Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species

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	86^e			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	128^f			45.6	0.5
Clade V
Pycnococcus provasolii CCMP 1203	PYCN	80,211		60.5	99^g		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.

ISSN: 1471-2164