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.

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.

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 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

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 79-85 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey
Keyword(s):  
Gene Diversity ◽  
5S Rdna ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
5S Dna ◽  
5S Rrna Gene ◽  
Polymerase Chain

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. Key words: 5S RNA gene, genomes, Triticeae, 5S DNA unit classes.

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.

The molecular diversity of the 5S rRNA gene in Kengyilia alatavica (Drobov) J.L. Yang, Yen &Baum (Poaceae: Triticeae): potential genomic assignment of different rDNA units

Genome ◽  
1997 ◽  
Vol 40 (2) ◽  
pp. 215-228 ◽  
Author(s):  
Bernard R. Baum ◽  
L. Grant Bailey
Keyword(s):  
Concerted Evolution ◽  
Molecular Diversity ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Gene ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Gene ◽  
Polymerase Chain ◽  
Rrna Sequences

5S rRNA sequences from several accessions of Kengyilia alatavica, a member of a tribe that includes wheat and wheat relatives, have been amplified by the polymerase chain reaction, cloned, and sequenced. From an evaluation of the aligned sequences, five 5S unit classes have been discerned. One class consists of short units, while the other four contain longer units. BLAST searches of the GenBank® database have allowed us to tentatively assign these to classes found in genomes of other species. For example, the short 5S unit class and one long 5S unit class were designated, respectively, "short P1" and "long P1" because of their match with the comparable sequenced 5S rDNA accessions of Agropyron cristatum, a carrier of the P genome. Another unit class, is coined as "long R1", because of its similarity to the units sequenced from Secale cereale and Secale vavilovii, carriers of the R genome. The third unit class was designated "long S1" and is found also in Elytrigia spicata, a carrier of the S genome. Implications of these findings on the possible association of some unit classes with cytological haplome and on concerted evolution are discussed.Key words: 5S RNA gene, genomes, concerted evolution, Triticeae.

Loss of 5S rDNA units in the evolution of Agropyron, Pseudoroegneria, and Douglasdeweya

Genome ◽  
2008 ◽  
Vol 51 (8) ◽  
pp. 589-598 ◽  
Author(s):  
B. R. Baum ◽  
T. Edwards ◽  
D. A. Johnson
Keyword(s):  
Single Unit ◽  
Gene Loss ◽  
5S Rdna ◽  
Lineage Sorting ◽  
Genomic Constitution ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Tribe Triticeae

We have investigated relationships among the three closely related genera Agropyron , Pseudoroegneria , and Douglasdeweya. Based upon grouping of 330 5S rDNA sequences into unit classes, we found that Douglasdeweya, with the genomic constitution PPStSt, has 2 unit classes, the long P1 and short S1, and Pseudoroegneria, with the genomic constitution StSt or StStStSt, has the long S1 and short S1 unit classes. In contrast, only the long P1 unit class was found in species of the genus Agropyron (PP). Having a single unit class is unique among all the genera of the tribe Triticeae investigated so far and may reflect gene loss or lineage sorting during its genesis. The presence of the short S1 and long P1 unit classes confirms the amphiploid origin of Douglasdeweya.

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.

Molecular diversity of the 5S rDNA units in the Elymus dahuricus complex (Poaceae: Triticeae) supports the genomic constitution of St, Y, and H haplomes

2003 ◽  
Vol 81 (11) ◽  
pp. 1091-1103 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey ◽  
Douglas A Johnson ◽  
Alex V Agafonov
Keyword(s):  
Molecular Diversity ◽  
5S Rdna ◽  
Rrna Gene ◽  
Genomic Constitution ◽  
Pseudoroegneria Spicata ◽  
Rdna Unit ◽  
Nontranscribed Spacer ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Gene

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.

scholarly journals Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the ‘next-generation’ Tree of Life

2019 ◽  
Vol 93 (3) ◽  
pp. 260-276 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
D.I. Hernández-Mena
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
28S Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Next Generation ◽  
Phylogenetic Classification ◽  
Rdna Sequences

AbstractDigenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.

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