This file README-MS PhD Thesis Supplementary Data was generated on 2022-02-04 by MARA SGROI

GENERAL INFORMATION


1. Title of Dataset: Supplementary Data for PhD thesis "Evolutionary conservation of host responses to arbuscular mycorrhizal symbiosis in liverworts" submitted by Mara Sgroi



2. Author Information

	A. Principal Investigator Contact Information

		Name: Uta Paszkowski

		Institution: Crop Science Centre - University of Cambridge

		Address: 96 Lawrence Weaver road, Cambridge, CB3 0LE

		Email: up220@cam.ac.uk



	B. Associate or Co-investigator Contact Information

		Name: 

		Institution: 

		Address: 

		Email: 



	C. Alternate Contact Information

		Name: Mara Sgroi

		Institution: Crop Science Centre - University of Cambridge

		Address: 96 Lawrence Weaver road, Cambridge, CB3 0LE

		Email: ms2370@cam.ac.uk



3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>: 

2017-05-01 to 2020-12-15

4. Geographic location of data collection <latitude, longiute, or city/region, State, Country, as appropriate>: 

Cambridge, UK

5. Information about funding sources that supported the collection of the data:

Biotechnology and Biological Sciences Research Council (BBSRC)


SHARING/ACCESS INFORMATION



1. Licenses/restrictions placed on the data: 

Data embargoed until 31-01-2023, then publicly available on the Apollo repository

2. Links to publications that cite or use the data:

"Evolutionary conservation of host responses to arbuscular mycorrhizal symbiosis in liverworts", PhD thesis, Mara Sgroi and Uta Paszkowski


3. Links to other publicly accessible locations of the data: 



4. Links/relationships to ancillary data sets: 



5. Was data derived from another source? no




6. Recommended citation for this dataset: 
Mara Sgroi, PhD thesis, University of Cambridge, 2021




DATA & FILE OVERVIEW



1. File List: 

Supplementary table 1: Results of differential expression analysis of RNA-seq data from M. paleacea thalli colonized by R. irregularis.
Supplementary table 2: GO enrichment analysis of differentially expressed genes during M. paleacea arbuscular mycorrhizal symbiosis 
Supplementary table 3: List of genomic resources used as input for orthology inference with the Orthofinder analysis pipeline 
Supplementary table 4: table of transcript IDs belonging to each orthogroup identified with the Orthofinder analysis pipeline 
Supplementary table 5: list of M. truncatula direct orthologs of M. paleacea transcripts identified with the Orthofinder analysis pipeline 
Supplementary table 6: M. paleacea and M. truncatula orthologs significantly differentially expressed during arbuscular mycorrhizal symbiosis 
Supplementary table 7: Amino-acid sequences of candidate M. paleacea pathogenesis-related and gibberellic acid biosynthetic genes, with corresponding M. polymorpha orthologs. 
Supplementary File 1: M. paleacea AMS transcriptome assembly, nucleotide sequences 
Supplementary File 2: M. paleacea AMS transcriptome assembly, predicted peptide sequences 
Supplementary File 3: Resolved unannotated gene trees for each orthogroup presented in Supplementary Table 4 


2. Relationship between files, if important: 

Discussed in point 1 


3. Additional related data collected that was not included in the current data package: 



4. Are there multiple versions of the dataset? yes/no yes

	A. If yes, name of file(s) that was updated: 

		i. Why was the file updated? newer versions of the data not updated but available on request

		ii. When was the file updated? newer versions of the data not updated but available on request


METHODOLOGICAL INFORMATION



1. Description of methods used for collection/generation of data: 

Read methods section of the associated PhD thesis' document


2. Methods for processing the data: 

Read methods section of the associated PhD thesis' document


3. Instrument- or software-specific information needed to interpret the data: 

Read methods section of the associated PhD thesis' document


4. Standards and calibration information, if appropriate: 

5. Environmental/experimental conditions: 

Marchantia paleacea adult (4 weeks) inoculated with R. irregularis crude inoculum or mock-inoculated with autoclaved incoulum


6. Describe any quality-assurance procedures performed on the data: 

Read methods section of the associated PhD thesis' document


7. People involved with sample collection, processing, analysis and/or submission: 

Mara Sgroi, Uta Paszkowski