The 5S DNA sequences in Hordeum bogdanii and in the H. brevisubulatum complex, and the evolution and the geographic dispersal of the diploid Hordeum species (Triticeae: Poaceae)

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Bernard R. Baum ◽  
Douglas A. Johnson
Keyword(s):  
Dna Sequences ◽  
Diploid Species ◽  
5S Rdna ◽  
Single Species ◽  
Gene Gain ◽  
The North ◽  
Unit Classes ◽  
Unit Class ◽  
Gain Loss ◽  
Hordeum Species

The molecular diversity of 5S rDNA from the closely related Asiatic diploid species, Hordeum bogdanii and the H. brevisubulatum complex has been catalogued and analysed. As in previous studies in Hordeum , we found that the sequences are constrained in such an manner that unit classes can be defined. The long H1 unit class, known to occur in all Eurasian species, was frequently found in these 2 taxa. In addition, we identified a new unit class, called the short H3 to reflect the H genome found in these 2 taxa. Although the 2 taxa are very close morphologically, the variation in the long H1 DNA units is constrained to such a great degree that, in many cases, the accessions in a unit class from a single species are clustered. In H. bogdanii, the majority of the sequences are grouped in this manner, whereas in the H. brevisubulatum complex, the tendency to be constrained is lower in some but not all subspecies. These results support keeping H. brevisubulatum ssp. violaceum and ssp. iranicum as 1 species with the long H1 and short H1 unit classes, while retaining ssp. nevskianum and ssp. turkestanicum in the H. brevisubulatum complex. We have summarized our work on the presence/absence of the 10 unit classes found in all diploid species of Hordeum. A phylogenetic analysis, based strictly on the presence/absence of unit classes, indicated clearly that all the South American diploids and all the North American diploids possess long H2 and long Y2 unit classes and, except for H. californicum and H. pusillum, which contain long H1 in addition to the long H2 and long Y2 classes, are devoid of the long H1 unit class. This suggests that the gene gain/loss process from a common ancestor has been concomitant with intercontinental dispersal between the Old and the New Worlds.

Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae)

Genome ◽  
2008 ◽  
Vol 51 (2) ◽  
pp. 137-154 ◽  
Author(s):  
Yuan-Ying Peng ◽  
Yu-Ming Wei ◽  
Bernard R. Baum ◽  
You-Liang Zheng
Keyword(s):  
Molecular Diversity ◽  
Diploid Species ◽  
5S Rdna ◽  
Rrna Gene ◽  
D Genome ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Hexaploid Species ◽  
Unit Class ◽  
C Genome

The molecular diversity of the rDNA sequences (5S rDNA units) in 71 accessions from 26 taxa of Avena was evaluated. The analyses, based on 553 sequenced clones, indicated that there were 6 unit classes, named according to the haplomes (genomes) they putatively represent, namely the long A1, long B1, long M1, short C1, short D1, and short M1 unit classes. The long and short M1 unit classes were found in the tetraploid A. macrostachya , the only perennial species. The long M1 unit class was closely related to the short C1 unit class, while the short M1 unit class was closely related to the long A1 and long B1 unit classes. However, the short D1 unit class was more divergent from the other unit classes. There was only one unit class per haplome in Avena, whereas haplomes in the Triticeae often have two. Most of the sequences captured belonged to the long A1 unit class. Sequences identified as the long B1 unit class were found in the tetraploids A. abyssinica and A. vaviloviana and the diploids A. atlantica and A. longiglumis . The short C1 unit class was found in the diploid species carrying the C genome, i.e., A. clauda, A. eriantha , and A. ventricosa , and also in the diploid A. longiglumis, the tetraploids A. insularis and A. maroccana , and all the hexaploid species. The short D1 unit class was found in all the hexaploid species and two clones of A. clauda. It is noteworthy that in previous studies the B genome was found only in tetraploid species and the D genome only in hexaploid species. Unexpectedly, we found that various diploid Avena species contained the B1 and D1 units. The long B1 unit class was found in 3 accessions of the diploid A. atlantica (CN25849, CN25864, and CN25887) collected in Morocco and in 2 accessions of A. longiglumis (CIav9087 and CIav9089) collected in Algeria and Libya, respectively, whereas only 1 clone of A. clauda (CN21378) had the short D1 unit. Thus there might be a clue as to where to search for diploids carrying the B and D genomes. Avena longiglumis was found to be the most diverse species, possibly harboring the A, B, and C haplomes. The long M1 and short M1 are the unit classes typical of A. macrostachya. These results could explain the roles of A. clauda, A. longiglumis, and A. atlantica in the evolution of the genus Avena. Furthermore, one clone of the tetraploid A. murphyi was found to have sequences belonging to the short D1 unit class, which could indicate that A. murphyi might have been the progenitor of hexaploid oats and not, as postulated earlier, A. insularis. The evolution of Avena did not follow the molecular clock. The path inferred is that the C genome is more ancient than the A and B genomes and closer to the genome of A. macrostachya, the only existing perennial, which is presumed to be the most ancestral species in the genus.

The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes – a test on cultivated wheat and wheat progenitors

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 590-599 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey ◽  
Alexander Belyayev ◽  
Olga Raskina ◽  
Eviatar Nevo
Keyword(s):  
Evolutionary Dynamics ◽  
Diploid Species ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Aegilops Speltoides ◽  
Mantel Tests ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Genes

Data is presented on the evolutionary dynamics of non-transcribed spacers (NTSs) of 5S rRNA genes in some diploid and polyploid Triticum and Aegilops species. FISH experiments with probes representing different unit classes revealed presence and (or) absence of these sequences in genomes or separate chromosomes of the species. Among the three diploid species only Aegilops speltoides has all of the different unit classes in ribosomal clusters as detected by the probes. Triticum urartu does not have the long D1 signals and Aegilops tauschii does not have the long A1 signals. Both polyploids possess all types of sequences, but because of genome rearrangements after polyploidization there is significant repatterning of single different rDNA unit classes in chromosomal positions when compared with those in diploid progenitors. Additional refined work is needed to ascertain if the sequences in the polyploids are mixed or are located in mini clusters in close proximity to each other. Mantel tests for association between the presence of the FISH signals of the A, B, and D genomes together and separately with the unit class data of the material, i.e., the probes used in FISH, indicated that all signals were associated with their respective probe material, but that there was no association of the unit classes found and the signals to each haplome. All combinations of the partial Mantel tests, e.g., between the A and B haplomes while controlling the effect of the all probes signals, with correlations ranging from 0.48 to 0.79 were all significant. Principal coordinate analysis showed that the signals of most unit class specific probes were more or less equally distant except for the long {S1 and short G1 signals, which were not different, and that the short A1 signals were closely related to the former two, whereas the signals of the long G1 were even less related.Key words: in situ hybridization, non-transcribed spacers, 5S rRNA genes, Triticeae.

scholarly journals Differences Between South American H Haplome Diploids and I Haplome Diploids from the Perspective of the 5S rDNA Gene in the Genus Hordeum

2011 ◽  
Vol 40 (No. 2) ◽  
pp. 45-50 ◽  
Author(s):  
R. Baum B ◽  
J. Johnson D
Keyword(s):  
Maximum Likelihood ◽  
Molecular Clock ◽  
Diploid Species ◽  
5S Rdna ◽  
South American ◽  
Rdna Gene ◽  
Unit Classes ◽  
Cultivated Barley ◽  
5S Rdna Sequence ◽  
Hordeum Species

Twelve South American diploid Hordeum species belonging to the H genome and three diploid species belonging to the I genome (including cultivated barley) were investigated for their 5S rDNA sequence diversity. The 374 sequenced clones were assigned to classes called “unit classes” which were further assigned to haplomes. Two unit classes were found to be present in each haplome. These were labelled to reflect the haplomes, viz. the long H1 and short I1 unit classes for the I haplome diploids, and the long H2 and long Y2 unit classes for the South American H genome diploids. The aligned sequences were subjected to a series of Maximum Likelihood analyses and various tests, including molecular clock, which are presented and discussed. The divergences among the unit classes suggest that the genus Hordeum might be of paleopolyploid origin.  

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

2000 ◽  
Vol 78 (12) ◽  
pp. 1590-1602 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Gene Tree ◽  
Cladistic Analysis ◽  
5S Rdna ◽  
Hordeum Spontaneum ◽  
Rrna Gene ◽  
South American Species ◽  
Hordeum Vulgare L ◽  
Unit Classes ◽  
Unit Class ◽  
Hordeum Species

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.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Comprehensive Picture ◽  
Host Parasite

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.

The 5S rRNA gene in sea barley (Hordeum marinum Hudson sensu lato): sequence variation among repeat units and relationship to the X haplome in barley (Hordeum)

Genome ◽  
1998 ◽  
Vol 41 (5) ◽  
pp. 652-661 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Sequence Variation ◽  
Current Knowledge ◽  
Cladistic Analysis ◽  
5S Rdna ◽  
The Other ◽  
Rrna Gene ◽  
Repeat Units ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Gene

We have investigated the molecular diversity of the 5S rDNA units in sea barley, comprising Hordeum marinum and Hordeum geniculatum. Although we were unable to detect "short" units after screening of 639 clones, we found two unit classes, one 602-607 bp long and the other 507-512 bp long. We classify the shortest unit class of the two as belonging to the "long H1" unit class, identified in previous papers. The longest unit class is not similar to any unit class so far identified, and is therefore unique. It was coined by us as the "long X1," to reflect the X haplome. We present a summary of all the unit classes so far described in Hordeum. We carried out a cladistic analysis, based on the "long H1" (orthologous) sequences, that included H. vulgare, H. spontaneum, H. bulbosum, H. marinum, H. geniculatum, and H. bogdanii. As a result, the first three grouped in one clade, and the other three in the other clade, with the latter clade being more isolated. These results reflect current knowledge of relationships based on morphology, cytology, and genome analysis. Furthermore, the sequences from the 5S unit classes may be potentially useful as DNA probes for genomic identification and genetic transfer in the Triticeae.Key words: 5S rDNA, genomes, X haplome, sea barley, Triticeae.

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)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 854-866 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Current Model ◽  
5S Rdna ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rdna Unit ◽  
Repeat Units ◽  
Unit Classes ◽  
Unit Class ◽  
Hordeum Murinum ◽  
Cladistic Analyses

The molecular diversity of the 5S rDNA units in 13 accessions of wall barley, which include Hordeum murinum, H. leporinum, and H. glaucum, is reported. Our analyses, based on 54 sequenced clones, indicate the presence of two sequence classes not previously seen in other barley species; namely, the long Y1 unit class and the short Y1 unit class. In addition, the accumulation of new sequence information has allowed us to refine previous groups. Using these new results, along with previously published work, we present a summary of all the unit classes described to date and potential correspondences between 5S rDNA unit classes and haplomes identified previously. In H. murinum, we found the long H1 and long X2 unit classes, and in one of six accessions referable to H. glaucum we found the unique short Y1 unit class. Our cladistic analyses, using orthologous sequences, provide support for the current model for the relationships among several species within the Triticeae.Key words: 5S rDNA, Y haplome, genomes, wall barley, Triticeae.

A comparison of the 5S rDNA diversity in the Hordeum brachyantherum–californicum complex with those of the eastern Asiatic Hordeum roshevitzii and the South American Hordeum cordobense (Triticeae: Poaceae)

2002 ◽  
Vol 80 (7) ◽  
pp. 752-762 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Species Recognition ◽  
Cladistic Analysis ◽  
Strong Support ◽  
5S Rdna ◽  
Hordeum Spontaneum ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
5S Dna

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.

scholarly journals The genome structure of Arachis hypogaea (Linnaeus, 1753) and an induced Arachis allotetraploid revealed by molecular cytogenetics

2018 ◽  
Vol 12 (1) ◽  
pp. 111-140 ◽  
Author(s):  
Eliza F. de M. B. do Nascimento ◽  
Bruna V. dos Santos ◽  
Lara O. C. Marques ◽  
Patricia M. Guimarães ◽  
Ana C. M. Brasileiro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Structure ◽  
Diploid Species ◽  
Molecular Cytogenetics ◽  
5S Rdna ◽  
Rdna Locus ◽  
Genetic Changes ◽  
Rdna Loci ◽  
Cultivated Plant ◽  
Fish Signal

Peanut,Arachishypogaea(Linnaeus, 1753) is an allotetraploid cultivated plant with two subgenomes derived from the hybridization between two diploid wild species,A.duranensis(Krapovickas & W. C. Gregory, 1994) andA.ipaensis(Krapovickas & W. C. Gregory, 1994), followed by spontaneous chromosomal duplication. To understand genome changes following polyploidy, the chromosomes ofA.hypogaea, IpaDur1, an induced allotetraploid (A.ipaensis×A.duranensis)4xand the diploid progenitor species were cytogenetically compared. The karyotypes of the allotetraploids share the number and general morphology of chromosomes; DAPI+bands pattern and number of 5S rDNA loci. However, one 5S rDNA locus presents a heteromorphic FISH signal in both allotetraploids, relative to corresponding progenitor. Whilst forA.hypogaeathe number of 45S rDNA loci was equivalent to the sum of those present in the diploid species, in IpaDur1, two loci have not been detected. Overall distribution of repetitive DNA sequences was similar in both allotetraploids, althoughA.hypogaeahad additional CMA3+bands and few slight differences in the LTR-retrotransposons distribution compared to IpaDur1. GISH showed that the chromosomes of both allotetraploids had preferential hybridization to their corresponding diploid genomes. Nevertheless, at least one pair of IpaDur1 chromosomes had a clear mosaic hybridization pattern indicating recombination between the subgenomes, clear evidence that the genome of IpaDur1 shows some instability comparing to the genome ofA.hypogaeathat shows no mosaic of subgenomes, although both allotetraploids derive from the same progenitor species. For some reasons, the chromosome structure ofA.hypogaeais inherently more stable, or, it has been at least, partially stabilized through genetic changes and selection.

The 5S rDNA units in Kengyilia (Poaceae: Triticeae): diversity of the nontranscribed spacer and genomic relationships

2000 ◽  
Vol 78 (12) ◽  
pp. 1571-1579 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey
Keyword(s):  
Concerted Evolution ◽  
Low Frequency ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Nontranscribed Spacer ◽  
Unit Classes ◽  
Unit Class ◽  
5S Dna ◽  
Genomic Relationships ◽  
Single Clone

The sequences of eighty 5S rDNA clones were obtained by polymerase chain reaction (PCR) amplification of DNA from 12 accessions representing eight species of Kengyilia. Orthologous sequences were grouped into five unit classes: long P1, long S1, long {Y1, short P1, and short S1. Both the long P1 and long S1 classes are prevalent in Kengyilia, whereas the rest are rare. The short S1 class has not been described previously in other Kengyilia species. Two clones represent the long {Y1 class, with only one clone reported previously in Kengyilia alatavica (Drobow) J.L. Yang, Yen & Baum and a single clone found in this investigation. The long H1 unit class reported earlier for Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen & Baum, but not for K. alatavica, was not found in any of the eight species investigated. Therefore, its presence in K. rigidula may be the result of introgression from Elymus nutans Grisebach, an HS-genome species containing the long H1 unit class; the two are often found growing together and are known to yield sterile hybrids in those populations. The specific 5S DNA unit classes, except for the ones that were found in very low frequency and in few samples, may have a potential not only as markers for the identification of haplomes but also of hybrids containing a combination of genomes. This investigation indicated, along with previous studies, that the 5S unit classes either form integral parts of haplomes or remain conserved and identifiable within haplomes originating from distant species, indicating that concerted evolution in the 5S gene plays only a partial role as an evolutionary force.Key words: 5S DNA gene, molecular diversity, Kengyilia, Triticeae, concerted evolution.

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