The endosymbiotic captures of free-living prokaryotes, leading to the evolution of two types of organelles, mitochondria and plastids, are considered to be key events in the establishment and success of extant eukaryotic lineages [1, 2]. If all mitochondria are likely to be derived from an α-proteobacterium-like ancestor, possibly due to a single and ancient endosymbiotic event, the history of plastid acquisition in the diverse photosynthetic eukaryotic lineages seems to be more complex [3–6]. It is now largely accepted that a single primary endosymbiotic event involving the capture of a cyanobacterium led to an ancestral primary plastid, which subsequently gave rise to the green plastids of the terrestrial plants and chlorophytes, the rhodoplasts of red algae and the cyanelles of the glaucophytes. Once established, primary red or green algal plastids later spread independently to other eukaryote lineages via secondary or tertiary endosymbioses, whereby a photosynthetic eukaryote was engulfed by another eukaryote. Subsequently, plastids have also been independently lost and/or replaced in several eukaryote lineages, making the reconstruction of plastid evolution very difficult.
The current consensus of eukaryote phylogeny recognizes six putative super-clusters: Opisthokonta, Amoebozoa, Plantae, Chromalveolata, Rhizaria, and Excavata [7, 8], but this division is still debated [9, 10]. The three primary plastid-containing lineages, Viridiplantae, Rhodophyta and Glaucophyta form the "Plantae" or "Archaeplastida" supergroup. Photosynthetic eukaryotes with secondary or tertiary plastids have evolved independently in the Chromalveolata, Rhizaria, and Excavata [3, 5]. Among the secondary plastids, chlorophyll c-containing plastids have been shown to be derived from an ancestral red alga via a secondary endosymbiotic process that took place around one billion years ago [11, 12]. This type of plastid is found in Cryptophyta, Haptophyta, Heterokonta (also called stramenopiles) and Dinophyceae algae [3, 4]. Cryptophyta, Haptophyta and Heterokonta eukaryotic lineages have been grouped under the name of "Chromista" by Cavalier-Smith , and were later associated with the Alveolata, which includes the apicomplexans, dinoflagellates and ciliates, to form the "Chromalveolata" supergroup. In 1999, Cavalier-Smith proposed that all the chlorophyll c-containing plastids were derived from a single secondary endosymbiotic event and that the common ancestor of chromalveolates was originally photosynthetic . During diversification of the four extant chromalveolates lineages, photosynthetic capacity and/or the plastid organelle would then have been independently lost several times in different eukaryotic lineages, such as oomycetes (non-photosynthetic heterokonts), apicomplexa or ciliates (non-photosynthetic alveolates). According to this so-called "chromalveolate" hypothesis, plastid and nuclear genomes have similar evolutionary histories and one would expect monophyly of chromalveolate lineages in both nuclear and plastid phylogenies. This hypothesis has been extensively debated over the last ten years (for recent references, [5, 6, 15–17]), in part because of incongruence between plastid and nuclear phylogenies .
At the nuclear level, both the monophyly of heterokonts and alveolates and that of cryptophytes and haptophytes have received increasing support in recent years (for recent review and references therein, ). Two contemporary phylogenetic analyses based on expressed sequences tag surveys of the cryptomonad Guillardia theta and the haptophyte Emiliania huxleyi supported the close relationship of cryptophyte and haptophyte host lineages [18, 19]. In nuclear phylogenies alveolates and heterokonts often form a sister group [9, 20]. Unexpectedly, several large scale nuclear phylogenies have also shown a very robust relationship between members of Rhizaria, cercozoans, and these two main clades of the "chromalveolates", but with the exclusion of haptophytes and cryptophytes [18, 21, 22]. The debate is becoming more complex with the emergence of this new putative SAR (stramenopiles/alveolata/rhizaria) supergroup, as proposed by Burki . Recent phylogenetic studies employing large gene- and taxon-rich datasets continue to question the reality of the "chromalveolate" supergroup, by placing the haptophyte-cryptophyte clade as a sister group to the Plantae [24, 25] or by having them emerging independently and separately from the SAR supergroup . It is however well known that reconstructing the evolution of host cell lineages can be difficult, especially because of the chimeric nature of nuclear genomes and because large-scale horizontal gene transfers have occurred in some lineages during evolution .
Plastid genomes are less affected by horizontal gene transfer, with some rare exceptions . At the plastid level, the monophyly of chromist plastids is supported by analyses of single genes , of small numbers of concatenated plastid genes [12, 29], and of larger datasets of plastid-associated genes, i.e. plastid and nuclear-encoded plastid-targeted genes [30–35]. The relationships among chlorophyll c-containing plastids are, however, particularly hard to resolve and the results obtained are sometimes incongruent with host cell phylogenies . Haptophyte plastid genes more often group with the heterokont/dinoflagellate clade, than with those of cryptophytes [30, 31, 33, 34]. A clade grouping haptophyte and cryptophyte species has been inferred from some plastid gene phylogenies [31, 33–35]. This clustering was not strongly supported and was highly dependent on the plastid gene dataset used [31, 35] and/or on taxon-sampling [33, 34]. Other variant topologies have included the placing of dinoflagellates either as a sister-group to haptophyte plastids [30, 33] or to heterokont plastids [34, 35]. However, a close evolutionary relationship between haptophyte and cryptophyte plastids would be consistent with the presence of a unique laterally transferred bacterial rpl36 gene in both plastid genomes . Other multigene analyses produced alternative results, such as low support for the chromist clade  or paraphyly of red-algal derived plastids [35, 36].
The inability to recover congruencies between plastid and nuclear phylogenies, especially concerning haptophyte and cryptophyte monophyly, may be explained by poor taxon sampling of red algal and chromist species [31, 36]. Until now, insufficient sequence data have been available for the chromalveolates, in terms of both nuclear and plastid genome sequences. In public databases, more than 110 complete plastid genomes are available from land plants and green algae, whereas less than 15 sequences belong to red algae or photosynthetic chromalveolate species. Only five complete plastid sequences have been reported for red algal species [36–39]. For the chromalveolates, with the exception of the highly diverged red-algal derived plastid genomes of non-photosynthetic apicomplexans  and those of dinoflagellates [41, 42], complete plastid sequences have been published for two cryptomonads, Guillardia theta and Rhodomonas salina [11, 31], one haptophyte, Emiliania huxleyi , 3 diatoms, Odontella sinensis, Phaeodactylum tricornutum and Thalassiosira pseudonana [44, 45], one raphidophyte Heterosigma akashiwo  and one xanthophyte Vaucheria litorea .
Here we report the complete sequences of the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. These sequences represent the first fully characterized plastid genomes from two distinct orders of Phaeophyceae, namely Ectocarpales and Fucales . We have performed phylogenetic studies using large sets of genes and different reconstruction methods. The results still do not resolve the question of the monophyly of chromist plastids. However the topologies of concatenated plastid protein phylogenetic trees support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies.