Reconstructing the Ancestral Gene Set of Bryophytes from Comparative Transcriptome Data

Transcriptome data generated for the 1KP Project has greatly increased the genomic resources for non-model organisms, especially bryophytes. Protein orthology in the 1KP Project does not account for gene families that are restricted to specific clades if the ortholog in a reference genome is single-copy. We describe a process for identifying valid protein families that are unique to bryophytes but absent in the sequenced genomes of the moss Physcomitrella and the liverwort Jungermannia. Reclustering of proteins not previously sorted into orthogroups reveals thousands of gene families that may be unique to the bryophytes among land plants. By identifying orthologous proteins across many species, we can rule out contamination and distinguish ancient gene families that have been lost in model species from novel gene families restricted to specific clades. Using these orthogroups we explore patterns of gene family expansion and loss of ancestral gene families within bryophytes with a focus on identifying gene families that may have originated through horizontal transfer from bacteria or fungi.