Genomics and Transcriptomics of Algae and Plants

Advances in sequencing technologies have permitted recently the investigation of complete plant genomes and the full complement of mRNAs produced by these genomes. In this work, the predicted proteomes of plant genomes were compared to identify proteins conserved within the plant lineage. An inventory of 597 proteins that is found in plants but not non-photosynthetic organisms was defined as the 'GreenCut2'. Sets of transcript and protein data were subjected to a meta-analysis to infer function for proteins of unknown function. While the majority of the GreenCut2 proteins are localized to plastids and the associated mRNAs are expressed in green tissues, some GreenCut2 proteins are involved in plant-specific processes independent of the plastid or photosynthetic metabolism. Additionally, newly sequenced plant genomes present the opportunity to discover new or dispensable facets of plant biochemistry, and so the genomes of the algae Porphyra umbilicalis and Asterochloris sp. Cgr/DAlpho were surveyed for proteins involved in processes such as photosynthesis and metal metabolism. The Porphyra genome was found to encode a full complement of metal transporters, while also encoding red plant-specific photosynthetic apparatus proteins. Asterochloris was also found to encode a standard set of metal transporters. Finally, transcriptome data acquired by RNA-seq methodology allows unprecedented depth of coverage of expressed mRNAs, which permitted improvements of over 100 gene models within the genome and subsequent searches for promoter elements. Biochemical pathways were also described at the level of mRNA abundance, indicating similar abundances for transcripts within the same pathway.