ABSTRACT: Purpose: RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. Methods: mRNA profiles of Aureococcus anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed by aligning to reference genome and transcript using SOAPaligner/SOAP2 (version 2.21). Results: Deconvolution and filtering of raw reads yielded a mean of 6,938,798 reads (range: 6,539,842 to 7,242,083 reads) per individual RNA-seq library (Table 1). Subsequent alignment of the clean reads to the A. anophagefferens reference genome yielded a mean of 5,852,408 reads (84.3%) for each sample that mapped to at least one location in the A. anophagefferens genome. However, of these mapped reads, only 47.4 to 50.9% of the total reads were mapped to the reference transcript for each sample (Table 2). In A. anophagefferens grown on three different N sources, 9148 to 9526 genes were detected for each sample. A comparison of gene expression among the three N sources was performed. 322 differentially expressed genes were detected between nitrate-grown and urea-grown cells, 237 between nitrate-grown and mixture N-grown cells and 29 between urea-grown and mixture N-grown cells. Fewer differentially expressed genes between urea-grown and mixture N-grown cells were identified, which further suggested the preferred utilization of cells for urea in media with mixture N. For nitrogen-limited and recovery experiments, 707 genes were up-regulated significantly, and 766 were down-regulated significantly in N-depleted cells relative to N-replete cells. N-depleted cells exhibited a broad transcriptional response to nitrogen re-addition, with 681 genes up-regulated and 874 genes down-regulated in urea recovery cells, and 312 genes up-regulated and 688 genes down-regulated in nitrate recovery cells. Conclusions: We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. Seven mRNA samples for Aureococcus anophagefferens were sequencd using Illumina HiSeqTM 2000, including three samples that was grown on urea, nitrate, and a mixture of urea and nitrate, and four samples that was under N-replete, limited and recovery conditions
