Table 1.
General Features of Schizomeris and Other Sequenced Chlorophycean cpDNAs
| OCC Clade |
CS Clade |
|||||||
| Oedogoniales | Chaetopeltidales | Chaetophorales |
Chlamydomonadales |
Sphaeropleales | ||||
| Feature | Oc | Ft | Sh | Sl | Cr | Vca | Ds | So |
| Size (bp) | ||||||||
| Total | 196,547 | 521,168 | 223,902 | 182,759 | 203,827 | 461,064 | 269,044 | 161,452 |
| IR | 35,492 | —b | —b | —b | 22,211 | 15,948 | 14,409 | 12,022 |
| SC1c | 80,363 | —b | —b | —b | 81,307 | 227,676 | 127,339 | 72,440 |
| SC2d | 45,200 | —b | —b | —b | 78,088 | 200,100 | 112,887 | 64,968 |
| A + T (%) | 70.5 | 65.5 | 71.1 | 72.8 | 65.5 | 57.0 | 67.9 | 73.1 |
| Sidedness index | 0.74 | 0.91 | 0.95 | 0.97 | 0.87 | 0.83 | 0.86 | 0.88 |
| Conserved genes (no.)e | 99 | 97 | 97 | 98 | 94 | 94 | 94 | 96 |
| Introns | ||||||||
| Fraction of genome (%) | 17.9 | 3.4 | 10.9 | 13.4 | 7.0 | 4.4 | 10.3 | 7.9 |
| Group I (no.) | 17 | 19 | 16 | 24 | 5 | 3 | 21 | 7 |
| Group II (no.) | 4 | 7 | 5 | 9 | 2 | 6 | 2 | 2 |
| Intergenic sequencesf | ||||||||
| Fraction of genome (%) | 22.6 | 77.8 | 44.4 | 31.5 | 49.2 | 75.3 | 54.1 | 34.3 |
| Average size (bp) | 370 | 3,824 | 975 | 538 | 937 | 3,405 | 1,347 | 517 |
| Short repeated sequencesg | ||||||||
| Fraction of genome (%) | 1.3 | 49.9 | 17.8 | 1.2 | 16.8 | 45.5 | 8.6 | 3.0 |
NOTE.—Abbreviations: Oc, Oedogonium cardiacum, NC_011031 (Brouard et al. 2008); Ft, Floydiella terrestris, NC_014346 (Brouard et al. 2010); Sh, Stigeoclonium helveticum, NC_008372 (Bélanger et al. 2006); Sl, Schizomeris leibleinii, HQ700713 (this study); Cr, Chlamydomonas reinhardtii, NC_005353 (Maul et al. 2002); Vc, Volvox carteri, GU084820 (Smith and Lee 2010); Ds, Dunaliella salina, GQ250046 (Smith et al. 2010); So, Scenedesmus obliquus, NC_008101 (de Cambiaire et al. 2006).
Values provided for the Volvox cpDNA should be considered as estimates because some intergenic regions could not be entirely sequenced.
Because the Floydiella, Stigeoclonium, and Schizomeris cpDNAs lack an IR, only the total sizes of these genomes are given.
Single-copy region with the larger size.
Single-copy region with the smaller size.
Conserved genes refer to free-standing coding sequences usually present in chloroplast genomes. Genes present in the IR as well as others duplicated were counted only once.
ORFs < 130 codons showing no sequence similarity with known genes were considered as intergenic sequences.
Nonoverlapping repeated elements ≥30 bp were identified as described in the Materials and Methods.