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Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region.

Brassac J, Jakob SS, Blattner FR - PLoS ONE (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Research, IPK, Gatersleben, Germany.

ABSTRACT
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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Scheme summarizing phylogenetic relationships of species and cytotypes in the genus Hordeum based on TOPO6.Diploid taxa were drawn directly at the tree, while tetra- and hexaploids were connected by lines to their inferred parental taxa. Dashed lines indicate uncertainties and double lines depict an autopolyploid origin. Colors refer to the ploidy level of the taxa (tetraploid blue lines, hexaploid green lines).
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pone-0033808-g003: Scheme summarizing phylogenetic relationships of species and cytotypes in the genus Hordeum based on TOPO6.Diploid taxa were drawn directly at the tree, while tetra- and hexaploids were connected by lines to their inferred parental taxa. Dashed lines indicate uncertainties and double lines depict an autopolyploid origin. Colors refer to the ploidy level of the taxa (tetraploid blue lines, hexaploid green lines).

Mentions: The TOPO6 sequences obtained in this study varied in lengths between 868 and 1057 bp and were stored in the EMBL nucleotide database under accession numbers HE655746-HE656023. The alignment of 278 TOPO6 sequences was 1275 bp long and contained 367 variable sites (281 for diploids only), of which 248 were parsimony-informative (205 for diploids only). All analysis algorithms resulted in very similar tree topologies, thus only the BI trees are presented (Fig. 1 for diploids only, Fig. 2 for the complete dataset), while results of the MP analyses are available as Figures S2 and S3. Both analyses are summarized in a scheme of the TOPO6-based species and cytotype relationships within Hordeum (Fig. 3). All analyses revealed the sequences derived from Hordeum species to be monophyletic with one exception (Fig. 1): two clone sequences from a single diploid H. brevisubulatum individual (PI229753) clustered outside the Hordeum clade, together with Eremopyrum triticeum. Sequences from the four genome groups in Hordeum (H, I, Xa, Xu) were mainly found monophyletic (Fig. 1) with few exceptions: (i) the H. brevisubulatum sequences already mentioned, (ii) a tetraploid individual of H. brevisubulatum (BG156/07) having one sequence falling outside of the I clade in a polytomy together with the Xa+I clade, and (iii) two diploid individuals of H. murinum (Xu genome, [12]) with two clones clustering with H-genome H. bulbosum (derived from H. murinum PI218078) and one clone clustering with I-genome H. pubiflorum (from H. murinum BCC2002). The Hordeum clade received strong support with a posterior probability (pp) of 0.99 in BI. The H-genome sequences formed the sistergroup to the remaining species, with Xu-genome sequences grouping as sister to the clade including sequences derived from Xa- and I-genome taxa.


Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region.

Brassac J, Jakob SS, Blattner FR - PLoS ONE (2012)

Scheme summarizing phylogenetic relationships of species and cytotypes in the genus Hordeum based on TOPO6.Diploid taxa were drawn directly at the tree, while tetra- and hexaploids were connected by lines to their inferred parental taxa. Dashed lines indicate uncertainties and double lines depict an autopolyploid origin. Colors refer to the ploidy level of the taxa (tetraploid blue lines, hexaploid green lines).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316500&req=5

pone-0033808-g003: Scheme summarizing phylogenetic relationships of species and cytotypes in the genus Hordeum based on TOPO6.Diploid taxa were drawn directly at the tree, while tetra- and hexaploids were connected by lines to their inferred parental taxa. Dashed lines indicate uncertainties and double lines depict an autopolyploid origin. Colors refer to the ploidy level of the taxa (tetraploid blue lines, hexaploid green lines).
Mentions: The TOPO6 sequences obtained in this study varied in lengths between 868 and 1057 bp and were stored in the EMBL nucleotide database under accession numbers HE655746-HE656023. The alignment of 278 TOPO6 sequences was 1275 bp long and contained 367 variable sites (281 for diploids only), of which 248 were parsimony-informative (205 for diploids only). All analysis algorithms resulted in very similar tree topologies, thus only the BI trees are presented (Fig. 1 for diploids only, Fig. 2 for the complete dataset), while results of the MP analyses are available as Figures S2 and S3. Both analyses are summarized in a scheme of the TOPO6-based species and cytotype relationships within Hordeum (Fig. 3). All analyses revealed the sequences derived from Hordeum species to be monophyletic with one exception (Fig. 1): two clone sequences from a single diploid H. brevisubulatum individual (PI229753) clustered outside the Hordeum clade, together with Eremopyrum triticeum. Sequences from the four genome groups in Hordeum (H, I, Xa, Xu) were mainly found monophyletic (Fig. 1) with few exceptions: (i) the H. brevisubulatum sequences already mentioned, (ii) a tetraploid individual of H. brevisubulatum (BG156/07) having one sequence falling outside of the I clade in a polytomy together with the Xa+I clade, and (iii) two diploid individuals of H. murinum (Xu genome, [12]) with two clones clustering with H-genome H. bulbosum (derived from H. murinum PI218078) and one clone clustering with I-genome H. pubiflorum (from H. murinum BCC2002). The Hordeum clade received strong support with a posterior probability (pp) of 0.99 in BI. The H-genome sequences formed the sistergroup to the remaining species, with Xu-genome sequences grouping as sister to the clade including sequences derived from Xa- and I-genome taxa.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Research, IPK, Gatersleben, Germany.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus