A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells.

BACKGROUND: The halophyte Suaeda aralocaspica performs complete C4 photosynthesis within individual cells (SCC4), which is distinct from typical C4 plants, which require the collaboration of 2 types of photosynthetic cells. However, despite SCC4 plants having features that are valuable in engineering higher photosynthetic efficiencies in agriculturally important C3 species such as rice, there are no reported sequenced SCC4 plant genomes, limiting our understanding of the mechanisms involved in, and evolution of, SCC4 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 SCC4 plant S. aralocaspica. Knowledge of the genome of S. aralocaspica should increase our understanding of the evolution of SCC4 photosynthesis and contribute to the engineering of C4 photosynthesis into economically important C3 crops.

Grape seed proanthocyanidins inhibit proliferation of pancreatic cancer cells by modulating microRNA expression.

MicroRNAs (miRNAs) are small non-coding RNAs of 18-25 nucleotides that modulate gene expression at the post-transcriptional level. Grape seed proanthocyanidins (GSPs), which are biologically active components in grape seeds, have been demonstrated to exhibit anticancer effects. The current study investigated whether GSPs can regulate miRNA expression and the possible anticancer molecular mechanisms of GSPs. Pancreatic cancer (PC) cell samples, SS3, SS12 and SS24, were treated with 20 µg/ml GSPs for 3, 12 and 24 h, respectively. Control samples, SC3, SC12 and SC24, were also prepared. Using miRNA-seq, transcriptome analysis identified 24, 83 and 83 differentially expressed (DE) miRNAs in SS3 vs. SC3, SS12 vs. SC12 and SS24 vs. SC24, respectively. This indicated that treatment with GSPs could modulate the expression of miRNAs. Subsequently, 74, 598 and 1,204 target genes for the three sets of DE miRNAs were predicted. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that multiple target genes were associated with the proliferation and apoptosis of PC cells. In addition, a network was constructed of the DE miRNAs and the target genes associated with PC. The associations identified suggested that treatment with GSPs may inhibit the proliferation of PC cells through the modulation of miRNA expression.