A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C(4) photosynthesis within individual cells

BACKGROUND: The halophyte Suaeda aralocaspica performs complete C(4) photosynthesis within individual cells (SCC(4)), which is distinct from typical C(4) plants, which require the collaboration of 2 types of photosynthetic cells. However, despite SCC(4) plants having features that are valuable in engineering higher photosynthetic efficiencies in agriculturally important C(3) species such as rice, there are no reported sequenced SCC(4) plant genomes, limiting our understanding of the mechanisms involved in, and evolution of, SCC(4) photosynthesis. FINDINGS: Using Illumina and Pacific Biosciences sequencing platforms, we generated ∼202 Gb of clean genomic DNA sequences having a 433-fold coverage based on the 467 Mb estimated genome size of S. aralocaspica. The final genome assembly was 452 Mb, consisting of 4,033 scaffolds, with a scaffold N50 length of 1.83 Mb. We annotated 29,604 protein-coding genes using Evidence Modeler based on the gene information from ab initio predictions, homology levels with known genes, and RNA sequencing–based transcriptome evidence. We also annotated noncoding genes, including 1,651 long noncoding RNAs, 21 microRNAs, 382 transfer RNAs, 88 small nuclear RNAs, and 325 ribosomal RNAs. A complete (circular with no gaps) chloroplast genome of S. aralocaspica 146,654 bp in length was also assembled. CONCLUSIONS: We have presented the genome sequence of the SCC(4) plant S. aralocaspica. Knowledge of the genome of S. aralocaspica should increase our understanding of the evolution of SCC(4) photosynthesis and contribute to the engineering of C(4) photosynthesis into economically important C(3) crops.