Table 1.

Gene content comparisons between plastid genomes.

Genes		Species
	No.	Heterokonts							Hapto	Crypto		Rhodophytes
		Esil	Fves	Vlit	Haka	Ptri	Osin	Tpse	Ehux	Gthe	Rsal	Gten	Ppur	Ccal	Cmer
83 genes listed in Table S3*, rpl36, rbcR, ccsA	86	+	+	+	+	+	+	+	+	+	+	+	+	+	+
rpoC1, rpoC2, ycf35, ycf46	4	+	+	+/-	+	+	+	+	+	+	+	+	+	+/-	-
cbbX, ccs1, tatC	3	+	+	+	+	+	+	+	+	+	+	+	-	+/-	+
petL, petM	2	+	+	+	+	+	+	+	+	+	+	-	+	-	+
thiG, thisS	2	+	+	+	+	+	+	+	+	-	-	+	+/-	+	+
dnaB, ftsH, petF, psaE, psbX, rpl1, rpl4, rpl11, rpl12, rpl13, rpl18, rpl24, rpl29, rpl32, rpl35, rps20, sufC, ycf33	18	+	+	+	+	+	+	+	-	+	+	+	+	+/-	+
psbY	1	+	+	+	+	+	-	+	-	-	+	-	-	-	+
ycf41, ycf42, ycf66	3	+	+	+	+/-	+	+/-	+	-	-	-	-	-	-	-
psbW, secG, tsf	3	+	+	+/-	-	+	+	+	+/-	+	+	+/-	+/-	+/-	+/-
ftrB, ilvB, ilvH	3	+	+	+	+	-	-	-	-	+	+	+	+	+/-	+/-
ycf65	1	+	+	+	+	-	-	-	+	-	-	+	-	+	+
acsF, petJ, rps1, ycf34, ycf54	5	+	+	+/-	+	-	-	-	-	-	-	+/-	+/-	+/-	+/-
chlB, chlL, chlN, rpl9	4	+	+	+	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-
ycf19, ycf37	2	+	+	+	-	-	-	-	+/-	+	+	+	+	+	+/-
Escp124 (FvORF76) ~ ycf60	1	+	+	+	-	-	-	-	+	-	-	+	-	+	+
Escp152 (FvORF501)	1	+	+	-	-	-	-	-	-	-	-	-	-	-	-
hlip ~ ycf17	1	+	-	+	-	-	-	-	-	+	+	-	+	+	+
syfB	1	+	-	-	-	+	-	-	-	-	-	+	+	-	-
Escp36, Escp117, Escp161	3	+	-	-	-	-	-	-	-	-	-	-	-	-	-

E. siliculosus (Esil) and F. vesiculosus (Fves) cpDNAs were compared with those of other heterokonts, haptophyte (Hapto), cryptophytes (Crypto) and rhodophytes. Presence (+), absence (-) or presence of only a subset (+/-) of the genes listed in the first column is indicated. Species abbreviations: Vaucheria litorea (Vlit), Heterosigma akashiwo (Haka), Phaeodactylum tricornutum (Ptri), Odontella sinensis (Osin), Thalassiosira pseudonana (Tpeu), Emiliania huxleyi (Ehux), Guillardia theta (Gthe), Rhodomonas salina (Rsal), Gracilaria tenuistitipata (Gten), Porphyra purpurea (Ppur), Cyanidium caldarium (Ccal), Cyanidioschyzon merolae (Cmer).

(*) see additional file 2.