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.     

八个四倍体鹅观草属物种的核型研究

对8个鹅观草属物种的核型进行了研究。核型公式如下:纤穗鹅观草2n=4x=28=20m+8sm(2sat);紫穗鹅观草2n=4x=28=22m(2sat)+6sm;假花鳞草2n=4x=28=24m(2sat)+4sm;肃草2n=4x=28=22m+6sm(2sat);小颖鹅观草2n=4x=28=22m+6sm(2sat);纤瘦鹅观草2n=4x=28=24m(4sat)+4sm;变颖鹅观草2n=4x=28=20m+8sm(2sat);毛花鹅观草2n=4x=28=24m(2sat)+4sm。它们的核型属1A或2A型。其中后5个物种的核型为首次报道。     

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 molecular evolution of the rbcL gene of St genome in Elymus sensu lato (Poaceae: Triticeae)

Analysis of the patterns and levels of diversity in duplicate gene not only traces evolutionary history of polyploids, but also provides insight into how the evolutionary process differs between lineages and between homoeologous loci within lineages. Elymus sensu lato is a group of allopolyploid species, which share a common St genome and with the different combinations of H, Y, P, and W genomes. To estimate the evolutionary process of the rbcL gene in species of Elymus s. l. and its putative dioploid relatives, 74 sequences were obtained from 21 species of Elymus s. l. together with 24 diploid taxa representing 19 basic genomes in Triticeae. Phylogeny and sequence diversity pattern analysis suggested that (1) species of Pseudoroegneria (Nevski) Á. Löve might serve as the maternal donor of the species of Elymus s. l; (2) differentiation of St genome were shown in the species of Elymus s. l. following polyploidy event; (3) divergences within the species might associate with geographic diversity and morphological variability; (4) differences in the levels and patterns of nucleotide diversity of the rbcL gene implied that the St genome lineages in the species of Elymus s. l. have differently evolutionary potentials.     

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.     

Genomic relationships within theElymus parviglumis group (Triticeae: Poaceae)

Genomic relationships of 13 tetraploid species within the AsiaticElymus parviglumis group containing the SY genomes were assessed by analysing chromosome pairing at metaphase I of the parental species and their interspecific hybrids. Two major genomic subgroups among the tetraploids were identified from the cluster analysis of the averaged c-values, namely, theE. caucasicus subgroup (two species) and theE. parviglumis subgroup (11 species). The genomic affinity of theElymus species is associated with the interspecific geographic distance.After October 1, 1993     

Molecular evolution and diversity of dimeric alpha-amylase inhibitor gene in Kengyilia species (Triticeae: Poaceae)

Kengyilia Yen et J. L. Yang is a group of allohexaploid species with StYP genomic constitutions in the wheat tribe. To investigate the evolution and diversity of dimeric alpha-amylase inhibitor genes in the Kengyilia, forty-five homoeologous DAAI gene sequences were isolated from sampled Kengyilia species and analyzed together with those of its close relatives. These results suggested that (1) Kengyilia species from Central Asia and the Qinghai–Tibetan Plateau had different origins from those of the geographically differentiated P genome; (2) the St and P genomes of Kengyilia were donated by Pseudoroegneria and Agropyron, respectively, and the Y genome had an independent origin and showed an affinity with the St genome; (3) purifying selection dominated the DAAI gene members and the St-DAAI gene was evolving at faster rate than the P- and Y-DAAI genes in Kengyilia; and (4) natural selection was the main factor on the codon usage pattern of the DAAI gene in Kengyilia.     

Identifying the genome of wood barley Hordelymus europaeus (Poaceae: Triticeae)

Wood barley, Hordelymus europaeus, was compared with other Triticeae species by Southern and fluorescence in situ hybridisation using total genomic DNA and repetitive sequences as probes. On Southern blots, the total genomic probe from H. europaeus hybridised strongly to DNA of its own species and to Leymus and Psathyrostachys, indicating the presence of Ns genome in H. europaeus. Furthermore, the total genomic probe from P. fragilis hybridised to DNA of H. europaeus as much as to all of the Psathyrostachys and Leymus species examined. Ns genome-specific DNA sequences isolated from L. mollis (pLmIs1, pLmIs44 and pLmIs53) hybridised essentially to H. europaeus and all of the species of Leymus and Psathyrostachys. Chromosomal localization of these clones on H. europaeus confirmed the presence of Ns genome-specific DNA on all chromosomes, indiscriminately. Under moderate hybridisation stringency the Ns genome-specific probes, together with repetitive sequences pTa71 and pAesKB7, produced species-specific RFLP banding profiles on Southern blots. A phenetic tree based on these profiles revealed a distinct Ns species cluster within the Triticeae, represented by Leymus and Psathyrostachys species. Hordelymus europaeus belonged to this Ns cluster. Chromosomal mapping of the 18S-25S and the 5S ribosomal genes, together with the repetitive sequence pLrTaiI, corroborated that H. europaeus was most probably related to Leymus, especially the European/Eurasian members of sect. Leymus. In an attempt to identify the genome of H. europaeus, different approaches were employed; the results clearly showed that wood barley had the Ns basic genome and nothing else.     

C-banding analysis of eight species ofKengyilia (Poaceae: Triticeae)

To characterize chromosomes and the interspecific relationships within the genus Kengyilia, 8 species were used for Giemsa C-banding analysis. Results indicated that the species differed in C-banding patterns. K. gobicola, K. alatavica and K. batalinii had distinct centromeric bands and no banded chromosomes, while K. hirsuta, K. longiglumis, K. melanthera, K. rigidula and K. thoroldiana had more abundant and diagnostic C-bands with interstitial and terminal bands.     

Higher-level phylogeny of Foraminifera inferred from the RNA polymerase II (RPB1) gene

Macroevolutionary relations among main lineages of Foraminifera have traditionally been inferred from the small subunit ribosomal genes (SSU rDNA). However, important discrepancies in the rates of SSU rDNA evolution between major lineages led to difficulties in accurate interpretation of SSU-based phylogenetic reconstructions. Recently, actin and beta-tubulin sequences have been used as alternative markers of foraminiferal phylogeny and their analyses globally confirm results obtained with SSU rDNA. In order to test new protein markers, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1), a nuclear encoded single copy gene, for 8 foraminiferal species representing major orders of Foraminifera. Analyses of our data robustly confirm previous SSU rDNA and actin phylogenies and show (i) the paraphyly and ancestral position of monothalamid Foraminifera; (ii) the independent origin of miliolids; (iii) the monophyly of rotaliids, including buliminids and globigerinids; and (iv) the polyphyly of planktonic families Globigerinidae and Candeinidae. Additionally, the RPB1 phylogeny suggests Allogromiidae as the most ancestral foraminiferal lineage. In the light of our study, RPB1 appears as a valuable phylogenetic marker, particularly useful for groups of protists showing extreme variations of evolutionary rates in ribosomal genes.     

Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae)

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing species. Twelve Spartina species have been sequenced for two nuclear DNA regions (ITS of ribosomal DNA, and part of the Waxy gene) and one chloroplast DNA spacer (trnT-trnL). Separate and conditional combined phylogenetic analyses using Cynodon dactylon as the outgroup have been conducted. Spartina is composed of two lineages. The first clade includes all hexaploid species: the Euro-African S. maritima (2n = 60), the East-American S. alterniflora (2n = 62) and the West-American S. foliosa (2n = 60). Spartina alterniflora appears as a closely related sister species to S. foliosa. Although belonging to the same lineage, Spartina maritima appears consistently more genetically differentiated from S. alterniflora than S. foliosa. The tetraploid species S. argentinensis (2n = 40) is placed at the base of this first clade according to the Waxy data, but its position is not well resolved by the other sequences. The second well-supported main lineage within genus Spartina includes the other tetraploid American species. Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora, suggesting a possible reticulate evolution for this species. The results agree with hybridization patterns occurring in Spartina: introgression involving closely related species (S. alterniflora and S. foliosa) on one hand, and alloploid speciation involving more differentiated species (S. alterniflora and S. maritima) on the other hand.     

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.     

利用RAPD分析披碱草属、鹅观草属和猬草属模式种的亲缘关系

利用随机扩增多态性DNA（RAPD）技术对小麦族披碱草属、鹅观草属和猬草属3个属的模式种进行了基因组DNA多态性分析。42个引物产物的290条谱带中,257条（88.62%)表现出多态性,说明披碱草属、鹅观草属和猬草属3个属的模式种间具有丰富的遗传多样性。利用290个RAPD标记,计算材料间Nei氏遗传相似性系和遗传距离,在NTSYS程序中利用UPGMA进行聚类。结果表明,Elymus sibiricus种不同居群间的遗传差异较小,遗传距离在0.097-0.180之间。E.sibiricus,Roegneria caucasica和Hystrix patula的种间遗传差异明显,遗传距离在0.458-0.605之间。H.patula与E.sibiricus的亲缘关系较近。R.caucasica与E.sibiricus的亲缘关系较远。     

Phylogenetic relationships of allotetraploid Hordelymus europaeus (L.) Harz (Poaceae: Triticeae)

Phylogenetic analyses of sequence data from two plastid genes (rbcL and ndhF) and two single-copy nuclear genes (DMC1 and EF-G) are used to elucidate the origin of the tetraploid, monotypic Hordelymus europaeus. Previous data have mostly shown an allopolyploid origin of Hordelymus, but very recently it was suggested that Hordelymus is autoploid. The present analysis, including representatives from all basic genome types accepted in the Triticeae, lends support to an alloploid origin. There is substantial support for the progenitor of Psathyrostachys as female genome donor of Hordelymus. Individual nuclear gene trees disagree about the male genome donor, but combined analysis of all data weakly supports the common progenitor of Pseudoroegneria and Henrardia as the male genome donor.     

Absence of the J genome in Leymus species (Poaceae: Triticeae): evidence from DNA hybridization and meiotic pairing.

To test the presence of a J genome in the type species of Leymus, L. arenarius, its total genomic DNA and that of tetraploids L. mollis, L. salinus ssp. salmonis, L. ambiguus, L. chinensis, L. secalinus, L. alaicus ssp. karataviensis, and L. innovatus were probed with the 277-bp insert of pLeUCD2, which can hybridize with the J, S, and P but not with the N, R, V, Q, I, T, and ABD genomes. The DNA probe hybridized with PalI- or TaqI-digested total DNAs from Thinopyrum elongatum (JeJe diploid) and T. elongatum x Psathyrostachys juncea (JeN hybrid), but not with those from L. arenarius (NNNNXXXX octoploid) and all tetraploid Leymus species (NNXX). Attempts to cross diploid Thinopyrum and tetraploid Leymus species yielded only one triploid hybrid, T. elongatum x L. salinus ssp. salmonis. Meiotic chromosome associations at metaphase I of pollen mother cells in the triploid hybrid averaged 19.69 univalents, 0.64 bivalents, and 0.01 trivalents per cell. Chromosome pairings in the tetraploid hybrids of L. mollis x L. salinus ssp. salmonis, and the reciprocal cross, indicate that L. mollis and L. salinus ssp. salmonis shae the same genomic constitution. Both the DNA probe and genome analysis results confirm the absence of the J genome in the seven additional Leymus species tested. Meiotic data indicated that tetraploid Leymus species could not have the genome formula N1N1N2N2; thus their genome formulas should remain as NNXX until the source of X is identified.     

RAPD Study on Inter species Relationships in Roegneria (Poaceae: Triticeae)

To assess the relationships among 26 species in Roegneria C. Koch, 34 random decamer primers were screened for RAPD fragments. 28 primers produced polymorphic RAPD products. Data from 16 primers were used for RAPD assay. By NTSYS-pc program, Jaccard' s genetic similarity coefficients were generated and dendrogram was constructed using UPGMA. It is concluded as follows: (1) Distinct genetic differences and extensive genetic diversity were present among the species. (2) There were some genetic differences between StY and StYH genomes, and StY and StYH had a certain degree of differentiations respectively which were related to geographic regions, the farther the geographic distribution between species, the less the similarity to each other. (3) When different accessions in a species, such as species with similar morphological characters, homologous genomes and similar geographic distribution, were clustered together respectively, it suggusted that they had closer relationships. (4) The awnless species R. alashanica Keng and R. magnicaespes (D. F. Cui) L. B. Cai, in Roegneria, were separated from the other species analysed in this study, indicating that these two species had intensive genetic differences from the others. (5) R. caucasica C. Koch, a species from Western Asia, was quite different from the other species contained StY genomes in Roegneria from Eastern Asia and Central Asia. (6) The results were in consistance with that of the analysis of morphology and chromosome pairing in the taxonomic treatments for R. ciliaris (Trin) Nevski and R. japonensis (Honda) Keng, R. tenuispica J. L. Yang et Y. H. Zhou and R. pendulina Nevski, and R. tsukushiensis (Honda) Ohwi and R. kamoji Ohwi. The present study discussed the usefulness of RAPD markers in the systematic study of Roegneria.     

Phylogeny of the StH genome species in Triticeae (Poaceae): Evidence from chloroplast trnL-F and mitochondria COXII intron sequences

The StH genome species in Triticeae exhibit different morphological variations and extensive geographic distribution. To estimate the phylogenetic relationship of the StH genome species in Triticeae, mitochondria COXII intron and chloroplast trnL-F sequences of 16 StH genome species were analyzed with those of four Pseudoroegneria species (St) and four Hordeum species (H). Sequence diversity and genealogical analysis suggested that (1) the trnL-F and COXII sequence may evolve faster in the polyploid species than in the diploids; (2) the COXII intron has a high evolutionary rate compared to trnL-F sequence and would provide potentially useful phylogenetic analysis in the StH genome species; (3) different Pseudoroegneria species might serve as the maternal donor during the polyploid speciation of the StH genome species; (4) phylogenetic relationships of the StH genome species may be not linked with the inter-continental disjunction between Eurasian and North American.     

Molecular phylogeny and maternal progenitor implication in the genus Kengyilia (Triticeae: Poaceae): Evidence from COXII intron sequences

Kengyilia is a perennial genus distributing in central and western Asia. Here, the levels of nucleotide diversity for COXII intron were obtained. The estimates of nucleotide diversity for different genome constitution ranged from θ = 0.00082 and π = 0.00082 for St genome species to π = 0.01227 and θ = 0.01229 for P genome species. Employing COXII intron sequences, the phylogenetic relationships within Kengyilia and between Kengyilia genus and its closely related genera were examined. The Maximum Parsimony analysis demonstrated that Kengyilia species were positioned into two clades corresponding to different maternal genomic donor. Kengyilia stenachyra, Kengyilia grandiglumis, Kengyilia hirsuta, Kengyilia melanthera, Kengyilia thoroldiana, Kengyilia alatavica and Kengyilia zhaosuensis were related to species of Agropyron, while Kengyilia kokonorica, Kengyilia rigidula, Kengyilia nana, Kengyilia mutica, Kengyilia longiglumis, Kengyilia laxiflora and Kengyilia gobicola were close to species of Roegneria and Pseudoroegneria. In addition, other three species of Kengyilia, such as Kengyilia batalinii, Kengyilia tahelacana and Kengyilia kaschgarica, were related to Douglasdeweya deweyi, Pseudoroegneria strigosa and Roegneria tibetica. This result indicated that there had been two phylogenetically divergent maternal donors within Kengyilia. Our new finding will help to understand the evolutionary history of the genus Kengyilia.     

Molecular phylogeny and reticulate origins of the polyploid Bromus species from section Genea (Poaceae)

The origin of polyploid Bromus species of section Genea was investigated using molecular data. This group of annual species native from the Old-World is composed of three diploids, two tetraploids, one hexaploid, and one octoploid. Molecular cloning, sequencing, and phylogenetic analyses were performed on several accessions per species. We used the low copy nuclear gene Waxy, repeated rDNA spacers ITS1 and ITS2 and chloroplast spacers trnT-trnL and trnL-trnF. Our analyses revealed four different lineages involved in the parentage of the polyploids and confirmed their reticulate origin. Three of these lineages are closely related to the diploid species B. sterilis, B. tectorum, and B. fasciculatus. The fourth lineage could not be related to any diploid according to the available data. Our data gave insights on the origin of all the polyploids of section Genea, and chloroplast data allowed us to identify the maternal lineages. The Waxy gene was the most informative regarding origin of the polyploids. The Waxy copies duplicated by polyploidy appear selectively maintained in the polyploid species. No sequence heterogeneity was encountered in the ITS region, where concerted evolution seems to have occurred toward either maternal or paternal repeats. These results provide new information about the origin and molecular evolution of these polyploids and will allow a more accurate taxonomic treatment of the concerned species, based on their evolutionary history.