An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution

Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of Tragopogon and obtained genome-edited T. porrifolius (2x) and T. mirus (4x) primary generation (T0) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (DFR) gene, which controls anthocyanin synthesis, in both T. porrifolius and T. mirus. All transgenic allotetraploid T. mirus individuals had at least one mutant DFR allele and 71.4% of the plants had all four DFR alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid Tragop..., This dataset contains the sequencing results of the DFR gene in CRISPR-mediated Tragopogon mutants. To genotype T. porrifolius, primers TragDFR-F1 and TragDFR-R2 were used to amplify a fragment (containing the CRISPR target sites) from TpoDFR. One microliter of genomic DNA (20-100 ng) was added into a 20‐μl PCR (1× Phusion HF Buffer [New England Biolabs, Ipswich, MA, USA], 200 μM dNTPs, 0.5 μM of each primer, 0.02 U/μl Phusion DNA polymerase [New England Biolabs, Ipswich, MA, USA]). The PCR conditions were as follows: one cycle of denaturation at 98°C for 30 s; 32 cycles at 98°C for 10 s, 59.5°C annealing for 30 s and 72°C extension for 1min 15 s; one cycle at 72°C for 10 min; and hold at 4°C. The PCR product was accessed via gel electrophoresis; the band with the expected size (~1.7 kb) was excised from the gel and purified using the Wizard Plus SV Minipreps DNA Purification System (Promega, Madison, WI, USA). PCR products were then sequenced at Eurofins Genomics (Louisville, KY, USA)...., , # An efficient CRISPR-mediated genome editing system in diploid and polyploid *Tragopogon* (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution

[https://doi.org/10.5061/dryad.5x69p8dcs](https://doi.org/10.5061/dryad.5x69p8dcs)

This dataset (24 ab1 files) contains the Sanger sequencing results of the *DFR* gene from *T. porrifolius* (D07) and *T. mirus* (D13) mutants.

## Description of the data and file structure

For each *T. porrifolius* individual, there is one ab1 file containing the Sanger sequencing result of the *DFR* gene. For each *T. mirus* individual, there are two ab1 files: one file contains the Sanger sequencing result of the *DFR* gene from the *T. dubius* homeolog, and the other file contains the sequencing result of the gene from the *T. porrifolius* homeolog.

For each *T. porrifolius* file, the format is: `T.porrifolius_[individual-id]_[sequencing-primer]_[date].ab1`

For each *T. mirus* file, the format is: `T.mirus_[individu...