Table 1.
General features of the prasinophyte cpDNAs compared in this study
| Taxon | Size | Introns b | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Name | Label | Total (bp) | IR (bp) | A + T (%) | Genes a | GI | GII | Intergenic c(%) | Repeats d(%) |
| Clade VI | |||||||||
| Prasinococcus sp. CCMP 1194 | PCUS | 85,590 | 67.9 | 115 | 14.3 | 0.9 | |||
| Prasinophyceae sp. MBIC 106222 | MBIC | 72,423 | 62.1 | 103 | 13.4 | 1.1 | |||
| Prasinoderma coloniale CCMP 1220 | PRMA | 77,750 | 65.9 | 106 | 16.0 | 0.4 | |||
| Clade I | |||||||||
| Pyramimonas parkeae CCMP 726 | PYRA | 101,605 | 13,057 | 65.3 | 110 | 1 | 22.4 | 0.5 | |
| Clade II | |||||||||
| Micromonas sp. RCC 299 | MICR | 72,585 | 7,307 | 61.2 | 86e | 19.0 | 0 | ||
| Monomastix sp. OKE-1 | MONO | 114,528 | 61.0 | 94 | 5 | 1 | 44.6 | 16.9 | |
| Ostreococcus tauri | OSTR | 71,666 | 6,824 | 60.1 | 88 | 1 | 15.1 | 0 | |
| Clade III | |||||||||
| Nephroselmis astigmatica NIES 252 | NAST | 125,042 | 13,742 | 59.5 | 123 | 2 | 18.6 | 0.3 | |
| Nephroselmis olivacea NIES 484 | NOLI | 200,801 | 46,137 | 57.9 | 128f | 45.6 | 0.5 | ||
| Clade V | |||||||||
| Pycnococcus provasolii CCMP 1203 | PYCN | 80,211 | 60.5 | 99g | 1 | 14.0 | 0 | ||
| Clade VII | |||||||||
| Picocystis salinarum CCMP 1897 | PICO | 81,133 | 10,364 | 62.7 | 114 | 1 | 9.2 | 0 | |
| Prasinophyceae sp. CCMP 1205 | 1205 | 64,335 | 63.3 | 100 | 10.0 | 0 | |||
aDuplicated genes were counted only once.
bNumber of group I (GI) and group II (GII) introns is given.
cOnly the ORFs coding for proteins of known functions or having recognized domains were considered as genes.
dNonoverlapping repeat elements were mapped on each genome with RepeatMasker [70] using the repeats ≥30 bp identified with REPuter [69] as input sequences.
eThis value is probably an underestimate because the genome sequence appears to be incomplete and missing three genes (see the legend of Figure 4).
fThe ycf20 pseudogene, which corresponds to the annotated orf111, was not counted.
gThis value differs from that reported previously [25] because an additional gene, rrf (coordinates 33313–33429 in [GenBank:NC_012097]), was identified using RNAmmer [64] in the course of this study.