File and code repository for the analysis of RNA-seq data of Fragaria x ananassa using Kallisto [1] and the new reference genome v1.0.a2 [2]
All the files containing the code used to carry on the analysis. Both .ipynb notebooks where made and used with Google Colab in mind so they should be perfectly reusable unless some Colab update breaks them
Reads_processing was used to download, asses, process, quantify and save all the transcriptomics data from the ENA accession PRJEB12420 [3]. It also has Google Drive functionality in case we want the final data to be saved there.
LAST_homeolog.ipynb was used to determine the posible list of homeolog tetrads between all the subgenomes of Fragaria x ananassa. It uses LAST [4] and other scripts [5]
DEG_homeolog_analysis.Rmd is an Rmarkdown script with all the code used to do the differential expression analysis, as well as some file processing for the Gene set enrichment analysis and the analysis of homeolog bias which can be found in the homeolog sheet in Comparisons.xlsx. This script uses both files coldata.txt and GOfragaria.txt to carry on some of these functions.
Comparisons.xlsx contains the aggregated data on some of the main comparisons carried out. Mainly, comparing the results of number of differentially expressed genes between the analysis carried out with kallisto, and the one carried out with featureCounts [2]. There is also data on the homeolog bias selection between conditions using statistical tests to determine wether there is differences.
Lists of the diferentially expressed genes in each condition with their respectives GO identitificators. These lists were made using some of the code in DEG_homeolog_analysis.Rmd and the GOfragaria.txt file
Files containing the CDS of Fragaria x ananassa classified by subgenome.
The file homeolog.ABCD.list is the result from the script in LAST_homeolog.ipynb, the file homeolog_clean.ABCD.list is the one used in the script DEG_homeologs_analysis.Rmd
High resolution images obtained from AgriGOv2.0 [6] for gene set enrichment of differentially expresed genes. Genes from each set with their GO ID can be obtained from the DEG annotated folder
Image name codes follow the pattern: Condition1Condition2 + tissue + geneset
Condition1Condition2 refers to which 2 conditions where being contrasted while doing the differential expression analysis (ie: WG means the stages that were being compared were White vs Green)
tissue refers to the plant tissue the samples were obtained from
geneset refers to the set of genes of each comparison, either up-regulated genes or down-regulated
Thus, the image with the code WGAup refers to the gene set enrichment of upregulated genes in achenes between the white and green stages.
- Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525-527.
- Liu, T., Li, M., Liu, Z., Ai, X., & Li, Y. (2021). Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture research, 8(1), 1-9.
- Sánchez-Sevilla, J. F., Vallarino, J. G., Osorio, S., Bombarely, A., Posé, D., Merchante, C., ... & Valpuesta, V. (2017). Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria× ananassa). Scientific reports, 7(1), 1-13.
- https://gitlab.com/mcfrith/last
- Kuo, T., Frith, M. C., Sese, J., & Horton, P. (2018). EAGLE: explicit alternative genome likelihood evaluator. BMC medical genomics, 11(2), 1-10.
- Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., ... & Su, Z. (2017). agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic acids research, 45(W1), W122-W129.