DOI: 10.5061/dryad.v6wwpzh1k
title: Multilevel analysis between Physcomitrium patens and Mortierella explores potential long-standing interaction among land plants and fungi

description: 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.
description: 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 1. Licenses/restrictions placed on the data:
 None 2. 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.
 1. 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); 2. Links/relationships to
 ancillary data set: None 3. 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. 
 Comparison 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.
 ``` Garcias-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.
 ``` Du, 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.
 4. Recommended 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.
 ## DATA & FILE OVERVIEW
 1. 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 image002.jpg
 image003.jpg image004.jpg image005.jpg image006.jpg image007.jpg
 image008.jpg image009.jpg image011.jpg image012.jpg image013.jpg
 image014.jpg image015.jpg image016.jpg image017.jpg image018.jpg
 image019.jpg image020.jpg image021.jpg image022.jpg image023.jpg
 image024.jpg image025.jpg image026.jpg image027.jpg image028.jpg
 image029.jpg L_elongata_CU image_001.jpg image_002.jpg image_003.jpg
 image_004.jpg image_005.jpg image_006.jpg image_007.jpg image_008.jpg
 image_009.jpg image_010.jpg image_011.jpg image_012.jpg image_013.jpg
 image_014.jpg image_015.jpg image_016.jpg NVP64cuglobules.jpg
 L_elongata_WT image_001.jpg image_002.jpg image_003.jpg image_004.jpg
 image_005.jpg image_006.jpg image_007.jpg image_008.jpg image_009.jpg
 image_010.jpg image_011.jpg image_012.jpg image_013.jpg image_014.jpg
 image_015.jpg image_016.jpg --- 1. 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 --- 1.
 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:
 () 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 --- 1. Cross P. patens Treatment
 Comparison with 99 Treatments against Perroud et al. 2018
 (). 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 () 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 --- 1. Media based effects
 on P. patens transcription 2. 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 --- 1. Linnemania elongata
 Genome Assembly Statistics 2. 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 --- 1. Differential
 expression of P. patens symbiosis gene orthologs 2. Genes identified as
 homologs for plant fungal symbiosis in P. patens based on the work
 presented in . 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 --- 1. 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:
 () 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:
 () 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 --- 1. All Gene Ontology
 Reports for Significant Genes 2. 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 ---