A lectin receptor-like kinase controls self-pollen recognition in Phlox
Data files
Jul 09, 2025 version files 1.74 GB
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A5_rnabloom.transcripts.fa
42.46 MB
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A6_rnabloom.transcripts.fa
55.76 MB
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A7_rnabloom.transcripts.fa
39.40 MB
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A9_rnabloom.transcripts.fa
48.19 MB
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DFR_floralscans.zip
814.37 MB
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diallelcross_fruitdata.csv
1.16 KB
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diallelcross_pollentubedata.csv
3.96 KB
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lecRLKtree_alignment.fasta
57.33 KB
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longread_multispecies_aligments.zip
12.06 KB
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README.md
9.12 KB
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RNAseq_normalized_expression.csv
2.27 MB
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S1_DFR_floralscans.zip
371.43 MB
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S4_DFR_floralscans.zip
365.13 MB
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shortread_drummondiionly_alignments.zip
85.82 KB
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tissuespecific_qpcr.csv
720 B
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vigs_fruitset.csv
39.48 KB
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vigs_pollentubes.csv
12.25 KB
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vigs_qpcr.csv
3.38 KB
Abstract
Self-incompatibility (SI) describes a widespread collection of genetic mechanisms in flowering plants used to specifically recognize and reject self-pollen. These mechanisms are fundamental to plant sexual reproduction and offer valuable insight into the molecular basis of cell-cell communication and self-recognition more broadly. Here, we leverage an independent evolution of SI in the lineage containing Phlox (Polemoniaceae) to characterize a novel gene causing self-pollen recognition which we name Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK). Recognition of self-pollen associates with a single genomic region containing the Phlox S-locus. We generate predictions regarding how S-loci must function and evolve to identify a single candidate gene within this S-associated region. This gene, PdPIRK, is highly and specifically expressed in the pistil and has exceptionally high polymorphism maintained by negative frequency dependent selection, two hallmarks of self-pollen recognition genes. Functional validation with gene silencing confirms that PdPIRK is necessary for self-incompatibility, and we further demonstrate allele specific activity, confirming its role in self-pollen recognition per se. PdPIRK encodes a G-type lectin receptor-like kinase, which is a member of the same gene family as SRK, the gene controlling self-pollen recognition in the distantly related Brassicaceae. Our findings suggest the presence of genetic constraints or paths of least resistance governing how S-loci evolve and add to our understanding of the diverse molecular mechanisms through which organisms achieve self-recognition.
Dataset DOI: 10.5061/dryad.zgmsbccr3
Description of the data and file structure
Identifying the Phlox S-locus using patterns of patterns of genetic association, gene expression, and genetic polymorphism with functional genetic validation.
Files and variables
File: shortread_drummondiionly_alignments.zip
Description: amino acid sequence alignments for the top 10% most highly expressed pistil genes within the S-associated region in* Phlox drummondii *
File: longread_multispecies_aligments.zip
Description: amino acid sequence alignments for three genes within the S-associated region using alleles of four *Phlox *species
File: lecRLKtree_alignment.fasta
Description: amino acid sequence alignment of lecRLKs
File: diallelcross_fruitdata.csv
Description: fruit set data for diallel crossing experiment associating cross-compatibility with* PdPIRK* genotype
Variables
- pistil: ID for the plant used as the pistil parent
- pollen: ID for the plant used as the pollen parent
- fruit set: the total number of fruits that set in each cross type
- number crosses: the total number of crosses performed for each cross type
File: diallelcross_pollentubedata.csv
Description: pollen tube data for diallel crossing experiment associating cross-compatibility with* Phlox drummondii* Pistil Identity Receptor Kinase (PdPIRK) genotype. One individual per predicted genotype was used to validate fruit set data.
Variables
- cross_ID: description of the cross type
- maternal: ID for the plant used as the pistil parent
- paternal: ID for the plant used as the pollen parent
- predicted_cross_type: prediction for whether the cross should be compatible or incompatible based on fruit set data in diallelcross_fruitdata.csv
- date_crossed: date cross was performed
- date_stained: date tubes were stained and imaged
- tubes_stigma: the total number of pollen tubes present on the stigma
File: DFR_floralscans.zip
Description: floral scans for all flowers crossed during the virus-induced gene silencing experiment using a silencing vector targeting dihydroflavonol 4-reductase (DFR) only.
File: S1_DFR_floralscans.zip
Description: floral scans for all flowers crossed during the virus-induced gene silencing experiment using a silencing vector targeting dihydroflavonol 4-reductase (DFR) and Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S1.
File: S4_DFR_floralscans.zip
Description: floral scans for all flowers crossed during the virus-induced gene silencing experiment using a silencing vector targeting dihydroflavonol 4-reductase (DFR) and Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S4.
File: RNAseq_normalized_expression.csv
Description: normalized expression for five tissue types: stigma/style, anther, pollen, leaf, and stem. Counts are given in TMM. Gene IDs are based on the* Phlox drummondii* genome annotation available at (doi.org/10.5281/zenodo.15498773).
File: tissuespecific_qpcr.csv
Description: qPCR confirming RNAseq
Variables
- Sample: ID for each sample which includes plant ID (number) and tissue type
- PdPIRK Genotype: genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Tissue: Tissue of origin for each sample (leaf, corolla, or stigma/style)
- Individual: Plant ID (number)
- S4 1 Ct (dRn): technical replicate 1 for PdPIRK allele S4 amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- S4 2 Ct (dRn): technical replicate 2 for PdPIRK allele S4 amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- S4 3 Ct (dRn): technical replicate 3 for PdPIRK allele S4 amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 1 Ct (dRn): technical replicate 1 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 2 Ct (dRn): technical replicate 2 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 3 Ct (dRn): technical replicate 3 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
File: vigs_pollentubes.csv
Description: pollen tube data for flowers crossed during the virus-induced gene silencing experiments using a silencing vector targeting 1) dihydroflavonol 4-reductase (DFR) only, 2)Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S4, or 3) Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S1
Variables
- Pistil_ID: plant ID for the pistil parent
- Flower_Number: ID for each flower crossed (corresponds to flower number in floral scan images)
- Flower_Color: color for each flower crossed, either pigmented or white
- Treatment: silencing status for each flower crossed, either silenced or unsilenced
- TRV2-vector: the silencing vector used to infect each plant
- Pistil_Genotype: pistil genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Pollen_Genotype: pollen genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Pollen_ID: plant ID for the pollen parent
- Number_Pollen_Tubes: the total number of pollen tubes present on the stigma
File: vigs_fruitset.csv
Description: fruit set data for flowers crossed during the virus-induced gene silencing experiments using a silencing vector targeting 1) dihydroflavonol 4-reductase (DFR) only, 2)Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S4, or 3) Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) allele S1
Variables
- Pistil_ID: plant ID for the pistil parent
- Flower_Number: ID for each flower crossed (corresponds to flower number in floral scan images)
- Flower_Color: color for each flower crossed, either pigmented or white
- Treatment: silencing status for each flower crossed, either silenced or unsilenced
- TRV2-vector: the silencing vector used to infect each plant
- Pistil_Genotype: pistil genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Pollen_Genotype: pollen genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Pollen_ID: plant ID for the pollen parent
- Fruit: binary indicator of fruit set (1 = fruit formed, 0 = no fruit formed)
File: vigs_qpcr.csv
Description: qPCR data for pistil tissue from silenced and unsilenced flowers for all individuals used in virus induced gene silencing experiments
Variables
- Sample: unique identifier for each sample that includes the plant ID (number) and its silencing status (u = unsilenced, i = silenced)
- PdPIRK Genotype: genotype at* PdPIRK* as confirmed by allele specific PCR amplification
- Individual: plant ID
- Treatment: silencing status for each sample
- Primer pair: the allele specific primers used to amplify PdPIRK for each sample
- PdPIRK 1 Ct (dRn): technical replicate 1 for PdPIRK amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- PdPIRK 2 Ct (dRn): technical replicate 2 for PdPIRK amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- PdPIRK 3 Ct (dRn): technical replicate 3 for PdPIRK amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 1 Ct (dRn): technical replicate 1 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 2 Ct (dRn): technical replicate 1 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
- Ef1a 3 Ct (dRn): technical replicate 1 for the housekeeping gene, Ef1alpha, amplification given in deltaRn, the baseline-corrected, normalized fluorescence signal.
File: A5_rnabloom.transcripts.fa
Description: pistil transcriptome for individual A5 from the diallel cross experiment (see diallelcross_fruitdata.csv) assembled using RNAbloom from PacBio IsoSeq HiFi reads
File: A6_rnabloom.transcripts.fa
Description: pistil transcriptome for individual A6 from the diallel cross experiment (see diallelcross_fruitdata.csv) assembled using RNAbloom from PacBio IsoSeq HiFi reads
File: A7_rnabloom.transcripts.fa
Description: pistil transcriptome for individual A7 from the diallel cross experiment (see diallelcross_fruitdata.csv) assembled using RNAbloom from PacBio IsoSeq HiFi reads
File: A9_rnabloom.transcripts.fa
Description: pistil transcriptome for individual A9 from the diallel cross experiment (see diallelcross_fruitdata.csv) assembled using RNAbloom from PacBio IsoSeq HiFi reads