Data from: A novel sperm-derived seminal fluid protein in Caenorhabditis nematodes
Data files
May 07, 2025 version files 493.44 MB
-
amplicon_processing.sh
1.83 KB
-
Analyze_Amplicon_BestBlast.R
7.20 KB
-
analyze_fecundity_staining.R
4.34 KB
-
FileS1_SupplementaryMethods.docx
32.29 KB
-
FileS2_IHSdata.txt
97.75 KB
-
FileS3_FecundityData.txt
1.72 KB
-
FileS4_BestBlast.txt.zip
21.51 MB
-
nspf001-deconv.nd2
67.38 MB
-
nspf001.nd2
67.49 MB
-
nspf005-deconv.nd2
92.57 MB
-
nspf005.nd2
92.68 MB
-
nspf006-deconv.nd2
75.78 MB
-
nspf006.nd2
75.88 MB
-
README.md
5.56 KB
-
TableS1_Primers.csv
694 B
-
TableS2_Strains.csv
418 B
-
TableS3_ModelComparison.csv
3.59 KB
Abstract
Nematode sperm contain subcellular vesicles known as membranous organelles (MOs) that fuse with the sperm cell membrane upon sperm activation to release their soluble contents into the extracellular space. The second most abundant proteins in the MOs belong to the conserved Nematode-Specific Peptide family, group F (NSPF) gene family. We hypothesize that these proteins contribute to seminal fluid and are part of post-insemination reproductive tract dynamics. We characterized the anatomical region where the NSPF proteins likely function during fertilization using dissected testes and whole-worm immunostaining of a His-tagged nspf-1 transgene. We confirmed that NSPF proteins are transferred to females during mating. NSPF proteins localize to the uterus lumen when transferred to mated females and in unmated adult hermaphrodites. These results suggest that the uterine localization of the NSPF proteins is likely a functional property of both male-derived sperm and self-sperm and not incidental to the point of transfer during mating. In males, we confirm that NSPF proteins are indeed sperm derived. We then used experimental evolution to compete the wildtype allele against a deletion allele in 10 replicate obligate-outcrossing populations. We calculated a mean selective disadvantage of 0.1% for the deletion allele, which indicated that the NSPF genes are beneficial to male fitness. This conclusion was reinforced by qualitative trends from lower-powered single-generation fertility assays. Together we demonstrate that nematodes use a novel approach for contributing proteins to seminal fluid and show that the highly abundant NSPF proteins likely have a beneficial impact on fitness.
Dataset DOI: 10.5061/dryad.5qfttdzj6
Description of the data and file structure
The oligonucleotides used in this study are available as Table S1. The immunostaining data are available in File S2 and the complete protocol is available in File S1. The fertility data are available in File S3. The raw amplicon data are available at NCBI SRA under accession number PRJNA1009866. The processed amplicon reads are available in File S4. The scripts used to analyze the amplicon data and immunostaining data are provided here as well as via the Cutter Lab GitHub repository NSPF (https://github.com/Cutterlab/NSPF).
Files and variables
File: analyze_fecundity_staining.R
Description: This R script analyzes the fecundity data in File S3 and the immunostaining data in File S2.
File: amplicon_processing.sh
Description: This script processes the raw amplicon sequence data and BLASTs each read to the wild type and deletion alleles.
File: Analyze_Amplicon_BestBlast.R
Description: This R script selects the best BLAST allele for each read (from the processed data) and analyzes the amplicon sequence data.
File: FileS1_SupplementaryMethods.docx
Description: Complete immunostaining protocols and buffer recipes.
File: FileS2_IHSdata.txt
Description: Immunostaining data across developmental stages and sexes. Each line represents an individual worm scored for fluorescence (1 = present; 0 = absent).
Variables
- Worm: Given as strain*-*stage-sex
- Head: pharynx region of the worms; present in all stages
- Upper gonad: distal gonad; meitoic region of the gonad; present in all stages but most prominent in L4 and older
- Mid gonad: proximal gonad; in hermaphrodites/females this is after the turn to the spermathecae; in males this is after the turn to the seminal vesicle; present in L4 and older
- lower gonad: uterus in hermaphrodites/females; vas deferens in males; present in L4 and older
- Vulva/cloaca: mating "opening"; present in all stages
- Tail: in males this includes the fan and rays
- None: no staining seen
- Eggs: presence or absence of eggs
File: FileS3_FecundityData.txt
Description: Late life fecundity data
Variables
- male: strain for the male used in the mating
- D5: fecundity on day 5 of adulthood
- D6: fecundity on day 6 of adulthood
- D7: fecundity on day 7 of adulthood
- D8: fecundity on day 8 of adulthood
- D9: fecundity on day 9 of adulthood
- D10: fecundity on day 10 of adulthood
- D11: fecundity on day 11 of adulthood
- D12: fecundity on day 12 of adulthood
File: FileS4_BestBlast.txt.zip
Description: Processed amplicon sequencing reads.
Variables
- ID: sequence ID
- Amplicon: Best BLAST allele (WT or DEL)
- Identity: Percent identity to called allele
- Alignment.length: Number of aligned base pairs
- Mismatches: Number of base pair mismatches
- gap.opens
- q.start: Query start
- q.end: Query end
- s.start: sequence start
- s.end: sequence end
- evalue
- bit.score
- replicate: generation.expevolrep.seqrep
- replicate2: generation.expevol.rep
File: TableS1_Primers.csv
Description: Primers used in this study.
Variables
- primer name
- sequence 5' to 3'
- purpose
File: TableS2_Strains.csv
Description: Strains used in this study.
Variables
- Strain Name: strain
- Primary Strain Background: genetic background for transgenics
- Genotype: full genotype
- Backcrossing/Inbreeding: number of generations backcrossed or inbred
- Method: method by which the strain was generated
- Source: strain source
File: TableS3_ModelComparison.csv
Description: Linear model comparisons for amplicon sequencing data. All six models fit are given along with their summaries (from R).
File: nspf001-deconv.nd2
Description: Deconvoluted image of stained, dissected gonads. To be analyzed along with file nspf001.nd2 to create Figure 1.
File: nspf001.nd2
Description: Confocal image of stained, dissected gonads. To be analyzed along with file nspf001-deconv.nd2 to create Figure 1.
File: nspf005-deconv.nd2
Description: Deconvoluted image of stained, dissected gonads. To be analyzed along with file nspf005.nd2 to create Figure 1.
File: nspf005.nd2
Description: Confocal image of stained, dissected gonads. To be analyzed along with file nspf005-deconv.nd2 to create Figure 1.
File: nspf006-deconv.nd2
Description: Deconvoluted image of stained, dissected gonads. To be analyzed along with file nspf006.nd2 to create Figure 1.
File: nspf006.nd2
Description: Confocal image of stained, dissected gonads. To be analyzed along with file nspf006-deconv.nd2 to create Figure 1.
Code/software
A bash script for processing the raw amplicon sequencing data is provided along with R scripts to analyze innumostaining, fecundity, and sequencing data.
Open source software needed are R and ImageJ.
Access information
Other publicly accessible locations of the data:
Data was derived from the following sources:
- Kasimatis, K.R., Moerdyk-Schauwecker, M.J., Timmermeyer, N. & Phillips, P.C. 2018. Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes. BMC Genomics 19: 593.
