Table 1. Identification of mRNAs translated after fertilization from RNA-Seq analysis of polysomal mRNAs. Each mRNA, associated with a transcript ID from the de novo assembly of the maternal transcriptome, is identified by its best BLASTn hit against a Strongylocentrotus purpuratus gene model (Echinobase; http://echinobase.org; (19,20)). The mRNA translation index (log2FC(F/Fpuro)) and its polysome fractions after fertilization (log2FC(F/UnF)) are indicated with their respective adjusted P-values (padj). Abundance of the transcript is expressed as fragments per kilobase million (FPKM). The mRNAs further verified in the polysome gradient analysis in Supplementary Figures S1C and S3 are shown in bold. The full translatome dataset is presented in Supplementary data 2.
| Transcript ID | Gene | F_vs_UnF | F_vs_Fpuro | FPKM | SPU best BLAST Hit | ||
|---|---|---|---|---|---|---|---|
| logFC | padj | logFC | padj | ||||
| Cell-cycle related genes | |||||||
| comp77341_c2_seq1 | Cyclin B | 2.964 | 2.14E-19 | 1.631 | 2.33E-07 | 3202.66 | SPU_015285 |
| comp80046_c1_seq2 | Ribonucleotide reductase small subunit R2 | 2.645 | 1.67E-12 | 1.195 | 7.15E-04 | 4679.83 | SPU_024933 |
| comp76547_c0_seq2 | Regulator of chromosome condensation 1 RCC1 | 2.426 | 9.07E-17 | 1.687 | 2.51E-09 | 103.06 | SPU_023992 |
| comp79240_c1_seq1 | Cyclin A | 2.339 | 5.65E-13 | 1.513 | 1.81E-06 | 649.47 | SPU_003528 |
| comp69502_c0_seq1 | 14–3-3 epsilon | 2.223 | 1.96E-10 | 0.864 | 1.17E-02 | 64.30 | SPU_003825 |
| comp79495_c0_seq1 | Cyclin dependent kinase 1 CDK1 | 1.583 | 8.41E-07 | 1.933 | 8.15E-10 | 62.15 | SPU_002210 |
| comp78419_c0_seq1 | Early mitotic inhibitor EMI1 | 1.417 | 2.56E-05 | 0.953 | 4.28E-03 | 14.66 | SPU_008889 |
| comp78987_c0_seq3 | DNA-replication factor cdt1 | 1.393 | 5.09E-07 | 1.192 | 1.30E-05 | 72.55 | SPU_002046 |
| comp77014_c0_seq1 | Polo-like kinase 1 PLK1 | 1.342 | 1.22E-06 | 1.033 | 1.51E-04 | 77.47 | SPU_017949 |
| comp79482_c0_seq1 | Cyclin B3 | 1.071 | 3.16E-04 | 1.400 | 1.25E-06 | 190.16 | SPU_006444 |
| comp79997_c3_seq5 | Geminin | 0.970 | 1.73E-03 | 1.211 | 5.63E-05 | 150.56 | SPU_005762 |
| comp79170_c0_seq2 | Cell division control protein 6 cdc6 | 0.944 | 5.07E-03 | 1.482 | 6.35E-06 | 154.35 | SPU_010595 |
| Maternal determinant of developmental patterning | |||||||
| comp77921_c0_seq1 | Gustavus | 2.582 | 2.03E-13 | 1.533 | 5.46E-06 | 75.98 | SPU_004717 |
| comp79094_c0_seq1 | Alk2 | 2.474 | 1.01E-12 | 1.859 | 2.63E-08 | 17.77 | SPU_016008 |
| comp76027_c0_seq8 | Transforming growth factor beta Univin | 2.311 | 1.16E-11 | 1.799 | 7.47E-08 | 18.28 | SPU_000668 |
| comp77686_c1_seq1 | SoxB1 | 1.713 | 3.74E-06 | 1.700 | 1.87E-06 | 1320.41 | SPU_022820 |
| comp73990_c1_seq1 | Beta-catenin | 1.490 | 1.49E-04 | 1.172 | 2.00E-03 | 194.50 | SPU_009155 |
| comp79158_c0_seq1 | Smad4 | 1.447 | 2.21E-06 | 1.401 | 3.58E-06 | 14.88 | SPU_004287 |
| comp79473_c0_seq3 | Transforming growth factor beta receptor | 1.131 | 1.64E-03 | 1.284 | 3.16E-04 | 6.38 | SPU_027380 |
| RNA-binding proteins (RNA-BPs) | |||||||
| comp70206_c1_seq4 | RBM4 | 3.427 | 3.15E-16 | 1.597 | 3.84E-05 | 100.80 | SPU_022878 |
| comp76265_c0_seq4 | Histone RNA hairpin-binding protein SLBP | 2.121 | 3.72E-08 | 1.246 | 8.67E-04 | 62.95 | SPU_009593 |
| comp68546_c0_seq1 | hnRNP K | 1.849 | 2.21E-09 | 1.666 | 3.54E-08 | 90.53 | SPU_008011 |
| comp66342_c1_seq4 | DAZAP Musashi | 1.757 | 6.76E-08 | 1.294 | 3.29E-05 | 85.10 | SPU_024306 |
| comp79981_c0_seq9 | CUG-BP | 1.401 | 3.26E-07 | 1.189 | 1.24E-05 | 7.74 | SPU_015850 |
| comp62631_c0_seq1 | hnRNP A | 1.191 | 2.06E-04 | 1.825 | 6.83E-09 | 115.70 | SPU_015676 |
| comp78371_c0_seq1 | Nova | 1.103 | 2.74E-04 | 1.592 | 8.14E-08 | 10.04 | SPU_003114 |
| comp76987_c1_seq1 | RKHD/Pem-3/Mex3B homolog | 1.072 | 4.34E-04 | 1.164 | 9.54E-05 | 854.27 | SPU_003290 |
| Translation regulation | |||||||
| comp73250_c0_seq1 | eIF4E binding protein Neuroguidin | 1.862 | 3.19E-04 | 1.366 | 6.29E-03 | 4.79 | SPU_019210 |
| comp78490_c0_seq1 | Termination factor eRF1 | 1.376 | 1.55E-05 | 1.847 | 1.61E-09 | 11.40 | SPU_023948 |
| comp79103_c1_seq1 | DAP5 | 1.339 | 4.26E-04 | 1.398 | 1.68E-04 | 87.12 | SPU_023932 |
| comp64074_c0_seq1 | Initiation factor eIF6 | 1.267 | 2.71E-02 | 1.554 | 4.25E-03 | 7.94 | SPU_012909 |
| comp78411_c2_seq1 | eIF4B | 1.111 | 6.02E-04 | 0.958 | 2.71E-03 | 94.72 | SPU_004840 |