprises a diverse assemblage of C₄ (NAD-ME and PCK) grasses with approx. 32 annual or perennial species. Evolutionary relationships and a modern classification of Leptochloa spp. based on the study of molecular characters have only been superficially investigated in four species. The goals of this study were to reconstruct the evolutionary history of Leptochloa s.l. with molecular data and broad taxon sampling.

Methods

A phylogenetic analysis was conducted of 130 species (mostly Chloridoideae), of which 22 are placed in Leptochloa, using five plastid (rpL32-trn-L, ndhA intron, rps16 intron, rps16-trnK and ccsA) and the nuclear ITS 1 and 2 (ribosomal internal transcribed spacer regions) to infer evolutionary relationships and revise the classification.

Key results

Leptochloa s.l. is polyphyletic and strong support was found for five lineages. Embedded within the Leptochloa sensu stricto (s.s.) clade are two Trichloris spp. and embedded in Dinebra are Drake-brockmania and 19 Leptochloa spp.

Conclusions

The molecular results support the dissolution of Leptochloa s.l. into the following five genera: Dinebra with 23 species, Diplachne with two species, Disakisperma with three species, Leptochloa s.s. with five species and a new genus, Trigonochloa, with two species.