Table 1. Summary of the 13 analyzed Cyanidiales genomes.
The existing genomes of Galdieria sulphuraria 074W, Cyanidioschyzon merolae 10D, and Galdieria phlegrea are marked with ‘#'. The remaining 10 genomes are novel. Genome Size (Mb): size of the genome assembly in Megabases. Contigs: number of contigs produced by the genome assembly. The contigs were polished with quiver Contig N50 (kb): Contig N50. %GC Content: GC content of the genome given in percent. Genes: transcriptome size of species. Orthogroups: All Cyanidiales genes were clustered into a total of 9075 OGs. Here we show how many OGs there are per species. HGT Orthogroups: Number of OGs derived from HGT. HGT Genes: Number of HGT gene candidates found in species. %GC Native: GC content of the native transcriptome given in percent. %GC HGT: GC content of the HGT gene candidates given in percent % Multiexon Native: % of multiallelic genes in the native transcriptome. % Multiexon HGT: percent of multiallelic genes in the HGT gene candidates. S/M Native: Ratio of Multiexonic vs Singleexonic genes in native transcriptome. S/M HGT: Ratio of Multiexonic vs Singleexonic genes in HGT candidates. Asterisks (*) denote a significant difference (p<=0.05) between native and HGT gene subsets. EC, PFAM, GO, KEGG: Number of species-specific annotations in EC, PFAM, GO, KEGG.
| Strain | Genome features | Gene and OG counts | HGTs | HGT vs native gene subsets | Annotations | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genome Size (Mb) | Contigs | Contig N50 (kb) | %GC Content | Genes | Orthogroups | HGT orthogroups | HGT genes | %GC Native | %GC HGT | (%) Multiexon Native | (%) Multiexon HGT | Exon/Gene Native | Exon/Gene HGT | EC | PFAM | KEGG | GO | |
| G. sulphuraria 074W# | 13.78 | 433 | 172.3 | 36.89 | 7174 | 5265 | 51 | 55 | 38.99 | 39.62* | 73.6 | 47.3* | 2.25 | 3.2* | 938 | 3073 | 3241 | 6572 |
| G. sulphuraria MS1 | 14.89 | 129 | 172.1 | 37.62 | 7441 | 5389 | 54 | 58 | 39.59 | 40.79* | 83.4 | 62.1* | 2.5 | 3.88* | 930 | 3077 | 3178 | 6564 |
| G. sulphuraria RT22 | 15.62 | 118 | 172.9 | 37.43 | 6982 | 5186 | 51 | 54 | 39.54 | 40.85* | 74.7 | 51.9* | 2.63 | 3.95* | 941 | 3118 | 3223 | 6504 |
| G. sulphuraria SAG21 | 14.31 | 135 | 158.2 | 37.92 | 5956 | 4732 | 44 | 47 | 40.04 | 41.47* | 84.8 | 83.0 | 4.02 | 5.03* | 931 | 3047 | 3143 | 6422 |
| G. sulphuraria MtSh | 14.95 | 101 | 186.6 | 40.04 | 6160 | 4746 | 46 | 47 | 41.33 | 42.48* | 79.7 | 63.8* | 3.15 | 4.32* | 939 | 3114 | 3244 | 6450 |
| G. sulphuraria Azora | 14.06 | 127 | 162.3 | 40.10 | 6305 | 4905 | 49 | 58 | 41.34 | 42.57* | 84.5 | 75.9* | 2.68 | 4.03* | 934 | 3072 | 3181 | 6474 |
| G. sulphuraria YNP5587.1 | 14.42 | 115 | 170.8 | 40.05 | 6118 | 4846 | 46 | 46 | 41.33 | 42.14* | 74.5 | 54.3* | 2.61 | 3.65* | 938 | 3084 | 3206 | 6516 |
| G. sulphuraria 5572 | 14.28 | 108 | 229.7 | 37.99 | 6472 | 5009 | 46 | 53 | 39.68 | 40.5* | 78.4 | 45.3* | 2.15 | 3.53* | 936 | 3108 | 3252 | 6540 |
| G. sulphuraria 002 | 14.11 | 107 | 189.3 | 39.16 | 5912 | 4701 | 46 | 52 | 40.76 | 41.35* | 97.1 | 50.0* | 2.37 | 3.73* | 927 | 3060 | 3184 | 6505 |
| G. phlegrea DBV009# | 11.41 | 9311 | 2.0 | 37.86 | 7836 | 5562 | 54 | 62 | 39.97 | 40.58* | na | na | na | na | 935 | 3018 | 3125 | 6512 |
| G. phlegrea Soos | 14.87 | 108 | 201.1 | 37.52 | 6125 | 4624 | 44 | 47 | 39.57 | 40.73* | 77.5 | 43.2* | 2.19 | 3.33* | 929 | 3034 | 3197 | 6493 |
| C. merolae 10D# | 16.73 | 22 | 859.1 | 54.81 | 4803 | 3980 | 33 | 33 | 56.57 | 56.57 | 0.5 | 0.0 | 1 | 1.01 | 883 | 2811 | 2832 | 6213 |
| C. merolae Soos | 12.33 | 35 | 567.5 | 54.33 | 4406 | 3574 | 34 | 34 | 54.84 | 54.26 | 9.4 | 2.9 | 1.06 | 1.1 | 886 | 2787 | 2823 | 6188 |