Table 2 Statistics of predicted genes in P. cordatum and other dinoflagellates
From: Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
Species | Prorocentrum cordatum | Amphidinium gibbosuma | Polarella glacialis | Symbiodinium natans | Durusdinium trenchii | Cladocopium proliferum | Amoebophrya ceratii | |
|---|---|---|---|---|---|---|---|---|
Isolate | CCMP1329 | Not defined | CCMP1383 | CCMP2548 | CCMP2556 | SCF055; formerly C. goreaui [53] | AT5.2 | |
Reference | This study | Beedessee et al. [23] | Stephens et al. [39] | González-Pech et al. [21] | Dougan et al. [40] | Chen et al. [41] | John et al. [42] | |
Number of predicted genes | 85,849 | 85,139 | 58,232 | 35,270 | 55,799 | 45,322 | 19,925 | |
Recovery of BUSCO proteins (%) [protein mode; alveolata_odb10] | 61.4 | 45.0 | 70.2 | 74.9 | 69.6 | 82.4 | 86.5 | |
Genes with transcript support (%) | 84.8 | 75.9 | 94.0 | 83.0 | 75.7 | 82.5 | 24.4 | |
Average gene length (bp) | 24,462 | 26,201 | 16,206 | 8780 | 15,334 | 15,745 | 2772 | |
Average CDS length (bp) | 2798 | 1193 | 1230 | 1660 | 1647 | 2018 | 1964 | |
CDS GC-content (%) | 65.9 | 54.9 | 57.8 | 58.2 | 55.7 | 54.2 | 60.8 | |
Number of exons per gene | 11.7 | 8.0 | 11.6 | 15.7 | 16.7 | 17.2 | 3.4 | |
Average exon length (bp) | 239.9 | 184.8 | 105.7 | 106 | 98.7 | 120.4 | 578.7 | |
Genes with introns (%) | 83.7 | 92.7 | 73.8 | 85.5 | 93.1 | 95.9 | 71.3 | |
Number of introns per gene | 9.8 | 7.0 | 10.6 | 14.7 | 15.7 | 16.2 | 2.4 | |
Average intron length (bp) | 4709 | 3732 | 1408 | 486 | 869 | 839 | 377 | |
Splice donor motif (%) | GT | 24.7 | 74.9 | 28.8 | 23.6 | 30.3 | 36.6 | 99.9 |
GC | 51.4 | 25.0 | 52.7 | 58 | 52.3 | 43.6 | < 0.1 | |
GA | 23.8 | 0.1 | 18.5 | 18.4 | 17.4 | 19.8 | 0 | |
Splice acceptor with AGG motif (%) | 79.7 | 93.2 | 96.9 | 97.1 | 96.5 | 96.1 | 56.5 | |
Number of intergenic regions | 48,574 | 47,727 | 35,271 | 33,042 | 47,452 | 39,720 | 17,856 | |
Average length of intergenic regions (bp) | 26,278 | 26,756 | 21,625 | 11,585 | 13,222 | 7388 | 1522 | |