Multilevel analysis between Physcomitrium patens and Mortierella explores potential long-standing interaction among land plants and fungi
Data files
Jun 28, 2023 version files 11.72 GB
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README.md
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Supp.1a.Physco_photos.tar.gz
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Supp.1b.Photo_Pixel_Quantification.csv
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Supp.2a.Physco_quants.tar.gz
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Supp.2b.Ppatens_Berionawt_DESeq.csv
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Supp.2c.Ppatens_Berionacu_DESeq.csv
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Supp.2d.Ppatens_Lelongatawt_DESeq.csv
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Supp.2e.Ppatens_Lelongatacu_DESeq.csv
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Supp.3a.Perroud_Mathieu.tar.gz
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Supp.3b.Perroud_Mathieu.csv
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Supp.3c.Significant_Perroud.csv
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Supp.3d.Novel_Expression_Perroud_v_Mathieu.csv
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Supp.3e.Novel_Silencing_Perroud_v_Mathieu.csv
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Supp.4.Gene_Ontology_Reports.xlsx
Dec 27, 2023 version files 11.88 GB
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README.md
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Supp.1.Additional_Microscopy_Photos.tar.gz
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Supp.2a.Physco_photos.tar.gz
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Supp.2b.Photo_Pixel_Quantification.csv
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Supp.3a.Physco_quants.tar.gz
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Supp.3b.Ppatens_Berionawt_DESeq.csv
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Supp.3c.Ppatens_Berionacu_DESeq.csv
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Supp.3d.Ppatens_Lelongatawt_DESeq.csv
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Supp.3e.Ppatens_Lelongatacu_DESeq.csv
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Supp.4a.Perroud_Mathieu.tar.gz
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Supp.4b.Perroud_Mathieu.csv
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Supp.4c.Significant_Perroud.csv
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Supp.4d.Novel_Expression_Perroud_v_Mathieu.csv
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Supp.4e.Novel_Silencing_Perroud_v_Mathieu.csv
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Supp.5.Media_Effects_On_Physco_Expression.pdf
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Supp.6.Mortierella_elongata_NVP64_genome_stats.xlsx
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Supp.7.SYM_gene_hits.txt
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Supp.8a.Arabidopsis_quants.tar.gz
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Supp.8b.Algae_quants.tar.gz
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Supp.8c.Orthogroups.tsv
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Supp.8d.SingleCopy_Orthogroups_all.tsv
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Supp.8e.SingleCopy_Orthogroups_AT_PP.tsv
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Supp.8f.SingleCopy_Orthogroups_CR_PP.tsv
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Supp.8g.Orthogroup_Significant_hits_overlap.xlsx
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Supp.9.Gene_Ontology_Reports.xlsx
Dec 26, 2023 version files 11.88 GB
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README.md
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Supp.1.Additional_Microscopy_Photos.tar.gz
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Supp.2a.Physco_photos.tar.gz
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Supp.2b.Photo_Pixel_Quantification.csv
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Supp.3a.Physco_quants.tar.gz
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Supp.3b.Ppatens_Berionawt_DESeq.csv
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Supp.3c.Ppatens_Berionacu_DESeq.csv
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Supp.3d.Ppatens_Lelongatawt_DESeq.csv
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Supp.3e.Ppatens_Lelongatacu_DESeq.csv
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Supp.4a.Perroud_Mathieu.tar.gz
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Supp.4b.Perroud_Mathieu.csv
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Supp.4c.Significant_Perroud.csv
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Supp.4d.Novel_Expression_Perroud_v_Mathieu.csv
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Supp.4e.Novel_Silencing_Perroud_v_Mathieu.csv
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Supp.5.Media_Effects_On_Physco_Expression.pdf
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Supp.6.Mortierella_elongata_NVP64_genome_stats.xlsx
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Supp.7.SYM_gene_hits.txt
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Supp.8a.Arabidopsis_quants.tar.gz
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Supp.8b.Algae_quants.tar.gz
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Supp.8c.Orthogroups.tsv
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Supp.8d.SingleCopy_Orthogroups_all.tsv
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Supp.8e.SingleCopy_Orthogroups_AT_PP.tsv
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Supp.8f.SingleCopy_Orthogroups_CR_PP.tsv
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Supp.8g.Orthogroup_Significant_hits_overlap.xlsx
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Supp.9.Gene_Ontology_Reports.xlsx
Abstract
The model moss species Physcomitrium patens has long been used for studying divergence and evolution of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes make it an ideal candidate for modeling plant terrestrialization 500 million years ago. Based on how plants and fungi interact today, it is predicted that early interactions may have aided in overcoming the barriers present for initial plant colonization on land. This may have manifested similar to present day, where fungi enabled easier uptake of nitrogen, phosphorous, micronutrients, and water retention in exchange for a reliable carbon source. However, identifiable fungal symbionts in P. patens, despite mutualistic interaction widespread among all present day embryophyte families, have remained elusive. To test modern representatives of early land fungal lineages, two Mortierella species (Linnemannia elongata and Benniella eriona), with strains lacking and containing endobacterial symbionts, were grown in coculture with P. patens. We illustrate the interaction between P. patens and Mortierella through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Our study provides insights into the earliest plant-fungal interactions may have looked like and ways P. patens and Mortierella communicate today.
README
This README file was generated on 2023-12-16 by Davis Mathieu
GENERAL INFORMATION
Title: Multilevel analysis between Physcomitrium patens and Mortierella explores potential
long-standing interaction among land plants and fungi.
Authors: Davis Mathieu, Abigail E. Bryson, Britta Hamberger, Vasanth Singan,
Keykhosrow Keymanesh, Mei Wang, Kerrie Barry, Stephen Mondo, Jasmyn Pangilinan,
Maxim Koriabine, Igor V Grigoriev, Gregory Bonito, Björn Hamberger
Prinicipal Investigator Contact Information
Name: Björn Hamberger
Intitution: Michigan State University
Address: East Lansing, MI USA
Email: hamberge@msu.edu
Associate or Co-investigator Contact Information
Name: Davis Mathieu
Institution: Michigan State University
Address: East Lansing, MI USA
Email: mathieud@msu.edu
Data Collecction Date: 2017-2021
Geographic Location of Data Collection: East Lansing MI, USA
Information about funding sources that supported the collection of the data: NSF (DEB
1737898); DOE (DE-AC02-05CH11231); GLBRC DOE (DE-SC0018409); MSU (MICL02454; MICL02416);
BSSD (LANLF59T);
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: None
Links to publications that cite or use this data:
Davis Mathieu, Abigail E. Bryson, Britta Hamberger, Vasanth Singan,
Keykhosrow Keymanesh, Mei Wang, Kerrie Barry, Stephen Mondo, Jasmyn Pangilinan,
Maxim Koriabine, Igor V Grigoriev, Gregory Bonito, Björn Hamberger (2023). Multilevel
analysis between Physcomitrium patens and Mortierella explores potential long-standing
interaction among land plants and fungi. The Plant Journal.
https://doi.org/10.1111/tpj.16605
Links to other publicly accessible locations of the data: NCBI P. patens SRA
Database (PRJNA807682); NCBI C. reinhardtii SRA (PRJNA809543); NCBI M. elongata (L. elongata
Genome Accession: (JAXBDG000000000);Links/relationships to ancillary data set: None
Was data derived from another source? YES
Large Scale Comparison between P. patens RNA Expression:
Perroud, P.-F., Haas, F. B., Hiss, M., Ullrich, K. K., Alboresi, A.,
Amirebrahimi,M., Barry, K., Bassi, R., Bonhomme, S., Chen, H., Coates,
J. C., Fujita, T., Guyon-Debast,A., Lang, D., Lin, J., Lipzen, A., Nogué,
F., Oliver, M. J., Ponce de León, I., … Rensing, S. A. (2018). The
Physcomitrella patens gene atlas project: Large-scale RNA-seq based
expression data. The Plant Journal, 95(1), 168–182. https://doi.org/10.1111/tpj.13940Comparison of Media Based effects of RNA Expression in P. patens:
Perroud, P.-F., Haas, F. B., Hiss, M., Ullrich, K. K., Alboresi, A.,
Amirebrahimi,M., Barry, K., Bassi, R., Bonhomme, S., Chen, H., Coates,
J. C., Fujita, T., Guyon-Debast,A., Lang, D., Lin, J., Lipzen, A., Nogué,
F., Oliver, M. J., Ponce de León, I., … Rensing, S. A. (2018). The
Physcomitrella patens gene atlas project: Large-scale RNA-seq based
expression data. The Plant Journal, 95(1), 168–182. https://doi.org/10.1111/tpj.13940Garcias-Morales, D., Palomar, V. M., Charlot, F., Nogué, F., Covarrubias, A. A., & Reyes, J. L. (2023). N6-Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens. The Plant Journal, 114(1), 7–22. https://doi.org/10.1111/tpj.16149 Otero-Blanca, A., Pérez-Llano, Y., Reboledo-Blanco, G., Lira-Ruan, V., Padilla-Chacon, D., Folch-Mallol, J. L., Sánchez-Carbente, M. D. R., Ponce De León, I., & Batista-García, R. A. (2021). Physcomitrium patens Infection by Colletotrichum gloeosporioides: Understanding the Fungal–Bryophyte Interaction by Microscopy, Phenomics and RNA Sequencing. Journal of Fungi, 7(8), 677. https://doi.org/10.3390/jof7080677 Causier, B., McKay, M., Hopes, T., Lloyd, J., Wang, D., Harrison, C. J., & Davies, B. (2023). The TOPLESS corepressor regulates developmental switches in the bryophyte Physcomitrium patens that were critical for plant terrestrialisation. The Plant Journal, 115(5), 1331–1344. https://doi.org/10.1111/tpj.16322
Orthologous expression comparison between A. thaliana, C. reinhardtii, and P. patens:
Vandepol, N., Liber, J., Yocca, A., Matlock, J., Edger, P., & Bonito, G.
(2022). Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis
thaliana aerial growth and responses to auxin, ethylene, and reactive
oxygen species. PLOS ONE, 17(4), e0261908.
https://doi.org/10.1371/journal.pone.0261908Du, Z.-Y., Zienkiewicz, K., Vande Pol, N., Ostrom, N. E., Benning, C., & Bonito, G. M. (2019). Algal-fungal symbiosis leads to photosynthetic mycelium. ELife, 8, e47815. https://doi.org/10.7554/eLife.47815
Investigation of SYM gene activation in P. patens based on former homologs
Delaux, P.-M., Radhakrishnan, G. V., Jayaraman, D., Cheema, J., Malbreil,
M., Volkening, J. D., Sekimoto, H., Nishiyama, T., Melkonian, M., Pokorny,
L., Rothfels, C. J., Sederoff, H. W., Stevenson, D. W., Surek, B., Zhang,
Y., Sussman, M. R., Dunand, C., Morris, R. J., Roux, C., … Ané, J.-M.
(2015). Algal ancestor of land plants was preadapted for symbiosis.
Proceedings of the National Academy of Sciences, 112(43), 13390–13395.
https://doi.org/10.1073/pnas.1515426112Recommended citation for this dataset:
Davis Mathieu, Abigail E. Bryson, Britta Hamberger, Vasanth Singan,
Keykhosrow Keymanesh, Mei Wang, Kerrie Barry, Stephen Mondo, Jasmyn Pangilinan,
Maxim Koriabine, Igor V Grigoriev, Gregory Bonito, Björn Hamberger (2023). Multilevel
analysis between Physcomitrium patens and Mortierella explores potential long-standing
interaction among land plants and fungi. The Plant Journal. Dryad Digital Repository.
https://doi.org/10.5281/zenodo.8067745
DATA & FILE OVERVIEW
- All microscopy photos that show or exemplify unique phenomenon from each coculture of P. patens and fungal species. Select photos were used in publication to represent observations. All samples were cocultured on BCD Agar and stained with Chlorazol Black E.
#DATA STRUCTURE
Supp.1.Additional_Microscopy_Photos.tar.gz
B_eriona_CU
image001.jpg
image002.jpg
image003.jpg
image004.jpg
image005.jpg
image006.jpg
B_eriona_WT
GBAus27p_ppatens_cell_rupture.1.jpg
image001.jpg
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L_elongata_CU
image_001.jpg
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NVP64cuglobules.jpg
L_elongata_WT
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- All Picture and Phenomic Data
2a. Raw phenomic Data: All P. patens and fungal coculture images captured with
Raspberry Pis and analyzed with PlantCV. Folder contains directories named after
the treatment and replicate. The file name contains the information on which
RaspberryPi, Camera, Date, and Time the image was captured.
*Number of conditions: 5
*P. patens isolates on soil, no coculture (control)
*P. patens in coculture with B. eriona cured of endobacteria CU (GBn)
*P. patens in coculture with B. eriona WT (GBp)
*P. patens in coculture with L. elongata cured of endobacteria CU (NVPn)
*P. patens in coculture with L. elongata WT (NVPp)
*Number of Sample Directories/replicates: 41
*Total Number of Photos: 2047
2b. Green pixel quantification: A .csv file containing the date the picture was taken,
the location of the raw file, the camera and raspberry pi number, the treatment,
the number of green pixels quantified with PlantCV, the estimated growth at day of
innoculation, and the growth ratio corrected for differences in starting culture
germination.
*Variables measured using PlantCV with dataset Supp.2a as an input:
*Date photo was taken
*Condition and replicate number
*Corresponding Device which captured the image
*Treatment Group
*Number of quantified green pixel count measured by PlantCV
*Start Day of innoculatin
*Pixel value at day 23 (day of innoculation) for correction based on
germination
*Corrected Ratio of growth compared to before and after innoculation Day 23
#DATA STRUCTURE
Supp.2a.Physco_photos.tar.gz
control_1/
control_2/
control_3/
control_4/
control_5/
control_6/
control_7/
control_8/
control_9/
control_10/
GBn_1/
GBn_2/
GBn_3/
GBn_4/
GBn_5/
GBn_6/
GBn_7/
GBp_1/
GBp_2/
GBp_3/
GBp_4/
GBp_5/
GBp_6/
GBp_7/
GBp_8/
NVPn_1/
NVPn_2/
NVPn_3/
NVPn_4/
NVPn_5/
NVPn_6/
NVPn_7/
NVPn_8/
NVPp_1/
NVPp_2/
NVPp_3/
NVPp_4/
NVPp_5/
NVPp_6/
NVPp_7/
NVPp_8/
Supp.2b.Photo_Pixel_Quantification.csv
- RNA-Seq Quantification and Analysis Files for P. patens with Mortierella
3a. P. patens RNA Seq Analysis Data: Folder containing the results from the quantified
mapped reads using Salmon to their subsequent treatments. File naming convention is
based on their indicated name on JGI. After the "|" describes the treatment
affiliated with each set of analyzed RNA-Seq reads. Additionally a tx2gene file
was generated with tximport for compressing multiple isoforms. These Salmon_quant
files were used in later anaylsis as input for the calling of differentially
expressed genes between P. patens and fungal treatments using DESeq2 and the
analysis with Perroud et al. 2018, A. thaliana, and C. reinhardtii.
Each Quant_file (i.e. CUTON) contains:
*aux_info (Directory): Contains information about how Salmon was
invoked for read quantification, including the approximation of
observed fragment length.
*cmd_info.json (JSON): A recording the main command line
paramenters invoked by Salmon at time of producing results
file (quant.sf).
*lib_format_counts.json (JSON): Report of number of fragments that
mapped (and didn't map) with the library format. Also includes
statistics on strand bias. Will additionally include areas where
the same read maps to multiple locations.
*libParams/flenDist.txt (text file): Contains the parameters of the
normalized distribution of observed fragment lengths.
*logs/salmon_quant.log (log file): The print out of Salmon usage
while running the program
*quant.sf (tsv file): Main output file containing:
*the transcript name
*length of the transcript (bp)
*normalized length of the transcript removing poly A tail
and identifying where reads map
*Transcripts per Million (TPM) value for relative abundance
*Number of mapped reads to that transcript
More information at: (https://salmon.readthedocs.io/en/latest/salmon.html)
3b. P. patens x B. eriona WT gene Results: All significantly differentially expressed
genes when P. patens is cocultured with B. eriona WT with an adjusted P-values
less than 0.01 identified with DESeq2.
*Total number of gene hits: 2586
*Variables measured:
*Physcomitrium patens [v3.3] gene name
*Base Mean expression level
*Log2 fold change in the presence of B. eriona WT
*Log2 fold standard error (lfcSE)
*stat measures the deviance between the reduced model and the
full model based on Log2 change and lfcSE
*P-value for expression change
*Bonferroni adjusted P-value for expression change
3c. P. patens x B. eriona CU gene Results: All significantly differentially expressed
genes when P. patens is cocultured with B. eriona CU with an adjusted P-values
less than 0.01 identified with DESeq2.
*Total number of gene hits: 65
*Variables measured:
*Physcomitrium patens [v3.3] gene name
*Base Mean expression level
*Log2 fold change in the presence of B. eriona CU
*Log2 fold standard error (lfcSE)
*stat measures the deviance between the reduced model and the
full model based on Log2 change and lfcSE
*P-value for expression change
*Bonferroni adjusted P-value for expression change
3d. P. patens x L. elongata WT gene Results: All significantly differentially expressed
genes when P. patens is cocultured with L. elongata WT with an adjusted P-values
less than 0.01 identified with DESeq2.
*Total number of gene hits: 802
*Variables measured:
*Physcomitrium patens [v3.3] gene name
*Base Mean expression level
*Log2 fold change in the presence of L. elongata WT
*Log2 fold standard error (lfcSE)
*stat measures the deviance between the reduced model and the
full model based on Log2 change and lfcSE
*P-value for expression change
*Bonferroni adjusted P-value for expression change
3e. P. patens x L. elongata CU gene Results: All significantly differentially expressed
genes when P. patens is cocultured with L. elongata CU with an adjusted P-values
less than 0.01 identified with DESeq2.
*Total number of gene hits: 1053
*Variables measured:
*Physcomitrium patens [v3.3] gene name
*Base Mean expression level
*Log2 fold change in the presence of L. elongata CU
*Log2 fold standard error (lfcSE)
*stat measures the deviance between the reduced model and the
full model based on Log2 change and lfcSE
*P-value for expression change
*Bonferroni adjusted P-value for expression change
#DATA STRUCTURE
Supp.3a.Physco_quants.tar.gz
Salmon_quants
CUTON/ | P. patens control 1
CUTOO/ | P. patens control 2
CUTOP/ | P. patens control 3
CUTOS/ | P. patens x B. eriona WT 1
CUTOT/ | P. patens x B. eriona WT 2
CUTOU/ | P. patens x B. eriona WT 3
CUTOW/ | P. patens x B. eriona CU 1
CUTOX/ | P. patens x B. eriona CU 2
CUTOZ/ | P. patens x L. elongata WT 1
CUTPA/ | P. patens x L. elongata WT 2
CUTPB/ | P. patens x L. elongata WT 3
CUTPC/ | P. patens x L. elongata CU 1
CUTPG/ | P. patens x L. elongata CU 2
CUTPH/ | P. patens x L. elongata CU 3
CWYAU/ | P. patens x B. eriona CU 3
tx2gene_ppatens.txt
Supp.3b.Ppatens_Berionawt_DESeq.csv
Supp.3c.Ppatens_Berionacu_DESeq.csv
Supp.3d.Ppatens_Lelongatawt_DESeq.csv
Supp.3e.Ppatens_Lelongatacu_DESeq.csv
- Cross P. patens Treatment Comparison with 99 Treatments against Perroud et al. 2018 (https://doi.org/10.1111/tpj.13940).
4a. Formatted Supplemental collected from Perroud et al. 2018: Contains the formatted
data of the RPKM values downloaded from the supplemental data found in Perroud et
al. 2018 (https://doi.org/10.1111/tpj.13940) and the file of those values converted
to TPM. These are intermediate files used in the conversion to TPM and are included
here mainly for rerunning of code if desired to repeat experimentation:
*Ppatens_RPKM.csv: Supplemental file of quantified reads (RPKM) from
Perroud et al. 2018
*Ppatens_TPM.csv: Supplemental file of quantified reads (RPKM) from Perroud
et al. 2018 converted to transcript per million (TPM)
4b. Combined document containing the P. patens fungal/soil treatment samples and the
Perroud et al. 2018 samples quantified gene expression in TPM.
Total Samples: 114
Total Treatments: 28
Total Treatment Groups and replicates:
*ctrl (3):P. patens whole plant (gametophore) isolates on soil
tested here
*GBp (3): P. patens whole plant (gametophore) cocultured with B.
eriona WT
*GBn (3): P. patens whole plant (gametophore) cocultured with B.
eriona CU
*NVPp (3):P. patens whole plant (gametophore) cocultured with L.
elongata WT
*NVPn (3):P. patens whole plant (gametophore) cocultured with L.
elongata CU
*Gametophores_a_Bsl (3): above ground P. paten gametophore tissue
on solid BCD media
*Gametophores_a_Ksl (1): above ground P. patens gametophore tissue
on Knop solid media
*Protonema_Bsl (2): P. patens protonema tissue on BCD solid media
*Protonema_Ksl (3): P. patens protonema tissue on Knop solid media
*Protonema_Bsl_cont (3): P. patens protenema tissue grown on BCD
solid media and under constant light
*Protonema_Bsl_const_Glc (3):P. patens protenema tissue grown with
constant light and with Glucose
*Protonema_BslA (3): P. patens protonema tissue grown on BCDA
(ammonium) solid media
*Protenema_Klq (5): P. patens protonema tissue grown on Knop liquid
media
*Protonema_Klq_RNeasy (3): P. patens protonema tisue grown on Knop
liquid media and extracted using the Qiagen Plant Mini Kit RNeasy
*Leaflet_Ksl (2): P. patens leaflet tissue grown on Knop solid agar
*Sporophyte_g_Ksl (3): P. patens green sporophyte tissue grown on
Knop solid media
*Sporophyte_b_Ksl (3): P. patens brown sporophyte tissue grown on
Knop solid media
*Spores_BslA_cont (3): P. patens germinating spores on BCDA
(ammonium) solid media and constant light
*Protoplast_p_BslA (3): P. patens protoplasts (protenema) grown on
BCDA (ammonium) solid media
*Protonema_Bsl_heat (3): P. patens protenema tissue grown on BCD
solid media (maybe supplemented with 5mM ammonium tartrate
(contrasting details from primary literature supplemental and
text)for 5 days with repeated heat shock cycles of 5h @22C then
1h @37C.
*Gametophores_Bsl_dehy (3): P. patens gametophore tissue grown on
BCD solid media for 5 weeks on cellophane disk. Gametophores were
transferred to dehydrating atmosphere until reaching constant
weight (150h) and sampled at 180h
*Gametophore_Bsl_rehy (3): P. patens gametophore tissue grown on
BCD solid media for 5 weeks on cellophane disk. Gametophores were
transferred to dehydrating atmosphere until reaching constant
weight (150h). Samples were then floated on sterile water for 5
min, then placed on back on solid BCD media for 2 hours before
extraction.
*Protonema_Bsl_lgt50_ABA24 (3): P. patens protonema tissues were
cultivated on solid BCD media for 6 days and then transferred to
solid BCD media supplemented with 50 uM Abscisic acid (ABA) for 24
hours
*Protonema_Ksl_hlgt850 (3): P. patens protonema tissue under high
light harvested 2 hours after lights were turned on (850 umol
m-2s-1) grown on Knop liquid media
*Protonema_Ksl_llgt10 (3): P. patens protonema tissue under low
light harvested 2 hours after lights were turned on (10 umol
m-2s-1) grown on Knop liquid media
*Protonema_BslA_Glc_UV.B (3): P. patens protonema tissue grown
under continuous 4umol m-2s-1 white light and 1umolm-2s-1 UV-B
light at 300-320 nm for 1-2 weeks then harvested.
*Protonema_BSl_Cont_GA9 (3): P. patens protonema tissue grown on
solid BCD media supplemented with GA9-methylester. Samples were
harvested after 7 days
*Protonema_BSl_lgt50_OPDA (3): P. patens protonema tissue grown on
solid BCD media supplemented with 5mM ammonium tartrate with 50 uM
12-oxo-phytodienoic acid (OPDA) and incubated for 6 h before
extraction.
*Protonema_BSlA_dark_Glc (3): P. patens protonema tissue grown on
solid BCD media supplemented with 5mM Ammonium and 0.5% glucose in
darkness for 1-2 weeks before extraction.
*Protonema_BSlA_Glc_red (3): P. patens protonema tissue grown on
solid BCD media supplemented with 5mM Ammonium in red light under
continuous 10umol m-2s-1 red light 660-680 nm for 1-2 weeks before
extraction.
*Protonema_BslA_Glc_blue (3): P. patens protonema tissue grown on
solid BCD media supplemented with 5mM Ammonium in blue light under
continuous 10umol m-2s-1 red light 660-680 nm for 1-2 weeks before
extraction.
*Protonema_BslA_Glc_red_f (3): P. patens protonema tissue grown on
solid BCD media supplemented with 5mM Ammonium in far red light
under continuous 2umol m-2s-1 far red light 720-740 nm for 1-2
weeks before extraction.\
*Protonema_BslA_strig (3): P. patens protonema tissue grown on
solid BCD media (Ammonium) cultivated for 21 days before being
transferred to 1uM racemic GR24 (synthetic strigolactone) for 24h.
*Protonema_KlqA_lgt2hrs (3): P. patens protonema tissue light
controls harvested 2 hours after lights were turned on (70 umol
m-2s-1) grown on Knop liquid (Ammonium) media
*Protonema_Klq_lgt2hrs (3): P. patens protonema tissue light
controls harvested 2 hours after lights were turned on (70 umol
m-2s-1) grown on Knop liquid media
*Protonema_Bsl_acetone (3): P. patens protonema tissue grown on
solid BCD media and then transfered after 21 days to a plate with
1uM acetone cellophane disk.
*gam_rhiz_Klq_hydr (3): P. patens gametophore rhizoid tissues
grown on Knop liquid media in a hydroponic setup.
*gam_rhiz_Klq_hydr_auxin (3): P. patens gametophore rhizoid tissues
grown on Knop liquid media with 10 uM napthaleneacetic acid (NAA) in a hydroponic setup.
4c. All significantly differentially expressed genes when P. patens fungal/soil samples
were compared to the 99 Perroud et al. 2018 treatments, representing only those
genes with an adjusted P-value less than 0.0001.
*Total number of gene hits: 7450
*Variables measured:
*Physcomitrium patens [v3.3] gene name
*Base Mean expression level
*Log2 fold change in the presence of L. elongata CU
*Log2 fold standard error (lfcSE)
*stat measures the deviance between the reduced model and the
full model based on Log2 change and lfcSE
*P-value for expression change
*Bonferroni adjusted P-value for expression change
4d. All genes that were identified to have 0 expression among all samples in Perroud
et al. 2018 and have some expression in P. patens fungal/soil treatment.
*Total number of gene hits: 822
4e. All genes that were identified to have 0 expression among all samples P. patens
fungal/soil treatment and have at least one sample with expression in Perroud et
al. 2018.
*Total number of gene hits: 2116
#DATA STRUCTURE
Supp.4a.Perroud_Mathieu.tar.gz
Ppatens_RPKM.csv
Ppatens_TPM.csv
Supp.4b.Perroud_Mathieu.csv
Supp.4c.Significant_Perroud.csv
Supp.4d.Novel_Expression_Perroud_v_Mathieu.csv
Supp.4e.Novel_Silencing_Perroud_v_Mathieu.csv
Media based effects on P. patens transcription
A summary of the effects based on different medias on P. patens transcription.
This investigated and illustrates the comparisons of media effects among control
samples under varying conditions. Samples were analyzed using Salmon and DESeq2 for
comparison. Contained within the pdf includes the BioProject number and SRA files
used for comparison
#DATA STRUCTURE
Supp.5.Media_effects_on_Physco_expression.pdf
Linnemania elongata Genome Assembly Statistics
Table with metrics for various Mortierella species sequenced at the same time,
including M. elongata NVP64 presented in this work with it's updated phylogeny
and latin name Linnemania elongata.
*Fungal Genomes: 5
*Genome Assembly Stats:
*Assembly Length
*Contig Number
*Contig N50
*Repeat length in Mb%
*Number of predicted genes
*Number of genes with Pfam support
*Number of CDS complete genes
*Pubmed ID (being this work here Mathieu et al.)
#DATA STRUCTURE
Supp.6.Mortierella_elongata_NVP64_genome_stats.xlsx
Differential expression of P. patens symbiosis gene orthologs
Genes identified as homologs for plant fungal symbiosis in P. patens based on the
work presented in https://doi.org/10.1073/pnas.1515426112. Genes are converted
from their previous annotation names to the update v3.3 genome names, then are
indicated as signficantly differentially expressed with either "UP" or "DOWN" to
indicate how the expressionwas different then control conditions based on Supp3b-e.
#DATA STRUCTURE
Supp.7.SYM_gene_hits.txt
- Homology and Gene Expression analysis between P. patens x A. thaliana x C. reinhardtii
8a. A. thaliana RNA Seq Analysis Data: Folder containing the results from the
quantified mapped reads generated using Salmon for their subsequenst treatments.
File naming convention was based on the treatment inacted on each sample. After the
"|" describes the treatment affiliated with the short hand set of analyzed RNA-Seq
reads.
Each Quant_file contains:
*aux_info (Directory): Contains information about how Salmon was
invoked for read quantification, including the approximation of
observed fragment length.
*cmd_info.json (JSON): A recording the main command line
paramenters invoked by Salmon at time of producing results
file (quant.sf).
*lib_format_counts.json (JSON): Report of number of fragments that
mapped (and didn't map) with the library format. Also includes
statistics on strand bias. Will additionally include areas where
the same read maps to multiple locations.
*libParams/flenDist.txt (text file): Contains the parameters of the
normalized distribution of observed fragment lengths.
*logs/salmon_quant.log (log file): The print out of Salmon usage
while running the program
*quant.sf (tsv file): Main output file containing:
*the transcript name
*length of the transcript (bp)
*normalized length of the transcript removing poly A tail
and identifying where reads map
*Transcripts per Million (TPM) value for relative abundance
*Number of mapped reads to that transcript
More information at: (https://salmon.readthedocs.io/en/latest/salmon.html)
8b. C.reinhardtii RNA Seq Analysis Data: Folder containing the results from the
quantified mapped reads generated using Salmon for their subsequenst treatments.
File naming convention was based on the short hand of the organisms in coculture
(C. reinhardtii strain 21gr, and L. elongata NVP64). After the "|" describes the
treatment affiliated with the short hand set of analyzed RNA-Seq reads.
Each Quant_file contains:
*aux_info (Directory): Contains information about how Salmon was
invoked for read quantification, including the approximation of
observed fragment length.
*cmd_info.json (JSON): A recording the main command line
paramenters invoked by Salmon at time of producing results
file (quant.sf).
*lib_format_counts.json (JSON): Report of number of fragments that
mapped (and didn't map) with the library format. Also includes
statistics on strand bias. Will additionally include areas where
the same read maps to multiple locations.
*libParams/flenDist.txt (text file): Contains the parameters of the
normalized distribution of observed fragment lengths.
*logs/salmon_quant.log (log file): The print out of Salmon usage
while running the program
*quant.sf (tsv file): Main output file containing:
*the transcript name
*length of the transcript (bp)
*normalized length of the transcript removing poly A tail
and identifying where reads map
*Transcripts per Million (TPM) value for relative abundance
*Number of mapped reads to that transcript
More information at: (https://salmon.readthedocs.io/en/latest/salmon.html)
8c. Raw Orthofinder Results for P. patens, A. thaliana, and C. reinhardtii: Output from
Orthofinder, not selected for Single copy orthogroups. File is a tab seperated file
containing all of the orthologs from P. patens, A. thaliana, and C. reinhardtii for
each orthogroup
Total Orthogroups: 13,358
8d. Shared Single Copy orthogroups between P. patens, A. thaliana, and C. reinhardtii:
Selected output from Orthofinder, where there is a single ortholog shared among
each of the three species. File is a tab seperated file containing all of the
single copy orthologs from P. patens, A. thaliana, and C. reinhardtii for
each orthogroup where 1 copy is present for all.
Total Orthogroups: 1,524
8e. Shared Single Copy orthogroups between P. patens and A. thaliana: The selected
single copy orthogroup output generated from Orthofinder when only using the
P. patens and A. thaliana amino acid sequences as input. File is a tab seperated
file containing all of the single copy orthologs from P. patens and A. thaliana
for each orthogroup where 1 copy is present for all.
Total Orthogroups: 3032
8f. Shared Single Copy orthogroups between P. patens and C. reinhardtii: The selected
single copy orthogroup output generated from Orthofinder when only using the
P. patens and C. reinhardtii amino acid sequences as input. File is a tab seperated
file containing all of the single copy orthologs from P. patens and C. reinhardtii
for each orthogroup where 1 copy is present for all.
Total Orthogroups: 2484
8g. Shared and Significantly Expressed Orthogroups among P. patens, A. thaliana, and
C. reinhardtii: Spreadsheet combining the single copy orthologs shared between
P. patens/A. thaliana/C. reinhardtii, P. patens/C. reinhardtii, and
P. patens/A. thaliana. Orthogroups were required to only have one copy in each
organism and have significant differential gene expression among at least one
fungal treatment per plant (56 total orthogroups to have significant expression).
#DATA STRUCTURE
Supp.8a.Arabidopsis_quants.tar.gz
Salmon_quants
control_1 | A. thaliana Control 1
control_2 | A. thaliana Control 2
control_3 | A. thaliana Control 3
NVP64cu_1 | A. thaliana x L. elongata CU 1
NVP64cu_2 | A. thaliana x L. elongata CU 2
NVP64cu_3 | A. thaliana x L. elongata CU 3
NVP64wt_1 | A. thaliana x L. elongata WT 1
NVP64wt_2 | A. thaliana x L. elongata WT 2
NVP64wt_3 | A. thaliana x L. elongata WT 3
Athaliana_NVPcu.csv
Athaliana_NVPwt.csv
tx2gene_athaliana.txt
Supp.8b.Algae_quants.tar.gz
Salmon_quants
21gr_Day0_1 | C. reinhardtii Control 1
21gr_Day0_2 | C. reinhardtii Control 2
21gr_Day0_3 | C. reinhardtii Control 3
21gr_Day0_4 | C. reinhardtii Control 4
21gr_Day0_5 | C. reinhardtii Control 5
21gr_NVP64cu_Day15_1 | C. reinhardtii x L. elongata CU 1
21gr_NVP64cu_Day15_2 | C. reinhardtii x L. elongata CU 2
21gr_NVP64cu_Day15_3 | C. reinhardtii x L. elongata CU 3
21gr_NVP64cu_Day15_4 | C. reinhardtii x L. elongata CU 4
21gr_NVP64wt_Day15_1 | C. reinhardtii x L. elongata WT 1
21gr_NVP64wt_Day15_2 | C. reinhardtii x L. elongata WT 2
21gr_NVP64wt_Day15_3 | C. reinhardtii x L. elongata WT 3
21gr_NVP64wt_Day15_4 | C. reinhardtii x L. elongata WT 4
Creinhardtii_NVPcu_csv
Creinhardtii_NVPwt.csv
tx2gene_chlamy.txt
Supp.8c.Orthogroups.tsv
Supp.8d.SingleCopy_Orthogroups_all.tsv
Supp.8e.SingleCopy_Orthogroups_AT_PP.tsv
Supp.8f.SingleCopy_Orthogroups_CR_PP.tsv
Supp.8g.Orthogroup_Significant_hits_overlap.xlsx
All Gene Ontology Reports for Significant Genes
GO Term Report(s): Links to all GO term reports identified as effected from
comparison with B.eriona WT, B. eriona CU, L. elongata WT, L. elongata CU, Perroud
et al. 2018 significant genes, Perroud et al. 2018 novel expression, Perroud et al.
2018 novel silencing, A. thaliana signifcant genes, and C. reinhardtii significant
genes. Genes were indicated as enriched if log fold was greater than 0 from
Supp3b-e, Supp4c-e, and Supp 8a-b. Links take you to G:Profiler website link to
enriched and depreciated ontologies in each condition based on which genes were
entered.
#DATA STRUCTURE
Supp.9.Gene_Ontology_Reports.xlsx