Additional file 4: of Genome-wide replication landscape of Candida glabrata

Additional experiment performed to confirm replication origins. The time course shown in this experiment was performed as described in “Methods” for the first experiment (Additional file 1). Top: FACS analyses and DNA content are shown. Time points T0 to T6 were sequenced on a MiSeq (Illumina) sequencer and 2.3–4.1 millions reads were obtained (175 bp single reads) for each time point. Bottom: Sequence coverage for time points T2, T3, T4, and T6, for each chromosome (smoothing span: 0.05–0.09, depending on chromosome size). Sequence mapping of two time points (T1 and T5) exhibited too many gaps to allow us to calculate non-linear regressions for each of the 12 millions nucleotides of the C. glabrata genome, in order to determine T50 values. However, using T6 and T0 coverage, which correspond respectively to S and G1 phases of the cell cycle, we were able to determine replication peak positions. A comparison of peaks detected in experiment #1 (Fig. 2) and experiment #2 (the present figure) was made in the bottom right table. Out of 83 bona fide origins, 73 were found in experiment #2 (88 %), and 241 replication origins were detected (instead of 253 in experiment #1). The average distance between bona fide replication peaks found in both experiments was 6.9 ± 2.4 kb (95 % confidence interval), consistent with what was deduced from comparisons between ARS positions and replication peaks (Fig. 5a). (PDF 1224 kb