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.
Highlights
Polyploidization, or whole genome duplication, is a major mechanism in plant evolution
In this study we report results from a phylogenetic analysis of all Hordeum species using cloned sequences of the nuclear low-copy region TOPO6 [12] that is a partial sequence of the Spo11 gene, a conserved plant homologue of the widespread archaean topoisomerase VI subunit A involved in inducing meiotic DNA doublestrand breaks during recombination [17,18]
All analysis algorithms resulted in very similar tree topologies, only the Bayesian inference (BI) trees are presented (Fig. 1 for diploids only, Fig. 2 for the complete dataset), while results of the maximum parsimony (MP) analyses are available as Figures S2 and S3
Summary
Polyploidization, or whole genome duplication, is a major mechanism in plant evolution. Otto and Whitton [5], analyzing the distribution of haploid chromosome numbers, estimated that polyploidy might be involved in about 2– 4% of speciation events, proposing that polyploidization ‘‘may be the single most common mechanism of sympatric speciation in plants’’ The second definition is based on a taxonomic concept, where polyploids formed through hybridization of different species (allopolyploids) contrast with hybrids formed through genome duplication or crossing of different genotypes from within a species (autopolyploids). Taxonomic allopolyploids are often termed segmental allopolyploids in the cytogenetic reference frame, indicating the presence of only locally differentiated chromosomes. We here use the taxonomic system of polyploid definition and explicitly refer to cytogenetic allopolyploids by indicating their genome composition
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