Data from: A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
Data files
Sep 08, 2026 version files 89.79 MB
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Haustorial_genes_by_orthogroup2.csv
2.91 MB
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Pgroenlandica.PG262426N0.functional_annotation.tsv
86.88 MB
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README.md
4.07 KB
Abstract
Two datasets associated with the article, 'A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants', published in Annals of Botany, May 2026. The first dataset includes the IDs of all haustoria-associated genes identified in the analysis for species: Pedicularis groenlandica, Phtheirospermum japonicum, Cuscuta campestris, Phelipanche aegyptiaca (syn. Orobanche aegyptiaca), and Striga hermonthica. The orthogroups each haustoria-associated gene was classed into are also included. The second dataset is the functional annotation of the Pedicularis groenlandica genome.
Novel traits frequently evolve by co-opting existing genetic pathways through either the direct repurposing of existing genes or neofunctionalization of duplicated genes. Parasitism represents a major innovation in plants, in which a novel organ, the haustorium, evolved to penetrate hosts to extract water and nutrients. Previous studies hypothesized that haustoria-associated genes evolved primarily from root and pollen-associated pathways by neofunctionalization following genome duplications
Dataset DOI: 10.5061/dryad.w3r228174
Description of the data and file structure
These datasets are associated with the publication "A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants", published in Annals of Botany in May, 2026.
Files and variables
File: Haustorial_genes_by_orthogroup2.csv
Description: includes the IDs of all haustoria-associated genes identified in the analysis for species
Variables
- orthogroup: orthogroup generated by running orthofinder with all of the species
- protein_id: protein id from the protein seqs of the genomes
- gene: gene ids from each genome
- baseMean: differential expression quantification generated with DESeq
- log2FoldChange: differential expression quantification generated with DESeq
- lfcSE: differential expression quantification generated with DESeq
- stat: differential expression quantification generated with DESeq
- pvalue: differential expression quantification generated with DESeq
- padj: differential expression quantification generated with DESeq
- timepoint: stage of haustorial development at which the RNA was collected
- species:
File: Pgroenlandica.PG262426N0.functional_annotation.tsv
Description: functional annotation of the Pedicularis groenlandica genome
Variables
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gene_id: Unique identifier of the predicted protein-coding gene or translated open reading frame (ORF) used as input for functional annotation.
md5_digest: MD5 checksum generated by InterProScan for the input protein sequence; used to uniquely identify sequences and detect duplicates.
sequence_length: Length of the input protein sequence in amino acids.
analysis: Database or annotation method used by InterProScan to identify the protein domain, family, or functional signature (e.g., PANTHER, Pfam, SMART, SUPERFAMILY).
signature_accession: Accession number of the matching signature in the source database.
signature_description: Description or name of the matched protein family, domain, motif, or functional signature.
start_location: Amino acid position at which the matched signature begins in the query protein sequence.
end_location: Amino acid position at which the matched signature ends in the query protein sequence.
score: Statistical significance metric reported by the source database, typically an E-value or match score indicating confidence in the annotation.
status: Match status assigned by InterProScan; "T" indicates a valid match.
date: Date associated with the annotation database release used by InterProScan.
interpro_accession: InterPro accession number corresponding to the integrated protein family or domain entry, if available. Missing values ("-") indicate that no InterPro entry was associated with the matched signature.
interpro_description: Description of the corresponding InterPro entry. Missing values ("-") indicate that no InterPro entry was associated with the matched signature.
go_terms: Gene Ontology (GO) terms associated with the matched signature, representing inferred molecular functions, biological processes, and/or cellular components. Multiple GO terms are separated by the pipe character ("|").
Access information
Other publicly accessible locations of the data:
- All genomic and transcriptomic data, including the reference genome, can be found on NCBI under BioProject PRJNA1461970
This work was supported by the National Science Foundation (NSF DEB-2046813) awarded to D.E., the Rocky Mountain Biological Laboratory Graduate Student Grant awarded to R.O.C. and the Botanical Society of America (Graduate Student Research Award) awarded to R.O.C.
To investigate the extent to which haustoria-associated genes in P. groenlandica are shared with other parasitic plant lineages, we examined differential expression and orthology with other haustoria development datasets. We restricted our analyses to four datasets with transcriptomic time-series of haustorial development analogous to our dataset (i.e., RNA sampled from at least stages 1-3). This included: Cuscuta campestris (Bawin et al., 2024), Phtheirospermum japonicum (Kokla et al., 2021), Striga hermonthica (Westwood et al., 2012), and Orobanche aegyptiaca (Westwood et al., 2012). The quality of these datasets varied—S. hermonthica and O. aegyptiaca were generated in 2012, whereas C. campestris and P. japonicum were generated using more modern technologies since 2020. We utilized the control haustorial dataset from Kokla et al. (2022) whose main research focus was repression of haustorial formation by nitrogen, rather than the process of haustorial formation itself. In order to identify haustoria-associated genes by stage in each of these datasets, we followed the same pipeline that was used in P. groenlandica. A publicly available reference genome is available for each species with the exception of O. aegyptiaca. For this taxon, we instead mapped reads to the O. cumana var. cumana genome (Xu et al., 2022). Because reads mapped at a sufficiently high rate (average 66.8% mapping rate across all tissues and stages), we proceeded with the remainder of the pipeline. Genes from P. groenlandica and the four published genomes were classified into orthogroups using Orthofinder v3.0.8 (Emms & Kelly, 2019). We quantified orthogroup overlap among species’ haustoria-associated genes, then functionally annotated the haustorial orthologs by identifying their A. thaliana orthologs, followed by conducting a Gene Ontology term enrichment analysis using clusterProfiler, as described above.
We functionally annotated the genome using InterProScan with the –goterms tag, and identified the closest Arabidopsis thaliana ortholog of each gene with BLAST v2.16.0 (Ye et al., 2006).