The Viridiplantae then branched into the Chlorophyta or green algae, which include the Volvocales (e.g., Chlamydomonas this website and Volvox) and Prasinophytes (e.g., Ostreococcus and Micromonas), and the lineage that gave rise to the Spermatophyta (angiosperms, gymnosperms, bryophytes); this divergence occurred over 1 billion years ago. Genes

common to the genomes of the Chlorophyta and Spermatophyta can be traced to the Viridiplantae ancestor of these lineages; a subset of genes in this category would be involved in photosynthesis and chloroplast function. This subset could potentially be identified by comparative genomic analyses. Mining Chlamydomonas genomic sequence information A comparative analysis Small molecule library was performed in which all predicted Chlamydomonas proteins (predicted from gene models) were compared against both Arabidopsis and human protein sequences using BLAST, and the best hit scores for each Chlamydomonas protein relative to the two genomes was

shown in the analysis presented in Fig. 4 in the manuscript by Merchant et al. (2007). Some subsets of Chlamydomonas proteins were more similar to those of Arabidopsis, while others were more similar to those of humans. For example, Chlamydomonas thylakoid and stromal proteins, many of which are associated with photosynthetic function, were significantly more similar to polypeptides in Arabidopsis than to those in humans, as expected. Hence, some specific processes, including photosynthesis,

have been preserved in Chlamydomonas and Arabidopsis but not in humans (animal lineage). In contrast, genes encoding proteins associated with the structure and function of Chlamydomonas flagella have been preserved in humans and other mammals, but not in seed plants. These observations indicate that the common ancestor to Chlamydomonas and Spermatophyta was ciliated, like animal cells. However, the cilia and the genes associated with their structure and assembly were lost during the evolution of the seed plants (Merchant et al. 2007). Researchers can now integrate the power of full genome sequence analyses with the wealth of information amassed over the past several decades on photosynthetic Non-specific serine/threonine protein kinase and acclimation processes. The genomic information can be used to identify those genes present on the Chlamydomonas genome that encode proteins specifically associated with the green plant lineage; such proteins have been placed into an assemblage designated the “GreenCut” (Merchant et al. 2007; Grossman et al. 2010). Various analyses of GreenCut proteins and levels of transcripts encoding those proteins are providing new insights into their potential functions. Specific informatic tools have helped determine whether individual GreenCut proteins have a presequence that predicts their subcellular location.