| Transcription factor (TF) profiles have been used to define a "toolkit" for the lineage-specific developmental programs using comparative genomics. Land-plant genomes from moss to angiosperms share a "land-plant toolkit" of TF families, many presumably serving different functions in ancestral lineages before being recruited to mediate more complex decisions in land-plant development. We searched for 65 TF families, previously found in land plant genomes, in 5 green algal genomes within the division Chlorophyta: four Prasinophyceae genomes (Ostreococcus tauri, O. lucimarinus, Micromonas pusilla strains RCC299 and CCMP1545) and the Chlorophycean Chlamydomonas reinhardtii and the incomplete Volvox carteri genome, looking for patterns of TF loss and emergence. Of the 65 families, about half (34/65) are found in non-green organisms as well, including animal/fungal lineages, and therefore were likely present in a deeper eukaryotic common ancestor. The other half (31/65) are limited to the green lineage (Viridiplantae). Of these, 21 are limited to land plants and hence were either lost during the Chlorophycean radiations or else "invented" during the radiations leading to land plants. The remaining 10 TF gene families are found in both chlorophyte and land-plant genomes, although not equally distributed within these divisions, and do not appear elsewhere. Thus, we propose that these 10 families were components of the ancestral green toolkit and that their absence in certain radiations is the consequence of gene-family loss.
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