Figure 4

Differences between the chloroplast gene repertoires displayed by prasinophytes and the deep-branching streptophytes Mesostigma viride and Chlorokybus atmophyticus . The conserved genes missing in one or more prasinophyte genome as well as the six conserved genes found in Mesostigma and/or Chlorokybus but absent from all prasinophytes are indicated in the figure; the streptophyte-specific genes are denoted by filled circles. The presence of a gene is indicated by a dark blue box and the presence of a pseudogene by a light blue box. Species names are abbreviated as in Table 1. Although rpl36, trnH (gug) and trnV (uac)) are recorded as missing in Micromonas, all three genes are probably present because three lines of evidence suggest that the genome sequence in the [GenBank:NC_012575] accession is partial and that a missing segment contains these genes: 1) the three genes are conserved in all other compared green algae, 2) given that chloroplast gene order is colinear in Ostreococcus and Micromonas, they are predicted to be contiguous and located between psbB and trnG (ucc) 3) these predicted positions correspond to the circularization endpoints of the genome assembly deposited in [GenBank:NC_012575]. Species names for prasinophytes are abbreviated as in Table 1. A total of 75 genes are shared by all compared prasinophyte cpDNAs: atpA, B, E, F, H, I, clpP, ftsH, petA, B, G, psaA, B, psbA, B, C, D, E, F, H, I, J, K, L, N, T, Z, rbcL, rpl2, 5, 14, 16, 20, 23, rpoA, C1, C2, rps2, 3, 4, 7, 8, 11, 12, 14, 18, 19, rrl, rrs, tufA, ycf1, 3, 12, trnA (ugc), C (gca), D (guc), E (uuc), F (gaa), G (ucc), I (gau), K (uuu), L (uaa), L (uag), Me (cau), Mf (cau), N (guu), P (ugg), Q (uug), R (acg), R (ucu), S (gcu), S (uga), T (ugu), W (cca) and Y (gua).