This is a GitHub repository associated with the manuscript "Timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae)" by K. Heyduk, E. McAssey, and J. Leebens-Mack. You can find the current version of BioRxiv: https://biorxiv.org/cgi/content/short/2021.11.10.468112v1
Description of data and directories:
- OrthoFinder - contains the OrthoFinder results, including separate text files for each of the 8 Agavoideae species, as well as the full .tsv output of the OrthoFinder orthogroup assignment. The latter file includes non-Agavoideae species used in the analysis.
- PPC evolution - contains fasta files (cds, amino acid, and cds aligned via Pal2Nal) for PPC1 and PPC2. Also contains newick files for PPC1 and PPC2 gene trees.
- RNAseq count matrices - contains the raw counts from RNAseq of the 8 focal Agavoideae species. Output of Kallisto.
- TPM matrices - contains the TPM values from RNAseq of the 8 focal Agavoideae species. Output of Kallisto.
Abbreviations were commonly used in files and filenames as follows:
- Agave bracteosa: agave, ag
- Beschorneria yuccoides: besch, be
- Polianthes tuberosa: poli, po
- Hesperaloe nocturna: heno, hn
- Hesperaloe parviflora: hepa, hp
- Hosta venusta: hove, ho
- Yucca aloifolia: ya
- Yucca filamentosa: yf