Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets.

Although the monogenomic genera of the Triticeae have been analyzed in numerous biosystematic studies, the allopolyploid genera have not been as extensively studied within a phylogenetic framework. We focus on North American species of Elymus, which, under the current genomic system of classification, are almost all allotetraploid, combining the St genome of Pseudoroegneria with the H genome of Hordeum. We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the maternal genome donor of Elymus. We also present a cpDNA phylogeny for the monogenomic genera that includes more data than, and thus builds on, those previously published. The chloroplast DNA data indicate that Pseudoroegneria is the maternal genome donor to all but one of the Elymus individuals. There is little divergence among the Elymus and Pseudoroegneria chloroplast genomes, and as a group, they show little divergence from the rest of the Triticeae. Within the monogenomic Triticeae, the problematic group Thinopyrum is resolved as monophyletic on the chloroplast DNA tree. At the intergeneric level, the data reveal several deeper-level relationships that were not resolved by previous cpDNA trees.     

Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis

BAUM, B. R. & SAVILE, D. B. O., 1985. Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis. Established evolutionary trends in Uredinales as a whole are reviewed, and primitive and advanced characters are presented. The rusts of all Poaceae arc presented in a table that strongly indicates Bambusoideae to be the oldest and Pooideae the youngest subfamily. The rusts of Triticeae and their ecogeography are outlined; the rusts of Cyperaceae, selected as an out-group, are beiefly summarized; and the available characters and character states for rusts of Triticeae are given. Host alternation complicates the analysis. The aerial host (never a grass) is ecologically associated with the unrelated telial (grass) host. There are no appropriate methods to permit analysis of the combined components: aecial host evolution, telial host evolution, rust evolution, and their coevolution. Also, several aecial hosts are unknown. Consequently it was necessary to omit aecial hosts from the analysis. Cladistic analysis of the rusts of Triticeae was performed using five methods and consisted of cycles of tree analysis and modification of character state trees. A cladogram put together from a Dollo and a Wagner cladogram was used as a basis for the classification of rusts given. Subsequently a cladistic analysis of genera of Triticeae, using presence/absence of rusts as characters (Brooks' approach) was performed. The Triticeae cladogram of Baum (1983) was also analysed. Distances between the cladogram generated by various methods and that of Baum were computed for each possible pair, using the method of Robinson & Foulds, and then the resulting distance matrix was reduced in dimensionality by principal components and non-metric multidimensional scaling. The results are discussed in light of the limitation of the analyses and the data. It is concluded that coevolution is limited and that frequent jumps to ecologically associated hosts explain the parallelism in evolution of rusts on Triticeae.     

Morphological variation and genome constitution in some perennial Triticeae

JARVIE, J. K. & BARKWORTH, M. E., 1992. Morphological variation and genome constitution in some perennial Triticeae. A numerical analysis of species of five genomically defined genera of the Triticeae was undertaken, based on 42 morphological characters and 142 operational taxonomic units (OTUs). The primary goal was to determine the degree of congruence between morphological variation and genomic constitution. The second goal was to determine which existing supraspecific classification, if any, best reflected the morphological variation encountered. The five genera investigated were Thinopyrum (J genome), Lophopyrum (E genome), Pseudoroegneria (S genome), Trichopyrum (EES genome) and Elytrigia (SJE/SSX genome). Both principal co-ordinate and cluster analysis of the data placed the OTUs in supraspecific groups that reflected their genomic constitution. Monogenomic taxa were clearly separated. Allotetraploids between the E and S genomes were situated between E and S monogenomic taxa. Allotetraploids between the J and E genomes were situated closest to J genome taxa. The EES taxa of Trichopyrum were placed closest to Lophopyrum. OTUs of Elytrigia overlapped those of Pseudoroegneria , but not those of Lophopyrum or Thinopyrum.     

Biosystematics and evolutionary relationships of perennial Triticeae species revealed by genomic analyses

Understanding the classification and biosystematics of species in Triticeae Dumort., an economically important tribe in the grass family (Poaceae), is not an easy task, particularly for some perennial species. Does genomic analysis facilitate the understanding of evolutionary relationships of these Triticeae species? We reviewed literature published after 1984 to address questions concerning: (1) genome relationships among the monogenomic diploid species; (2) progenitors of the unknown Y genome in Elymus polyploids, X genome in Thinopyrum intermedium, and Xm genome in Leymus; and (3) genome constitutions of some perennial Triticeae species that were unknown or misidentified. A majority of publications have substantiated the close affinity of the E^b and E^e genomes in Th. bessarabicumand Th. elongatum, supporting the use of a common basic genome symbol. The E genome is close to the St genome of Pseudoroegneria and ABD genomes ofTriticum/Aegilops complex, providing an explanation for transferring genes from the E to ABD genomes with relative ease. Although the solid proof is still lacking, theW, P, and especially Xp genomes are possible origins for the Y genome of polyploid Elymus. The absence of the E genome and the allopolyploidy nature of tetraploidLeymus species have been unequivocally confirmed by both cytogenetic and molecular studies. However, the donor of the Xm genomes of Leymus was only speculated to be related to the P genome of Agropyron and F genome of Eremopyrum. Intermediate wheatgrass (Th. intermedium) has been extensively studied. The presence of the St (as the previously designated X) genome in Th. intermedium is now unequivocal. Its two more closely related E₁ and E₂ genomes are shown to be older versions of the E genome rather than the current E^b and E^e genomes. Speciation of Th. intermedium was similar to that of Triticum aestivum, in which the J^s/E^s(like B) genomes had the greatest differentiation from the current J (E^b) genome owning to repetitive sequences of the V genome, whereas its St (like D) had the least differentiation from the current St genome. Species with unknown or misidentified genomes have been correctly designated, including those with the ESt, StP, StPY,StWY, EStP, HW, StYHW, and NsXm genomes. Some of those species have been transferred to and renamed in appropriate genera.     

A study of 28 Elymus species using repetitive DNA sequences.

Four repetitive DNA sequences cloned from the barley (Hordeum vulgare) genome and common for different Triticeae species were used for a molecular study of phylogenetic relationships among 28 Elymus species. Two wild Hordeum species (H genome), two Pseudoroegneria species (S genome), Agropyron cristatum (P genome), and Australopyrum velutinum (W genome) were included as genomic representatives for the genomes that supposedly were involved in the evolution of the genus Elymus. Our results are essentially congruent with the genomic classification system. This study demonstrates that Elymus is not a monophyletic genus. Based on an analysis of Southern blot hybridization we could discriminate between SY and SH species owing to the strong specific hybridization pattern of the H genome. Hexaploid SYH species gave a hybridization pattern similar to SH species for the same reason. The results support the genomic composition of Elymus batalinii as SYP and also indicated the presence of at least one H genome in Elymus enysii with a hitherto unknown genomic constitution. Elymus erianthus had a hybridization pattern distinctly different from all other species in the investigation. Key words : Elymus, RFLP, phylogeny, repetitive DNA.     

禾本科牧草的同工酶分析

本文分析了23种禾本科牧草的酯酶同工酶和过氧化物酶同工酶。结果表明,如果统一取材标准及实验条件严格,酶谱资料是稳定可比较的,有一定的系统分类价值。酶谱并结合其它资料证明了成立鼠茅属(Vulpia)的合理性。酶谱资料还表明,黑麦草属(Lolium)可能是小麦族和羊茅族相互联系的桥梁。根据酶谱距离的资料,讨论了小麦族的某些属间关系。例如,作者发现,酶谱资料显示出鹅观草属与披碱草属赖草与披碱草属之间有更近的亲缘关系。     

COMMENTS ON GENOMIC GENERA IN THE TRITICEAE (POACEAE)

Generic delimitation in the Triticeae has long been problematical because the extensive hybridization in the group is not readily accomodated in a hierarchical classification. The genomic genera of Löve (1984) are one solution, but fully one-third of them are polyphyletic, incorporating 2 or more genomes. The suggestion that the tribe be considered a single genus (Stebbins, 1956) is theoretically defensible—the genus would be strictly monophyletic—but probably impractical. This paper presents a cladistic analysis of the tribe that differs from previous analyses in that it uses only strictly monophyletic (monogenomic) groups as terminal taxa; hybrids (heterogenomic groups) are shown as reticulations. Monophyletic groups can then be delimited to minimize the number of polyphyletic genera. A classification incorporating genomic information is derived from the phylogeny.     

Genetic Relationships Among Five Basic Genomes St,E,A,B and D in Triticeae Revealed by Genomic Southern and in situ Hybridization

The St and E are two important basic genomes in the perennial tribe Triticeae (Poaceae). They exist in many perennialspecies and are very closely related to the A, B and D genomes of bread wheat (Triticum aestivum L.). Genomic Southernhybridization and genomic in situ hybridization (GISH) were used to analyze the genomic relationships between the twogenomes (St and E) and the three basic genomes (A, B and D) of T. aestivum. The semi-quantitative analysis of the Southernhybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, andrelatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion.St and E are the two basic genomes of Thinopyrum ponticum (StStE~eE~bE~x) and Th. intermedium (StE~eE~b), two perennialspecies successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of thespontaneous wheat-Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genomeand rarely in the B genome. This would develop further use of alien species for wheat improvement, especially thosecontaining St or E in their genome components.     

Editorial: Taking genetics seriously

Since 2007, consumer genomics companies have marketed personal genome scanning services to assess users' genetic predispositions to a variety of complex diseases and traits. This study investigates early users' reasons for utilizing personal genome services, their evaluation of the technology, how they interpret the results, and how they incorporate the results into health-related decision-making. The analysis contextualizes early users' relationships to the technology, the knowledge generated by it, and how it mediates their relationship to their own health and to biomedicine more broadly. The results reveal that early users approach personal genome scanning with both optimism for genomic research and skepticism about the technology's current capabilities, which runs contrary to concerns that consumers may be ill equipped to interpret and understand genome scan results. These findings provide important qualitative insight into early users' conceptualizations of personal genomic risk assessment and illuminate their involvement in configuring this technology in the making.     

AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS

Abstract— Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2—4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.     

Phylogenetic relationships in Leymus (Poaceae: Triticeae) revealed by the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences

Using the nuclear ribosomal internal transcribed spacer (ITS) sequences and the chloroplasttrnL-F sequence, phylogeneic analysis was performed on 57 accessions of species in the tribe Triticeae including 13 Leymus species (N(s)) with different ploidy levels and 40 diploid species from 18 genera. The ITS sequences revealed that ployploid Leymus has close phylogentic relationships with Psathyrostachys and an undefined genus in Triticeae. The trnL-F tree demonstrated close relationships between certain Leymus species and Psathyrostachys, and other Leymus species distributed in North America were far from Psathyrostachys. Based on these results, it is unlikely that the unknown genome in Leymus species originated from one of the sampled diploid species in the present study. The maternal donor of all the Leymus species with a natural distribution in Eurasia were N(s) genome. Furthermore, Elymus californicus should be transferred from the genus Elymus to Leymus.     

Genetic Relationships Among Five Basic Genomes St, E, A, B and D in Triticeae Revealed by Genomic Southern and in situ Hybridization

The St and E are two important basic genomes in the perennial tribe Triticeae （Poaceae）. They exist in many perennial species and are very closely related to the A, B and D genomes of bread wheat （Triticum aestivum L.）. Genomic Southern hybridization and genomic in situ hybridization （GISH） were used to analyze the genomic relationships between the two genomes （St and E） and the three basic genomes （A, B and D） of T. aestivum. The semi-quantitative analysis of the Southern hybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, and relatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion. St and E are the two basic genomes of Thinopyrum ponticum （StStE^eE^bE^x） and Th. intermedium （StE^eE^b）, two perennial species successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of the spontaneous wheat-Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genome and rarely in the B genome. This would develop further use of alien species for wheat improvement, especially those containing St or E in their genome components.     

A linkage map of meadow fescue (<Emphasis Type="Italic">Festuca pratensis</Emphasis> Huds.) and comparative mapping with other Poaceae species

A genetic linkage map has been constructed for meadow fescue (Festuca pratensis Huds.) (2n=2x=14) using a full-sib family of a cross between a genotype from a Norwegian population (HF2) and a genotype from a Yugoslavian cultivar (B14). The two-way pseudo-testcross procedure has been used to develop separate maps for each parent, as well as a combined map. A total number of 550 loci have been mapped using homologous and heterologous RFLPs, AFLPs, isozymes and SSRs. The combined map consists of 466 markers, has a total length of 658.8 cM with an average marker density of 1.4 cM/marker. A high degree of orthology and colinearity was observed between meadow fescue and the Triticeae genome(s) for all linkage groups, and the individual linkage groups were designated 1F–7F in accordance with the orthologous Triticeae chromosomes. As expected, the meadow fescue linkage groups were highly orthologous and co-linear with Lolium, and with oat, maize and sorghum, generally in the same manner as the Triticeae chromosomes. It was shown that the evolutionary 4AL/5AL translocation, which characterises some of the Triticeae species, is not present in the meadow fescue genome. A putative insertion of a segment orthologous to Triticeae 2 at the top of 6F, similar to the rearrangement found in the wheat B and the rye R genome, was also observed. In addition, chromosome 4F is completely orthologous to rice chromosome 3 in contrast to the Triticeae where this rice chromosome is distributed over homoeologous group 4 and 5 chromosomes. The meadow fescue genome thus has a more ancestral configuration than any of the Triticeae genomes. The extended meadow fescue map reported here provides the opportunity for beneficial cross-species transfer of genetic knowledge, particularly from the complete genome sequence of rice.Communicated by P. Langridge     

Multidisciplinary approach to genome analysis in the diploid species,Thinopyrum bessarabicum and Th. elongatum (Lophopyrum elongatum), of the Triticeae

Summary The J and E genome species of the Triticeae are invaluable sources of salt tolerance. The evidence concerning the phyletic relatedness of the J genome of diploid Thinopyrum bessarabicum and the E genome of diploid Th. elongatum (=Lophopyrum elongatum) is discussed. Low level of chromosome pairing between J and E at different ploidy levels, suppression of J-E pairing by the Ph1 pairing regulator that inhibits homoeologous pairing, complete sterility of the diploid hybrids (JE), karyotypic divergence of the two genomes, differences in total content and distribution of heterochromatin along their chromosomes, and marked differences in gliadin proteins, isozymes, 5S DNA, and rDNA indicate that J and E are distinct genomes. Well-defined biochemical markers have been identified in the two genomes and may be useful in plant breeding. The level of distinction between J and E is comparable to that among the universally accepted homoeologous genomes A, B, and D of wheat. Therefore, the J and E genomes are homoeologous and not homologous, although some workers continue to call them homologous. The previous workers' data on chromosome pairing in diploid hybrids and/ or karyotypic differences in the conventionally stained chromosomes do not provide sufficient evidence for the proposed merger of J and E genomes (and, hence, of the genera Thinopyrum and Lophopyrum) specifically and for establishing genome relationships generally. Extra precautions should be exercised before changing the designation of an established genome and before merging two genera. A uniform, standardized system of genomic nomenclature for the entire Triticeae is proposed, which should benefit cytogeneticists, plant breeders, taxonomists, and evolutionists.Cooperative investigations of the USDA-Agricultural Research Service and the Utah Agricultural Experiment Station, Logan, UT 84322, USA. Approved as Journal Paper no. 3832     

Rapid evolutionary dynamics in a 2.8‐Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii

Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi‐gene families, the DNA sequence of a 2.8‐Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance‐like gene families, was analyzed in the diploid grass Aegilops tauschii, the D‐genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non‐syntenic genes and only 13 ancestral genes are shared among these grass species. These non‐syntenic genes, including prolamin and resistance‐like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non‐syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin‐related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance‐like genes and subsequent differential expansion of each R gene family. The high frequency of non‐syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8‐Mb region with nine‐fold higher than the genome‐wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.     

Phylogeny of a Genomically Diverse Group of Elymus (Poaceae) Allopolyploids Reveals Multiple Levels of Reticulation

The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.     

Evidence for widespread reticulate evolution within human duplicons

Approximately 5% of the human genome consists of segmental duplications that can cause genomic mutations and may play a role in gene innovation. Reticulate evolutionary processes, such as unequal crossing-over and gene conversion, are known to occur within specific duplicon families, but the broader contribution of these processes to the evolution of human duplications remains poorly characterized. Here, we use phylogenetic profiling to analyze multiple alignments of 24 human duplicon families that span >8 Mb of DNA. Our results indicate that none of them are evolving independently, with all alignments showing sharp discontinuities in phylogenetic signal consistent with reticulation. To analyze these results in more detail, we have developed a quartet method that estimates the relative contribution of nucleotide substitution and reticulate processes to sequence evolution. Our data indicate that most of the duplications show a highly significant excess of sites consistent with reticulate evolution, compared with the number expected by nucleotide substitution alone, with 15 of 30 alignments showing a >20-fold excess over that expected. Using permutation tests, we also show that at least 5% of the total sequence shares 100% sequence identity because of reticulation, a figure that includes 74 independent tracts of perfect identity >2 kb in length. Furthermore, analysis of a subset of alignments indicates that the density of reticulation events is as high as 1 every 4 kb. These results indicate that phylogenetic relationships within recently duplicated human DNA can be rapidly disrupted by reticulate evolution. This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution.     

Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed. Electronic Supplementary Material Supplementary material is available for this article at