DOI: 10.5061/dryad.7m0cfxq5j
title: Origin of subgenomes in the circumboreal allopolyploid carnivorous plant Drosera anglica (Droseraceae)

description: Premise of Study The parentage of one of the most widespread members of
 the carnivorous sundew genus Drosera, the enigmatic allopolyploid
 Drosera anglica, remains uncertain despite over 100 years of
 morphological, cytological, and more recently, molecular study. Methods
 Using transcriptomic and genomic data from 12 species and 20 populations
 across Drosera sect. Drosera including four D. anglica populations and a
 disjunct Idaho population of D. intermedia, we carried out reference-based
 assembly in HybPiper and phased sequences in HybPhaser. We estimated a
 species tree and quantified gene tree discordance; we calculated
 heterozygosity statistics and pairwise divergence between individuals. In
 addition to genome-wide analyses, we extracted and assembled rbcL and ITS
 reads from genome and transcriptome datasets to compare to previous Sanger
 sequencing data. We also generated flow cytometry data to verify the
 ploidy levels of D. anglica and D. rotundifolia populations. Key Results
 Sequences from phased subgenomes of D. anglica were sister to D.
 rotundifolia and D. linearis with high support. Both ITS and rbcL
 sequences of D. anglica were the most similar to D. linearis. Drosera
 anglica is intermediate between both parents in leaf shape and
 microhabitat; however, across D. sect. Drosera, neither leaf shape nor
 biogeographic distribution were a reliable indicator of phylogenetic
 relationships. Despite a range-wide sampling, we did not find evidence for
 multiple origins of D. anglica. Our results differed from previous
 parentage analyses based on chromosome pairing and Sanger sequencing with
 limited taxon sampling. Additionally, we found that the Idaho population
 previously identified as D. intermedia is D. anglica. Conclusions Drosera
 anglica arose from allopolyploidy between D. linearis (the chloroplast
 donor) and D. rotundifolia. Our study demonstrates the importance of taxon
 sampling, visualizing and careful examination of complex phylogenomic
 data, and presents an exemplar of detecting and analyzing allopolyploid
 relationships in plant lineages in general.
description: This repository contains data and analysis files for Mohn, RA, Yang, Y.
 Origin of subgenomes in the circumboreal allopolyploid carnivorous plant
 Drosera anglica (Droseraceae). ### Drosera_anglica_Dryad_Nov2025.zip The
 full dataset ### Dspat_6443_refgenes.fa The 6443 reference genes from D.
 spatulata used for input to HybPiper The genes are labeled with their
 Drosera spatulata names as published in Palfalvi et al., 2020 Current
 Biology.
 [https://doi.org/10.1016/j.cub.2020.04.051](https://doi.org/10.1016/j.cub.2020.04.051) They are in a fasta format. The complete list of Drosera spatulata genes were obtained here: [https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/](https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/) ### finalAlnPreCleaning The alignments of recovered genes after phasing of D. anglica subgenomes before trimming with Phyx This zipped folder contains a separate file for each gene, titled by the D. spatulata name. All samples with that gene are included in the gene alignment file in FASTA format. ### finalConcatAlign.fa The trimmed and concatenated alignment of genes used as input for RAxML. This is in a fasta file format. The cleaned gene alignments were concatenated by sample to enable input into RAxML to estimate a species tree. ### finalTreesPhased The one-to-one ortholog trees from phased data used for ASTRAL tree estimation The tree file estimated in RAxML from each gene with only one copy of a gene for each sample (or subgenome in the case of D. anglica). ### Astral_finalSpTree.tre The ASTRAL tree from phased data A coalescence tree estimated from the gene trees in finalTreesPhased using ASTRAL ### RAxML_finalConcatTree.tre The RAxML tree from phased data A tree estimated from the finalConcatAlign.fa file using RAxML. ### DataVis_KsPlot_DistMat A folder that contains the script, input files, and output files for everything calculated and visualized in R #### D_ang_R_Dryad.R R scripts that 1. makes the map figure from GBIF data 2. makes the figure of the % heterozygous loci vs. % Allele divergence 3. makes the Ks plots 4. calculates the pairwise distance matrix #### anglica_rot_lin_inttiled.pdf the output of the map figure script #### 4_Summary_table_combined.csv the HybPhaser output reformated slightly for making the figure of heterozygous loci and allele divergence ### ks_files This folder contains the ks (ks_yn) files calculated for each sample in the Ks plots It also contains a text document which is a match up between file name and species name This is all for use with the D_ang_R_Dryad Ks plot visualization section. #### KsPlot_Grid.pdf and KsPlot_Grid2.5.pdf The output of the Ks Plot script with 2 different axes #### 1000_noamb The cleaned fasta alignments of all genes used for calculating the pairwise distance between samples. This is the input for calculating the distance matrix #### 1000_noamb_matrix An output of the Rscript -- The pairwise distance matrices for each gene in 1000_noamb ### 1000_noamb_dist_mat.csv All the gene pairwise matrices flattened into one table Each column is a gene Each row is the distance between two samples #### 1000_noamb_mean_dist_mat.csv the mean pairwise distance across all genes #### 1000_noamb_median_dist_mat.csv the median pairwise distance across all genes ### rbcL_and_ITS This folder contains the alignments for rbcL and ITS. #### Full_rbcL_alignment.txt The alignment of all rbcL samples longer than 300 bps #### Final_rbcL_alignment.txt The alignment of the final rbcL samples presented after filtering #### Full_rRNA_variants.txt The alignment of the ITS and rRNA for all samples. #### rRNA_alignment.vcf The variants called against MT784099.1 ITS from Drosera rotundifolia ### FrozenScripts Folder containing the two frozen copies of the phylogenomic_dataset_construction scripts from [https://bitbucket.org/yanglab/phylogenomic_dataset_construction/src/master/](https://bitbucket.org/yanglab/phylogenomic_dataset_construction/src/master/) used in this analysis. v1 was used for the cleaning of RM207A, RM208A, RM209A, RM210A, RM214, RM217, RM218, RM240, RM241, RM242, and for transcriptome assembly for all transcriptomes. v2 was used for cleaning the remaining samples and for post-assembly processing.