Table S3.
Cleaning of RNA-seq reads, and mapping of clean reads to the P. placenta genome
| Samples* | Reads before trimming | Clean paired reads† | Concordant pair alignment rate,‡ % | Multiple alignments | Discordant alignments |
| 0–5 mm_0 | 30,753,156 | 29,884,512 (97.18%) | 87.0 | 5,777,018 (21.9%) | 424,076 (1.6%) |
| 0–5 mm_1 | 28,731,524 | 27,999,535 (97.45%) | 86.3 | 5,587,014 (22.8%) | 377,835 (1.5%) |
| 0–5 mm_2 | 31,600,067 | 30,805,100 (97.48%) | 86.8 | 5,961,761 (21.9%) | 439,525 (1.6%) |
| 15–20 mm_0 | 31,077,840 | 30,304,779 (97.51%) | 87.7 | 6,435,079 (23.8%) | 435,145 (1.6%) |
| 15–20 mm_1 | 28,128,765 | 27,433,981 (97.53%) | 87.2 | 5,784,636 (23.8%) | 382,660 (1.6%) |
| 15–20 mm_2 | 31,365,488 | 30,531,214 (97.34%) | 87.2 | 6,422,959 (23.7%) | 426,672 (1.6%) |
| 30–35 mm_0 | 29,726,771 | 28,927,543 (97.31%) | 86.4 | 6,403,817 (25.2%) | 390,088 (1.5%) |
| 30–35 mm_1 | 29,527,548 | 28,787,751 (97.49%) | 87.1 | 6,143,924 (24.1%) | 390,410 (1.5%) |
| 30–35 mm_2 | 32,265,990 | 31,454,831 (97.49%) | 86.5% | 6,801,996 (24.6%) | 448,067 (1.6%) |
The reference genome of P. placenta MAD 698-R v1.0 was used in this work (genome.jgi.doe.gov/Pospl1/Pospl1.home.html).
*
The 0, 1, and 2 represent three bioreplicates.
†
Clean reads were obtained after trimming with Trimmomatic (v0.3 in Galaxy platform through University of Minnesota).
‡
The cleaned reads were mapped against the genome of P. placenta MAD 698-R (v1.0) (Postia_placenta.fasta) with Tophat (v2.0.13) (methods are provided in SI Materials and Methods).