The second-strand cDNA was
synthesized with DNA polymerase I. Short fragments were purified with QiaQuick PCR extraction kit (Qiagen), and then were sequenced under the Illumina HiSeq™ 2000 platform at Shenzhen BGI. The full sequencing technical details can be inspected in the services of BGI (http://www.genomics.cn). This yielded approximately six million 90-bp pair-end reads for each sample (Table 1). Then pair-end reads were mapped to the Prochlorococcus MED4 genome (accession number: NC_005072) using Bowtie2 [60] with at most one mismatch. The coverage of each nucleotide was calculated by counting the number of reads mapped at corresponding nucleotide AZD8931 manufacturer positions in the genome. The number of reads that were perfectly mapped to a gene region was calculated using BEDTools [61], and then it was normalized by gene length and total mapped Nutlin3a reads, Epigenetics inhibitor namely RPKM as the gene expression value [26]. The gene annotations for Prochlorococcus MED4 were downloaded from MicrobesOnline [62] with modifications for non-annotated
genes that were designated “HyPMM#”. New ORFs identified in this study were annotated with “TibPMM#” (Sheet 2 of Additional file 3). Sequences generated by this study are available in the Gene Expression Omnibus (GEO) under accession number GSE49517. Identification of operons and UTRs Using a priori knowledge of the translation start and stop site from Additional file 3, the coverage of ORF upstream and downstream regions was scanned to identify a point of sharp coverage
decline. To define the boundary, we applied criteria modified from Vijayan et al.[24]. Briefly, a transcript’s boundary (translation start or stop site was defined as i = 0, and “i + 1” is the upstream or downstream of position “i”) was defined when position “i” satisfied one of the following three criteria: (1) coverage(i)/coverage(i + 1) ≥ 2, binomialcdf (coverage(i + 1), coverage(i) + coverage(i + 1), 0.5) < 0.01 and coverage(i + 1) > coverage(i:(i-89))/(90 × 7); (2) tuclazepam coverage(i)/coverage(i + 1) ≥ 5 or coverage(i)/coverage(i + 2) ≥ 5, and coverage(i + 1) < coverage(i:(i-89))/(90 × 7); (3) coverage(i + 1) ≤ background. Where binomialcdf (x, n, p) is the probability of observing up to x successes in n independent trials when success probability for each trial is p. We assumed reads were uniformly distributed on position “i” and “i + 1” (p = 0.5). If a sharp coverage reduction occurred, coverage(i + 1) would be much smaller than coverage(i); that was, the success of coverage(i + 1) became a small probability event in the events of all reads mapped to “i” and “i + 1” (binomialcdf < 0.01). The strictest criterion (1) was used for highly transcribed genes.