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Frank R Blattner - One of the best experts on this subject based on the ideXlab platform.
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Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region
2016Co-Authors: Jonathan Brassac, Sabine S Jakob, Frank R BlattnerAbstract:Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (46, 66) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (46, 66) wa
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species level phylogeny and polyploid relationships in Hordeum poaceae inferred by next generation sequencing and in silico cloning of multiple nuclear loci
Systematic Biology, 2015Co-Authors: Jonathan Brassac, Frank R BlattnerAbstract:Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.
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Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region
2012Co-Authors: Jonathan Brassac, Sabine S Jakob, Frank R BlattnerAbstract:Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.
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progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum poaceae triticeae
Breeding Science, 2009Co-Authors: Frank R BlattnerAbstract:During the last decade several phylogenetic studies of Hordeum were published using a multitude of loci from the chloroplast and nuclear genomes. In many studies taxon sampling was not representative and, thus, does not allow the inference of relationships among species. Generally, chloroplast data seem not suitable for reliable phylogenetic results, as far reaching incomplete lineage sorting result in nearly arbitrary species relationships within narrow species groups, depending on the individuals included in the analyses. Nuclear loci initially resulted at contradictory phylogenetic hypotheses. However, combining at least three nuclear loci in total evidence analyses finally provides consistent relationships among Hordeum species groups, and supports data from earlier cytological and karyological studies. Thus, recently published phylogenies agree on the monophyly of the four Hordeum genome groups (H, I, Xa, Xu), monophyly of the H/Xu and I/Xa groups, and separation between Asian and American members within the I-genome group. A new infrageneric classification of Hordeum is proposed, dividing the genus in subgenus Hordeum comprising sections Hordeum and Trichostachys, and subgenus Hordeastrum with sections Marina, Nodosa, and Stenostachys. The latter consists of two series reflecting the geographical distribution of the taxa, i.e. series Sibirica with Central Asian taxa and series Critesion comprising native taxa from the Americas. In section Nodosa all allopolyploid taxa are grouped, which are characterized by I/Xa genome combinations.
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phylogeographic analyses and paleodistribution modeling indicate pleistocene in situ survival of Hordeum species poaceae in southern patagonia without genetic or spatial restriction
Molecular Biology and Evolution, 2009Co-Authors: Sabine S Jakob, Enrique Martinezmeyer, Frank R BlattnerAbstract:Although many phylogeographic studies have been conducted to analyze the impact of the ice age on species history of Northern Hemisphere mountain plants, such studies are nearly absent for plants of the Southern Hemisphere, particularly for lowland vegetation units. These species should have been primarily influenced by climate cooling and changes in precipitation regime instead of glaciers covering their distribution areas. It is thought that New World lowland species generally evaded climate changes by equatorial migration during Pleistocene cold cycles and recolonized their habitats at higher latitudes when climate warmed up again. In contrast to Eurasia, latitudinal orientation of the major mountain ranges in the Americas made these migrations easily possible. In the huge steppe of the Patagonian plains and adjacent Andes of southern South America thrives a group of three sympatrically distributed diploid species of the barley genus Hordeum, which originated during the last 1.3 million years (My) from a common progenitor. To get insights into the speciation mode of the taxa and to test the hypothesis of longitudinal migration of steppe vegetation during the Pleistocene, we conducted population genetic and phylogeographic analyses based on sequences of the chloroplast trnL-F region from 922 individuals. We found a high number of chloroplast haplotypes shared among species, which indicate speciation through vicariance events. Analysis of the distribution of genetic diversity within and among species inferred an origin of Hordeum comosum in the Central Argentine Andes, whereas Hordeum patagonicum and Hordeum pubiflorum originated in southern Patagonia. The extant occurrence of H. comosum in southern Patagonia and H. pubiflorum northward along the Argentine Andes was caused by reciprocal migration after the origin of the species. Surprisingly, molecular data provided no evidence for range shifts toward the north during the last glacial maximum and recolonization of southerly habitats afterward, but indicated in situ survival of large populations of Hordeum species within their extant distribution ranges even in southernmost Patagonia and Tierra del Fuego. Ecoclimatic niche modeling used to reconstruct the potential paleodistribution areas of the species during the last glacial maximum shows that climate conditions were sufficient for the species to survive Pleistocene cold cycles in Patagonia without significant geographic restrictions. Molecular data together with ecological niche modeling indicate stable geographic distribution areas in two of the three species for at least the Holocene. As the Hordeum species are characteristic taxa of different steppe habitats, we speculate that the Patagonian steppe might be an old vegetation unit occurring for up to 4.5 My in southern South America.
Sabine S Jakob - One of the best experts on this subject based on the ideXlab platform.
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Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region
2016Co-Authors: Jonathan Brassac, Sabine S Jakob, Frank R BlattnerAbstract:Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (46, 66) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (46, 66) wa
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Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region
2012Co-Authors: Jonathan Brassac, Sabine S Jakob, Frank R BlattnerAbstract:Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.
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phylogeographic analyses and paleodistribution modeling indicate pleistocene in situ survival of Hordeum species poaceae in southern patagonia without genetic or spatial restriction
Molecular Biology and Evolution, 2009Co-Authors: Sabine S Jakob, Enrique Martinezmeyer, Frank R BlattnerAbstract:Although many phylogeographic studies have been conducted to analyze the impact of the ice age on species history of Northern Hemisphere mountain plants, such studies are nearly absent for plants of the Southern Hemisphere, particularly for lowland vegetation units. These species should have been primarily influenced by climate cooling and changes in precipitation regime instead of glaciers covering their distribution areas. It is thought that New World lowland species generally evaded climate changes by equatorial migration during Pleistocene cold cycles and recolonized their habitats at higher latitudes when climate warmed up again. In contrast to Eurasia, latitudinal orientation of the major mountain ranges in the Americas made these migrations easily possible. In the huge steppe of the Patagonian plains and adjacent Andes of southern South America thrives a group of three sympatrically distributed diploid species of the barley genus Hordeum, which originated during the last 1.3 million years (My) from a common progenitor. To get insights into the speciation mode of the taxa and to test the hypothesis of longitudinal migration of steppe vegetation during the Pleistocene, we conducted population genetic and phylogeographic analyses based on sequences of the chloroplast trnL-F region from 922 individuals. We found a high number of chloroplast haplotypes shared among species, which indicate speciation through vicariance events. Analysis of the distribution of genetic diversity within and among species inferred an origin of Hordeum comosum in the Central Argentine Andes, whereas Hordeum patagonicum and Hordeum pubiflorum originated in southern Patagonia. The extant occurrence of H. comosum in southern Patagonia and H. pubiflorum northward along the Argentine Andes was caused by reciprocal migration after the origin of the species. Surprisingly, molecular data provided no evidence for range shifts toward the north during the last glacial maximum and recolonization of southerly habitats afterward, but indicated in situ survival of large populations of Hordeum species within their extant distribution ranges even in southernmost Patagonia and Tierra del Fuego. Ecoclimatic niche modeling used to reconstruct the potential paleodistribution areas of the species during the last glacial maximum shows that climate conditions were sufficient for the species to survive Pleistocene cold cycles in Patagonia without significant geographic restrictions. Molecular data together with ecological niche modeling indicate stable geographic distribution areas in two of the three species for at least the Holocene. As the Hordeum species are characteristic taxa of different steppe habitats, we speculate that the Patagonian steppe might be an old vegetation unit occurring for up to 4.5 My in southern South America.
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a chloroplast genealogy of Hordeum poaceae long term persisting haplotypes incomplete lineage sorting regional extinction and the consequences for phylogenetic inference
Molecular Biology and Evolution, 2006Co-Authors: Sabine S Jakob, Frank R BlattnerAbstract:To analyze reasons for inconclusive results of earlier chloroplast phylogenies in the grass genus Hordeum, we established a genealogy of chloroplast haplotypes by sequencing the trnL-trnF region in 875 individuals, covering all 31 species of the genus. Although the outcomes of phenetic and parsimony analyses of 88 haplotypes were ambiguous, a network approach showed that in Hordeum ancient chloroplast types co-occur with their descendants. Moreover, we found up to 18 different chloroplast haplotypes within a single species and up to 6 species sharing single haplotypes. Persisting polymorphisms together with incomplete lineage sorting occurred preferentially in the rapidly speciating New World taxa of the genus, where ancient chloroplast types have survived for at least 4 Myr. Lineages-through-time plots and a high number of missing chloroplast haplotypes indicated far-reaching extinction of chloroplast lineages in Europe and particularly the Mediterranean. Survival of these lineages in East Asia and North America resulted in chloroplast relationships that markedly differed from nuclear estimations of species relationships. Thus, even for the deepest splits in the genus, reaching back more than 9 Myr, no safe phylogenetic inference from chloroplast data is possible in Hordeum. The chloroplast genealogy, however, revealed biogeographic patterns and indicated processes involved in speciation in Hordeum. We conclude that the described phenomena are not restricted to Hordeum and that the knowledge of the chloroplast relationships within a genus is indispensable to prevent misinterpretation of phylogeographic data within single species.
K Kanyuka - One of the best experts on this subject based on the ideXlab platform.
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barley stripe mosaic virus mediated tools for investigating gene function in cereal plants and their pathogens virus induced gene silencing host mediated gene silencing and virus mediated overexpression of heterologous protein
Plant Physiology, 2012Co-Authors: K E Hammondkosack, K KanyukaAbstract:Barley stripe mosaic virus ([BSMV][1]), the Hordeivirus type member, is the most intensely studied virus that naturally infects two major monocot crops, wheat ( Triticum aestivum ) and barley ( Hordeum vulgare ). The tripartite genome of this virus, comprising RNAα, RNAβ, and RNAγ, was sequenced
K E Hammondkosack - One of the best experts on this subject based on the ideXlab platform.
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barley stripe mosaic virus mediated tools for investigating gene function in cereal plants and their pathogens virus induced gene silencing host mediated gene silencing and virus mediated overexpression of heterologous protein
Plant Physiology, 2012Co-Authors: K E Hammondkosack, K KanyukaAbstract:Barley stripe mosaic virus ([BSMV][1]), the Hordeivirus type member, is the most intensely studied virus that naturally infects two major monocot crops, wheat ( Triticum aestivum ) and barley ( Hordeum vulgare ). The tripartite genome of this virus, comprising RNAα, RNAβ, and RNAγ, was sequenced
Roberta J. Mason-gamer - One of the best experts on this subject based on the ideXlab platform.
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Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae).
Molecular phylogenetics and evolution, 2008Co-Authors: Roberta J. Mason-gamerAbstract:The phylogenetic position of hexaploid Elymus repens within the tribe Triticeae (Poaceae) was examined using cloned sequences from the low-copy nuclear genes encoding phosphoenolpyruvate carboxylase (pepC) and β-amylase. A previous analysis of E. repens using data from the nuclear granule-bound starch synthase I (GBSSI) gene had yielded five phylogenetically distinct gene copies, two more than expected from hexaploidy alone. The three gene trees share three distinct E. repens clades, suggesting that E. repens contains three phylogenetically divergent genomes, contributed by Hordeum, Pseudoroegneria, and an unknown donor. The two additional GBSSI sequences, including one that was apparently derived from outside of the tribe, appear to reflect past introgression of GBSSI sequences into the E. repens genome. On all three trees, the Hordeum-like E. repens sequences are polyphyletic within Hordeum, and the trees are in conflict with regard to the placement of these sequences within Hordeum, highlighting multiple contributions from Hordeum to E. repens.
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The Evolution of North American Elymus (Triticeae, Poaceae) Allotetraploids: Evidence from Phosphoenolpyruvate Carboxylase Gene Sequences
Systematic Botany, 2004Co-Authors: D. Megan Helfgott, Roberta J. Mason-gamerAbstract:Abstract Cytogenetic studies of North American Elymus suggest that the genus is an allopolyploid derivative of Pseudoroegneria (St) and Hordeum (H). To test this, we conducted a phylogenetic analysis of North American Elymus species within a broad sample of diploid Triticeae taxa using cloned sequences from one member of the nuclear gene family encoding phosphoenolpyruvate carboxylase. The phylogeny supports the hypothesis that Pseudoroegneria and Hordeum are the diploid progenitors of the North American Elymus tetraploids. Each tetraploid Elymus individual has two distinct forms of the gene, and each form is in a strongly supported clade with sequences from either Pseudoroegneria or Hordeum, suggesting that these Elymus species have an St + H genomic content. This pattern is consistent with a single (or multiple very similar) polyploid ancestor(s) of the North American tetraploids, confirming earlier results based on granule-bound starch synthase I gene sequence data. We also examined the utility of the ...
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Origin of North American Elymus (Poaceae: Triticeae) Allotetraploids Based on Granule-bound Starch Synthase Gene Sequences
Systematic Botany, 2001Co-Authors: Roberta J. Mason-gamerAbstract:The current circumscription of Elymus based on cytogenetic analyses includes all allopolyploid Triticeae species containing the St (Pseudoroegneria) genome. In North American Elymus ,t heSt genome is combined with H (from Hordeum) in an allotetraploid (StStHH) configuration. The goal of this study is to determine whether molecular phylogenetic analyses support existing cytogenetic data with regard to the evolutionary origin of North American Elymus. Analyses were performed using sequences from the nuclear starch synthase gene, and include multiple species of Elymus, Pseudoroegneria, and Hordeum, along with representatives of most of the other monogenomic genera in the Triticeae. The results support the hypothesis that Pseudoroegneria and Hordeum are the genome donors to the North American Elymus tetraploids. One species currently placed in Elymus (an octoploid, Elymus californicus) appears to be unrelated to the rest. The close relationships among Elymus H-genome sequences, with one exception, are consistent with a single origin of the group. The St-genome group consists of two well-defined clades, but support for the monophyly of the entire St group is weak. There are short- comings associated with the current dependence on genome pairing data for grouping and ranking in the Triticeae, but molecular phylogenetic data suggest that, in many cases, groups delimited by cytogenetic data do in fact correspond to evolutionary lineages.
