Table 1.
Genome Assembly and Annotation Statistics for the Nine Assembled Clownfish Species and Pomacentrus moluccensis
| De Novo Assembly |
Reference-Guided Assembly |
|||||
|---|---|---|---|---|---|---|
| Amphiprion ocellaris | A. ocellaris | A. bicinctus | A. nigripes | A. polymnus | A. sebae | |
| Total assembly size (Mb) | 744 | 798 | 799 | 800 | 800 | 799 |
| Number of scaffolds | 27,951 | 16,543 | 16,953 | 16,995 | 17,050 | 16,941 |
| N50 (bp) | 136,417 | 246,482 | 246,127 | 246,124 | 246,119 | 245,870 |
| non-ATGC characters (%) | 4.6 | 3.6 | 2.8 | 2.7 | 2.7 | 2.9 |
| Paired-ends mapping rate (%) | 95.3 | 98.2 | 98.9 | 98.9 | 99.0 | 99.0 |
| Number of genes | 24,383 | 29,913 | 28,891 | 28,558 | 28,640 | 28,727 |
| Number of proteins | 27,606 | 33,845 | 33,219 | 32,905 | 33,128 | 33,271 |
| Functional annotated proteins (%) | 94.0 | 92.7 | 93.2 | 93.1 | 92.9 | 92.9 |
| CEGMA genes in assembly (%) | 97.2 | 99.6 | 99.6 | 99.6 | 99.6 | 100 |
| BUSCOs genes in annotation (%) | 87 | 93 | 94 | 95 | 95 | 95 |
|
Reference-guided assembly |
||||||
| A. akallopisos | A. perideraion | A. melanopus | P. biaculeatus | P. moluccensis | ||
| Total Assembly Size (Mb) | 801 | 801 | 803 | 797 | 794 | |
| Number of scaffolds | 17,172 | 17,212 | 17,399 | 16,164 | 15,505 | |
| N50 (bp) | 246,052 | 246,037 | 245,703 | 247,121 | 246,470 | |
| non-ATGC characters (%) | 1.9 | 2.0 | 1.4 | 2.9 | 7.9 | |
| Paired-ends mapping rate (%) | 99.0 | 99.0 | 97.4 | 96.9 | 81.2 | |
| Number of genes | 28,730 | 29,014 | 29,408 | 28,170 | 28,885 | |
| Number of proteins | 33,120 | 33,320 | 33,768 | 32,385 | 32,027 | |
| Functional annotated proteins (%) | 93.1 | 92.9 | 92.7 | 93.8 | 94.0 | |
| CEGMA genes in assembly (%) | 99.6 | 99.6 | 99.6 | 99 | 99.6 | |
| BUSCOs genes in annotation (%) | 95 | 94 | 94 | 95 | 89 | |
Note.—For A. ocellaris, statistics of both de novo and reference-guided assemblies are reported. Reference-guided assemblies were obtained using A. frenatus (Marcionetti et al. 2018) as reference genome. N50 index indicates the shortest scaffold length above which 50% of the genome is assembled. CEGMA and BUSCOs genes represent the completeness of the genome assemblies and annotations, respectively.