Unraveling Unique Modes of Photosynthesis in Suaedoideae Using Genetic Networks Developed From Diverse Genomic and Transcriptomic Resources

Suaedoideae is the only known subfamily to contain single cell C₄, Kranz C₄ and C₃ photosynthetic type species. This provides a unique opportunity to investigate gene expression of photosynthetic processes, dimorphic chloroplast development and chloroplast/nuclear interaction. Lack of sequence information for the single cell C₄ species Bienertia sinuspersici and Suaeda aralocaspica, the C₄ Kranz Suaeda eltonica and the C₃ Suaeda maritima presented the opportunity to utilize the various capabilities of Life Science’s 454, Illumina’s HiSeq 2000 and Pacific Biosciences’ RS sequencing technologies to construct transcriptomes and chloroplast genomes. Genomic DNA was sequenced with PacBio RS and HiSeq 2000 and cDNA was sequenced with 454 and HiSeq 2000 technologies. Chloroplast genomes were assembled and annotated utilizing the sequence information from the PacBio RS and HiSeq2000 and transcriptomes were assembled and annotated from the sequence information from the 454 and HiSeq2000 technologies. Assembly was performed with DNAStar’s SeqMan NGen and CLC Bio’s Genomic Workbench. Genomes require technology that can deal with multiple repeats. The PacBio RS platform, with characteristic long reads, coupled with 454 and HiSeq 2000 reads performed well while chloroplast genomes could be built with HiSeq 2000 reads mapped to a related species alone. Information from Blast2GO annotations and enzyme mapping of the transcriptome data lead to indicators of gene interactivity. Read count data, obtained by mapping to the transcriptome, coupled with gene interactivity information set the foundation for construction of genetic networks by which comparative studies can be made in these diverse photosynthetic species.