README

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.

Species abbreviations

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