For dataset 1, the files included here are: • 76_GUN1.alignment.fasta — FASTA format file containing aligned GUN1 sequences from 76 phylogenetically diverse land plants • 76_GUN1. conserved_region.alignment.fasta — FASTA format file containing aligned GUN1 sequences (central conserved region only) from 76 phylogenetically diverse land plants; corresponds to the alignment shown in Figure 1. • GUN1.hmm — Hidden Markov model profile generated by hmmbuild using the 76 GUN1 sequences in 76_GUN1. conserved_region.alignment.fasta • GUN1s.domt — ‘domain table’ output from hmmsearch listing the GUN1 profile matches found in the 76 GUN1 sequences • taxonomy.csv — CSV file with taxonomical metadata on 1KP samples needed to run the analyses in GUN1 classification.ipynb • GUN1 classification.ipynb — Jupyter notebook (Julia code) used to identify GUN1 sequences from the 1KP dataset and to generate Fig. S2 and Table S2 • 893_GUN1.alignment.fasta — FASTA format file containing 893 aligned GUN1 sequences (includes both those found in the 1KP dataset, which are often partial sequences, and the 76 full-length sequences from 76_GUN1.alignment.fasta) For dataset 2, the files included here are: • Mpdata_spec.csv — table of read counts extracted from Salmon output. Gene_ID column contains gene IDs corresponding to the MpTak_v6.1 reference genome. Columns M1 to M12 contain the read count data for each biological replicate transcriptome. Transcriptomes M1 to M3 were from wild type spores grown on control media, M4 to M6 were from wild type spores grown on spectinomycin-containing media, M7 to M9 were from gun1 mutant spores grown on control media and M10 to M12 were from gun1 mutant spores grown on spectinomycin-containing media. • MpTak1_v5.1r2_func_annotation_1line.csv - Functional annotations for MpTak_v5.1 genome release used to identify M. polymorpha photosynthesis-associated nuclear genes. This file was downloaded from https://marchantia.info/download/MpTak1_v5.1r2/ • mp_sample_table — text file containing experimental design used for identifying differentially expressed genes (supplemental table S3 from the paper) • mp_sample_table2 — text file containing experimental design used for making Figure 7a • RNAseq_WT_gun1_spores_spec.ipynb — Jupyter notebook (Python code) to reproduce supplemental table S3 from the paper — DEseq2 analysis identifying differentially expressed genes between all genotype and treatment combinations using the salmon quants (Mpdata_spec.csv). Requires Python packages pandas, numpy, matplotlib, seaborn and diffexpr (https://github.com/wckdouglas/diffexpr). • Figure_7a.ipynb — Jupyter notebook (Python code) to reproduce Figure 7a from the paper using the salmon quants (Mpdata_spec.csv). Requires Python packages pandas, numpy, matplotlib, seaborn and diffexpr (https://github.com/wckdouglas/diffexpr).