Orthogroup Identification and Enrichment Patterns

Orthologous genes across a subset of 19 land plant species were analyzed to identify gene families that are expanded in desiccation tolerant lineages. The gene family analysis included nine monocot (Ananas comosus, Brachypodium distachyon, Oryza sativa, Oropetium thomaeum, Panicum virgatum, Sorghum bicolor, Setaria italic, Xerophyta viscosa, Zostera marina), six eudicot (Lindernia brevidens, Lindernia subracemosa, Arabidopsis [Arabidopsis thaliana], Medicago truncatula, Solanum lycopersicum, Vitis vinifera), two bryophyte (Marchantia polymorpha and Physcomitrella patens), and two lycophyte genomes (Selaginella lepidophylla and Selaginella moellendorffii). This includes three desiccation-tolerant angiosperms and two bryophytes with ABA-induced desiccation tolerance. The predicted protein sequences for each species were first clustered into orthologous groups using Orthofinder (v2.2.6; Emms and Kelly, 2015). Diamond (v0.9.24; Buchfink et al., 2015) was used to conduct pairwise protein alignments, and all other parameters were set to defaults. The resulting 26,406 orthogroups were filtered to include only the 4,625 groups with at least one ortholog in all 19 species. For each orthogroup, the following values were calculated: the proportion of genes in that orthogroup among the 7 desiccation-tolerant plants, the proportion of genes in that orthogroup among the 14 DS plants, and the combined proportion using the following formulas:

The two proportions were then compared using a z-score calculated as follows:

A 1-sided hypothesis test was calculated by comparing the Z-score to a normal distribution. The resulting p-value was then adjusted using the Benjamini and Hochberg procedure (Benjamini and Hochberg, 1995) to obtain q-values. Orthogroups with a q-value of less than 0.05 were considered to be significantly enriched.