Abstract
TOPO6, a nuclear gene-marker region of subunit B of the plant homolog of archaean topoisomerase VI, occurs as single-copy locus in the haploid genome of most plant groups. The gene consists mainly of 19 exons and 18 introns, which provide conserved primer binding sites for PCR amplification in many angiosperm families combined with variable sequence stretches that can be explored in molecular systematics. Here intron/exon structure, sequence diversity, and a set of amplification primers are described to use TOPO6 as single-copy phylogenetic marker region in a wide range of plant taxa, either through PCR amplification or hybridization-based sequence capture.
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The author declares that he has no conflict of interest.
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Parts of this study were funded by the German Research Foundation (DFG) through Grant JA1938/2.
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Handling editor: Marcus Koch.
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Supplementary material 1 Alignment of the topoisomerase VI B coding regions of 36 plant taxa (FASTA format) used to infer sequence homology and positions of potentially conserved priming sites for amplification of TOPO6 parts by PCR. The genomic sequence of A. thaliana was included to indicate positions of introns and exons. The alignment can be explored with any sequence-alignment or editor program. Primer positions (Table 1) are indicated by stretches of ‘N’ in the first line (TXT 163 kb)
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Supplementary material 2 Alignment of coding and genomic sequences of Oryza sativa, Arabidopsis thaliana, Vitis vinifera, Ricinus communis, and Malus domestica (FASTA format) used to provide information on the range of intron length variation in angiosperm taxa (TXT 107 kb)
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Supplementary material 3 Neighbor-joining tree of 96 topoisomerase VI B sequences obtained from GeneBank to infer the occurrence of deep paralogs (PDF 4682 kb)
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Supplementary material 4 Bayesian phylogenetic tree derived from coding regions of topoisomerase VI B sequences of diverse land plants (PDF 367 kb)
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Blattner, F.R. TOPO6: a nuclear single-copy gene for plant phylogenetic inference. Plant Syst Evol 302, 239–244 (2016). https://doi.org/10.1007/s00606-015-1259-1
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DOI: https://doi.org/10.1007/s00606-015-1259-1