The 5S rRNA gene in wall barley (Hordeum murinum L. sensu lato): sequence variation among repeat units and relationship to the Y haplome in the genus Hordeum (Poaceae: Triticeae)

What does the 5S rRNA multigene family tell us about the origin of the annual Triticeae (Poaceae)?

We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The "long" unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the "short" unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.

Diversity and evolution of the Hordeum murinum polyploid complex in Algeria

Population diversity and evolutionary relationships in the Hordeum murinum L. polyploid complex were explored in contrasted bioclimatic conditions from Algeria. A multidisciplinary approach based on morphological, cytogenetic, and molecular data was conducted on a large population sampling. Distribution of diploids (subsp. glaucum) and tetraploids (subsp. leporinum) revealed a strong correlation with a North-South aridity gradient. Most cytotypes exhibit regular meiosis with variable irregularities in some tetraploid populations. Morphological analyses indicate no differentiation among taxa but high variability correlated with bioclimatic parameters. Two and three different nuclear sequences (gene coding for an unspliced genomic protein kinase domain) were isolated in tetraploid and hexaploid cytotypes, respectively, among which one was identical with that found in the diploid subsp. glaucum. The tetraploids (subsp. leporinum and subsp. murinum) do not exhibit additivity for 5S and 45S rDNA loci comparative with the number observed in the related diploid (subsp. glaucum). The subgenomes in the tetraploid taxa could not be differentiated using genomic in situ hybridization (GISH). Results support an allotetraploid origin for subsp. leporinum and subsp. murinum that derives from the diploid subsp. glaucum and another unidentified diploid parent. The hexaploid (subsp. leporinum) has an allohexaploid origin involving the two genomes present in the allotetraploids and another unidentified third diploid progenitor.

Ancient differentiation of the H and I haplomes in diploid Hordeum species based on 5S rDNA

5S rDNA clones from 12 South American diploid Hordeum species containing the HH genome and 3 Eurasian diploid Hordeum species containing the II genome, including the cultivated barley Hordeum vulgare, were sequenced and their sequence diversity was analyzed. The 374 sequenced clones were assigned to "unit classes", which were further assigned to haplomes. Each haplome contained 2 unit classes. The naming of the unit classes reflected the haplomes, viz. both the long H1 and short I1 unit classes were identified with II genome diploids, and both the long H2 and long Y2 unit classes were recognized in South American HH genome diploids. Based upon an alignment of all sequences or alignments of representative sequences, we tested several evolutionary models, and then subjected the parameters of the models to a series of maximum likelihood (ML) analyses and various tests, including the molecular clock, and to a Bayesian evolutionary inference analysis using Markov chain Monte Carlo (MCMC). The best fitting model of nucleotide substitution was the HKY+G (Hasegawa, Kishino, Yano 1985 model with the Gamma distribution rates of nucleotide substitutions). Results from both ML and MCMC imply that the long H1 and short I unit classes found in the II genome diploids diverged from each other at the same rate as the long H2 and long Y2 unit classes found in the HH genome diploids. The divergence among the unit classes, estimated to be circa 7 million years, suggests that the genus Hordeum may be a paleopolyploid.

The external promoter in the guinea pig 5S rRNA gene is different from the rodent promoter

The guinea pig has about 100 copies of the 5S rRNA gene per haploid genome and they are present in 2.1 kb tandem repeats. Three bona fide 5S rRNA genes and four pseudo genes were sequenced. The conserved external promoter (D box) found in rodents and primates is only partially present in the guinea pig. The "D box like" sequence in guinea pig only has eight of the 12 nucleotides in the conserved D box. The results are in accordance with investigations showing that the guinea pig is not a rodent. Conserved sequences in the non-transcribed spacer can therefore be useful in phylogenetic studies.

Molecular diversity of the 5S rDNA units in theElymus dahuricuscomplex (Poaceae: Triticeae) supports the genomic constitution ofSt,Y, andHhaplomes

The phylogenetic analysis of 118 5S rRNA gene sequences cloned from members of the Elymus dahuricus complex containing the St, Y, and H haplomes, and of several related species containing at least one of these three haplomes, is reported. Differences in sequence pattern, primarily within the nontranscribed spacer, enabled the identification of six putative orthologous groups that we refer to as unit classes. In previous publications, we have been able to assign unit classes to haplomes. In addition to four unit classes previously identified in other genera, namely the long H1, long S1, long P1, and long {Y1, here we document two new unit classes called the long S2 and long W1. Most sequences of the E. dahuricus complex and related tetraploid species are classified as long S1 and assigned to the St haplome. Both long S1 and long S2 unit classes were identified in the diploid Pseudoroegneria spicata (Pursh) Á. Löve with the St haplome. The long S2 unit class was also identified in the hexaploid Elymus scabrus (R. Br.) Á. Löve with the St,Y,and W haplomes. The long P1 was known from the diploid Agropyron cristatum Gaertn. with the P haplome, and the long W1 was determined in Australopyrum retrofractum (Vickery) Á. Löve, known to contain the W haplome, but was not yet detected in E. scabrus, a hexaploid species with W being one of the three haplomes. The long H1 reported earlier from Hordeum was identified in several clones of the E. dahuricus complex. As previously reported, the long {Y1 unit class was found to be rare overall, but we identified it in a few clones of Elymus drobovii and in the E. dahuricus complex.Key words: 5S rDNA, unit classes, haplomes, concerted evolution.

The South African Hordeum capense is more closely related to some American Hordeum species than to the European Hordeum secalinum: a perspective based on the 5S DNA units (Triticeae: Poaceae)

Several authors have proposed that the European Hordeum secalinum and the morphologically similar South African Hordeum capense are conspecific. In this paper we provide evidence that the two species differ in their 5S DNA unit class composition. We also report on the diversity of 5S DNA units in Hordeum muticum, a South American species. When the 5S rDNA unit class composition for these three species is compared with the unit class composition for all Hordeum species thus far investigated, it appears that H. capense is more closely related to the American Hordeum species containing the long Y2 unit class, than to H. secalinum, which lacks the long Y2 unit class but contains the long X2 unit class found in H. marinum. This analysis suggests H. capense may have originated from a stock common to the South American species, such as H. muticum.Key words: 5S DNA unit class, Hordeum capense, Hordeum secalinum, Hordeum muticum, continental drift.

Defining orthologous groups among multicopy genes prior to inferring phylogeny, with special emphasis on the Triticeae (Poaceae)

Sequence information from multicopy genes has been widely used for phylogenetic inference. Among those sequences analyzed, nuclear 5S rRNA genes, the two internal transcribed spacer regions (ITS1 and ITS2) of the 18S-26S rDNA genes, and the intergenic spacer (IGS) regions of the same 18S-26S rDNA genes have all been used at the specific, generic, familial and tribal levels. Many investigations have used direct sequencing of PCR products to generate sequence data. The merits of an alternate approach, namely, cloning prior to sequencing followed by careful alignment of numerous cloned sequences to discern groups of putative orthologous sequences that may then be useful for the inference of relationships among species and genera, are examined and discussed. This process discerns patterns resulting from several cycles of careful alignment followed by manual editing conducted by eye--an exacting operation especially when sequences are unequal in length due to the presence of additions/deletions. Based upon examples taken from our work on the sequencing of individual 5S rDNA clones from several wheat and barley species (Triticum and Hordeum respectively), and the re-analysis of data of others taken from several studies using the nuclear genes mentioned above, we are able to identify groups of putative orthologous sequences that we have named "unit classes". Furthermore, comparisons between provisional orthologous sequences isolated from different species are required for the inference of phylogenetic relationships between them. Paralogous sequences from different unit classes can be compared to infer evolutionary relationships among repeat types only, i.e. among unit classes. In several cases, the analysis of the sequence diversity obtained from different clones permitted the assignment of unit classes to specific haplomes.

A comparison of the 5S rDNA diversity in theHordeum brachyantherum–californicumcomplex with those of the eastern AsiaticHordeum roshevitziiand the South AmericanHordeum cordobense(Triticeae: Poaceae)

Amplification of the 5S rDNA gene by the polymerase chain reaction, followed by cloning and sequencing, was used to generate data from 23 seed accessions of Hordeum brachyantherum Nevski, Hordeum californicum Covas et Stebbins, Hordeum cordobense Bothmer, Jacobsen et Nicora, and Hordeum roshevitzii Bowden. One hundred and fourteen clones were analyzed, resulting in the detection of four different 5S DNA unit classes. Three of them, long H1, long H2, and long Y2, had been previously reported. The long H3 class, described for the first time, is present only in H. roshevitzii but can be grouped with previously unassigned units of Hordeum bulbosum L. and Hordeum spontaneum C. Koch. Based upon the analyses of 5S rDNA sequences, we found that (i) the long H2 unit class was not found in the Asiatic H. roshevitzii and therefore may be restricted to the American species, (ii) there is no strong support that H. brachyantherum and H. californicum are worthy of species recognition, and (iii) cladistic analysis of the consensus sequences of the four paralogous unit classes demonstrated that long Y2 is the most distant from the three long H classes.Key words: 5S DNA gene, Hordeum, unit classes.

Species relationships between antifungal chitinase and nuclear rDNA (internal transcribed spacer) sequences in the genus Hordeum

The sequences of the chitinase gene (Chi-26) and the internal transcribed spacer of 18S - 5.8S - 26S rDNA (ITS1) were determined to analyze the phylogenetic relationships among species representing the four basic genomes of the genus Hordeum. Grouping analysis based on data for Chi-26 gene sequences placed Hordeum secalinum (H genome) near the Hordeum murinum complex (Xu genome), and Hordeum bulbosum distant from the other species that carried the I genome. ITS sequence data showed the expected grouping based on the genome classification of the species studied. Different sequences of ITS were detected even in the genomes of the diploid species. The results are interpreted in terms of defective or unfinished concerted evolution processes in each taxon.

The 5S rRNA gene units in the native New World annual Hordeum species (Triticeae: Poaceae)

We have employed a polymerase chain reaction (PCR) based approach to amplify 5S rDNA sequences from 20 accessions representing five Hordeum species native to the Americas. Sequence analysis of 88 clones revealed three sets of orthologous sequences in Hordeum pusillum Nutt. and two sets in the other four species. The long H1 unit class, previously known in Hordeum bulbosum L., Hordeum marinum L. s.l., Hordeum murinum L. s.l., Hordeum spontaneum Boiss., and Hordeum vulgare L., was found also in Hordeum depressum (Scribner & Smith) Rydberg and in H. pusillum; however, the majority of the sequences fell within two new classes of orthologous sequences. Sequences of the long H2 unit class were found in four species but not in H. depressum. Sequences of the long Y2 unit class were found in all five species. The long H2 and long Y2 unit classes appear to be unique to this group of five, mostly annual, North and South American species. Cladistic analysis of the orthologous sequences from the species with the long H1 unit class places the long H1 sequence of Hordeum flexuosum Steudel in the same clade with H. murinum, whereas H. depressum is more closely related to the perennial species, Hordeum bogdanii Wilenski and H. bulbosum. This association differs from previously described species relationships and it may be that the gene tree differs from the species tree. A cladistic analysis of paralogous sequences of the two new unit classes defined in this study together with the long H1, the long Y1 and the long X2 unit classes uncovered in previous work in Hordeum, was performed. Based upon these analyses, we hypothesize that the possible order of divergence was first the division into two branches leading to the long H1 unit class and the long H2 unit class; the lineage leading to the long H2 class was further divided to give rise to branches leading to the long Y1, the long Y2 and the long X2 classes.Key words: 5S rDNA, genomes, haplomes, unit classes, Hordeum, Triticeae.

The 5S rRNA gene diversity in Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen, and Baum (Poaceae: Triticeae): possible contribution of the H genome to the origin of Kengyilia

Fifty-three units of 5S rDNA sequences from five accessions of Kengyilia rigidula, a member of the tribe Triticeae that also includes wheat, barley, rye, and their wild relatives, have been amplified by the polymerase chain reaction (PCR), cloned, and sequenced. The genome of K. rigidula consists of three haplomes, St, P, and Y. An evaluation of the aligned sequences of the diverse 53 different 5S DNA units yielded three 5S-unit classes. One unit class, Long S1, was assignable to the St haplome, one unit class, the Long P1, was assignable to the P haplome, and a third unit class, Long H1, was assignable to the H haplome. The last was expected to be assignable to the Y haplome, based on previous knowledge. Evolutionary scenarios are put forward to explain this finding. Among those possibilities is that the number of copies of units assignable to the Y haplome is very small and difficult to detect. Short units, reported earlier in K. alatavica, were not found in K. rigidula.