ALGAE CONTAINING CHLOROPHYLLS a + c ARE PARAPHYLETIC: MOLECULAR EVOLUTIONARY ANALYSIS OF THE CHROMOPHYTA

Sequence comparisons of small subunit ribosomal RNA coding regions from 12 chlorophylls a + c-containing algae were used to infer phylogenetic relationships within the Chromophyta. Three chromophyte lines of descent, delineated by the Bacillariophyceae, the Phaeophyceae/Xanthophyceae, and the Chrysophyceae/Eustigmatophyceae/Synurophyceae are members of a complex evolutionary assemblage, which also includes representatives of the Oomycota (“lower” fungi). Maximum parsimony and distance matrix methods demonstrate a common evolutionary history for these lineages but their relative branching order could not be determined. Other algal species with chlorophylls a + c, including dinoflagellates and prymnesiophytes, are not members of this complex assemblage. Dinoflagellates are specifically related to apicomplexans and ciliates, and the prymnesiophyte, Emiliania huxleyi, represents an independent photosynthetic lineage that separated from other eukaryotes during the nearly simultaneous divergence of plants, animals, fungi, and a number of other protist lineages. The small subunit rRNA phylogenies of chromophytes/oomycetes were compared to those derived from comparisons of ultrastructural characters. Only tubular, tripartite mastigonemes (flagellar hairs) characterized all studied taxa of chromophytes/oomycetes as a monophyletic assemblage.     

Immunogold-labeling analysis of alginate distributions in the cell walls of chromophyte algae

The immunogold electron microscopy technique was employed to detect the presence of alginates in the cell walls of selected chromophyte species. Anti-alginate antiserum labeled the cell walls of Sphacelaria and Scytosiphon (Phaeophyceae), Tribonema, Vaucheria, Botrydium, Botrydiopsis (Xanthophyceae) and an‘un-described filamentous species’ (incertae cedis), but it did not label those of Giraudyopsis, Phaeosaccion (Chrysomeridales), Antithamnion (Rhodophyceae) and Bryopsis (Ulvophyceae). This is the first report of the occurrence of alginates in the chromophyte outside Phaeophyceae. The absence of alginates in Chrysomeridales, which has an unclear phylogenetic position, implies a rather distant phylogenetic relationship of the order Chrysomeridales from Phaeophyceae/Xanthophyceae.     

A "Total Evidence" Analysis of the Phylogenetic Relationships among the Photosynthetic Stramenopiles

Phylogenetic relationships among the nine major autotrophic stramenopile taxa were inferred in a combined analysis of the rbcL, SSU rDNA, partial LSU rRNA, carotenoid, and ultrastructural data sets. The structure of the shortest combined tree is: (Outgroup, ((((Bacillariophyceae, (Pelagophyceae, Dictyochophyceae)),((Phaeophyceae, Xanthophyceae), Raphidophyceae)), Eustigmatophyceae),(Chrysophyceae, Synurophyceae))). The Synurophyceae/Chrysophyceae is the best supported group followed by the Phaeophyceae/Xanthophyceae and the Pelagophyceae/Dictyochophyceae clades. The monophyletic groups composed of Bacillariophyceae/Pelagophyceae/Dictyochophyceae and Phaeophyceae/Xanthophyceae/Raphidophyceae received the lowest Bremer support values. The optimal combined tree suggests that the diatom frustule is derived from the siliceous "skeleton" in Dictyochophyceae, that the reduced flagellar apparatus arose once in the Bacillariophyceae/Dictyochophyceae/Pelagophyceae clade, and that the specific photoreceptor-eyespot apparatus in Chrysophyceae and the Phaeophyceae/Xantophyceae clade originated independently within the autotrophic stramenopiles. Despite conflicts in tree structure between the most-parsimonious combined phylogeny and the optimal tree(s) of each data partition, it cannot be concluded that extensive incongruence exists between the data sets.     

The structure and phylogenetic significance of the flagellar transition region in the chlorophyll c-containing algae.

An electron-dense helix is the most conspicuous structure in the flagellar transition region of members of the algal class Chrysophyceae. This “transitional helix” (TH) lies immediately distal to a partition across the flagellar axoneme which occurs exactly at the level at which the flagellum enters the cell body. The helix surrounds the central axonemal pair and lies at a distance of 10 nm from the 9 peripheral doublets. From the new data presented and a survey of published observations on the structure of the transition region of all the chlorophyll c-containing classes of algae, it is shown that a TH characteristic of the Chrysophyceae, Xanthophyceae and Eustigmatophyceae. The number of TH gyres varies from 3 to 6 in the Xanthophyceae and from 1 to 8 in the Chrysophyceae. In any one species, however, the TH is the same size in both the long flagellum which bears tubular mastigonemes and in the short smooth flagellum, though in some chrysophytes where the short flagellum is vestigial the number is fewer than in the normal flagellum. A TH appears to be absent from the Rhaphidophyceae and zoids of the Bacillariophyceae and Phaeophyceae though the structure of the transition region in these groups otherwise resembles that of the Chrysophyceae, Xanthophyceae and Eustigmatophyceae.The value of transition region variation in determining evolutionary relationships among the chlorophyll c-containing algal classes is assessed against a background of current ideas on their taxonomy and phylogeny. The relevant structural and biochemical features are tabled, and a phylogenetic scheme is presented which appears most logically to interpret these data. It is suggested that the line leading to the Eustigmatophyceae probably diverged from that leading to the strictly heterokont classes Xanthophyceae, Chrysophyceae, Phaeophyceae and Bacillariophyceae before evolution of a girdle lamella in the chloroplast and a photoreceptor apparatus involving a swelling at the proximal end of the short flagellum and an intraplastidial eyespot. The possession of a TH by both the Chrysophyceae and Xanthophyceae adds further support to the concept of their close relationship based on a range of other features. The exceptional absence of a TH from the chrysophycean genera Pedinella and Pseudopedinella reinforces the idea that these taxa are remote from the main chrysophycean line. Absence of a TH from the Phaeophyceae and Bacillariophyceae which otherwise share many important features with the Chrysophyceae and Xanthophyceae is probably a result of loss owing to the functional and morphological specialization of the zoids of these two groups. Transition region structure does not clarify the possible relationships of the Rhaphidophyceae, Prymnesiophyceae, Cryptophyceae or Dinophyceae.The proposed phylogeny supports the idea of a mutually related “heterokont” protist assemblage comprising the Chrysophyceae, Xanthophyceae, Phaeophyceae, Bacillariophyceae and possibly Rhaphidophyceae and the Oomycetes (water moulds) though in the latter the TH is replaced by a dense cylinder with a corrugated wall which may or may not be homologous with it. Structures resembling a TH have been described in a wide variety of other flagellated cells including the prasinophyte Pyraminonas orientalis, one species of the colourless flagellate genus Bicosoeca and the proteromonads Karotomorpha and Proteromonas. Only in the latter genera does homology with a TH seem likely on present evidence, suggesting that flagellates of this type may have evolved from chrysomonad-like ancestors.     

SYNUROPHYCEAE CLASSIS NOV., A NEW CLASS OF ALGAE

The silica-scaled algae (Synuraceae, Chrysophyceae sensu lato) are compared to other Chrysophyceae, Phaeophyceae and Bacillariophyceae with occasional comparisons to other chlorophyll c-containing algae, scaled protozoa and oomycete fungi. The silica-scaled algae have several unique characters which separate them from the above groups and based upon these differences a new order, Synurales ord. nov., and a new class, Synurophyceae class. nov., are described. The major distinguishing characters of the Synurophyceae class. nov. are: they have chlorophylls a and c₁ but lack chlorophyll c₂; their flagellar apparatus includes a microtubular root that loops around two parallel flagella and a flagellar root system which occurs in four absolute orientations; the photoreceptor consists of paired flagellar swellings which are not associated with the cell membrane and chloroplast; no eyespot is present; the nuclear envelope is not or is only weakly associated with the chloroplast endoplasmic reticulum. The Synurophyceae class. nov. are about equally distinct from the Chrysophyceae sensu stricto, Phaeophyceae and Bacillariophyceae when the class level characters are compared. Although the Phaeophyceae have a long history of being placed by themselves in the division Phaeophyta, and the Bacillariophyceae and Chrysophyceae have recently been placed alone in the Bacillariophyta and Chrysophyta, respectively, the similarities found among these classes suggest these algae are not so distinct that they require separate divisions. Tentatively, therefore, the Synurophyceae are placed in the division Phaeophyta along with the Bacillariophyceae and Chrysophyceae sensu stricto.     

A MOLECULAR PHYLOGENY OF THE HETEROKONT ALGAE BASED ON ANALYSES OF CHLOROPLAST-ENCODED rbcL SEQUENCE DATA1

Nearly complete ribulose-1,5-bisphosphate carboxylase/ oxygenase (rbcL)sequences from 27 taxa of heterokont algae were determined and combined with rbcL sequences obtained from GenBank for four other heterokont algae and three red algae. The phylogeny of the morphologically diverse haterokont algae was inferred from an unambiguously aligned data matrix using the red algae as the root, Significantly higher levels of mutational saturation in third codon positions were found when plotting the pair-wise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In light of this observation, third codon positions were excluded from phylogenetic analyses. Both weighted-parsimony and maximum-likelihood analyses supported with high bootstrap values the monophyly of the nine currently recognized classes of heterokont algae. The Eustigmatophyceae were the most basal group, and the Dictyochophyceae branched off as the second most basal group. The branching pattern for the other classes was well supported in terms of bootstrap values in the weightedparsimony analysis but was weakly supported in the maximum-likelihood analysis (<50%). In the parsimony analysis, the diatoms formed a sister group to the branch containing the Chrysophyceae and Synurophyceae. This clade, charactetized by siliceous structures (frustules, cysts, scales), was the sister group to the Pelagophyceae/Sarcinochrysidales and Phaeo-/Xantho-/ Raphidophyceae clades. In the latter clade, the raphido-phytes were sister to the Phaeophyceae and Xanthophyceae. A relative rate test revealed that the rbcL gene in the Chrysophyceae and Synurophyceae has experienced a significantly different rate of substitutions compared to other classes of heterokont algae. The branch lengths in the maximum-likelihood reconstruction suggest that these two classes have evolved at an accelerated rate. Six major carotenoids were analyzed cladistically to study the usefulness of carotenoid pigmentation as a class-level character in the heterokont algae. In addition, each carotenoid was mapped onto both the rbcL tree and a consensus tree derived from nuclear-encoded small-subunit ribosomal DNA (SSU rDNA) sequences. Carotenoid pigmentation does not provide unambiguous phylogenetic information, whether analyzed cladistically by itself or when mapped onto phylogenetic trees based upon molecular sequence data.     

CHARACTERIZATION AND PHYLOGENETIC POSITION OF THE ENIGMATIC GOLDEN ALGA PHAEOTHAMNION CONFERVICOLA: ULTRASTRUCTURE, PIGMENT COMPOSITION AND PARTIAL SSU rDNA SEQUENCE

The morphology, ultrastructure, photosynthetic pigments, and nuclear-encoded small subunit ribosomal DNA (SSU rDNA) were examined for Phaeothamnion confervicola Lagerheim strain SAG119.79. The morphology of the vegetative filaments, as viewed under light microscopy, was indistinguishable from the isotype. Light microscopy, including epifluorescence microscopy, also revealed the presence of one to three chloroplasts in both vegetative cells and zoospores. Vegetative filaments occasionally transformed to a palmelloid stage in old cultures. An eyespot was not visible in zoospores when examined with light microscopy, but small droplets, similar to eyespot droplets, were apparent beneath the shorter flagellum when cells were viewed with electron microscopy. Zoospores had two flagella that were laterally inserted in the cell approximately one-third of the cell length from the apex. The longer flagellum was directed anteriorly and the shorter flagellum was directed posteriorly. Electron microscopy revealed the presence of tubular tripartite flagellar hairs on the longer flagellum, but no lateral filaments were found on the tripartite hairs. The general organization of the flagellar root system was similar to that of zoospores belonging to the Xanthophyceae and Phaeophyceae. However, the transitional region of the flagella contained a transitional helix with four to six gyres. Microtubular root R₁ consisted of six microtubules at its proximal end and one microtubule at its distal end. Roots R₂ and R₄ consisted of one microtubule each and root R₃ consisted of two microtubules. No rhizoplast was found. Thin-layer chromatography revealed the presence of fucoxanthin, diadinoxanthin, neoxanthin, and heteroxanthin as well as chlorophylls a, c₁ and c₂. High-performance liquid chromatography revealed the presence of fucoxanthin, diadinoxanthin, diatoxanthin, heteroxanthin, and β,β-carotene as well as chlorophylls a and c. The complete sequence of the SSU rDNA could not be obtained, but a partial sequence (1201 bases) was determined. Parsimony and neighbor-joining distance analyses of SSU rDNA from Phaeothamnion and 36 other chromophyte algae (with two Öomycete fungi as the outgroup) indicated that Phaeothamnion was a weakly supported (bootstrap = <50%, 52%) sister taxon to the Xanthophyceae representatives and that this combined clade was in turn a weakly supported (bootstrap = <50%, 67%) sister to the Phaeophyceae. Based upon ultrastructural observations, pigment analysis, and SSU rDNA phylogenetic analysis, Phaeothamnion is not a member of the Chrysophyceae and should be classified as incertae sedis with affinities to the Xanthophyceae and Phaeophyceae.     

Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles

Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.     

Green flagellar autofluorescence in brown algal swarmers and their phototactic responses

A flavin-like green autofluorescent substance is noticed to occur in one of the flagella of flagellated cells in the Phaeophyceae, Chrysophyceae, Synurophyceae, Xanthophyceae and Prymnesiophyceae. In the phaeophycean swarmers the autofluorescence occurs in the posterior flagellum throughout its length. It is considered to be involved in the photoreception of phototaxis, since it almost always occurs in the swarmers which have a flagellar swelling and stigma and show phototaxis. In the phaeophycean swarmers, the stigma is shown to act as a concave reflector mirror focusing the reflection light onto the flagellar swelling. In the action spectrum studies, phaeophycean swarmers showed phototaxis between 370 and 520 nm, having two major peaks at 420 or 430 nm and 450 or 460 nm. Their responses were true phototactic and not photophobic. Rotation of the swarmer was shown to be essential in the photoreception ofEctocarpus gametes. Recipient of the Botanical Society Award for Young Scientists, 1991.     

The cytoskeleton of chromophyte algae

Summary The cytoskeleton of flagellate chromophyte algae, zoospores and gametes is active during swimming, phototaxis, several types of phagotrophic feeding, the formation, secretion and deployment of silica-scales, and the abrupt movement of spine-scales. The flagellar basal bodies are anchored by microtubular roots and/or fibrous roots. The kinds, numbers, and paths of these roots are characteristic of different taxonomic groups within the chromophytes. There are more differences in flagellar apparatuses for taxonomic classes dominated by flagellates as compared to classes dominated by coccoid, filamentous, or parenchymatous forms. Swimming cells that exhibit phototaxis often contain an autofluorescent substance that is located at the base of one flagellum. Phagotrophy occurs in flagellates of several distantly related taxonomic classes, suggesting that phagotrophy evolved independently several times. The most complex phagotrophic process occurs in the Chrysophyceae where one microtubule of a flagellar root forms a feeding basket or pouch into which food particles are moved. The silica-scales of the Synurophyceae are formed, secreted and finally moved into position outside the cell by cytoskeletal components. The six spinescales ofApedinella (Pedinellophyceae) lie outside the plasma membrane, but they are attached by microligaments and are repositioned almost instantly by a cytoskeletal complex of actin, centrin, and microtubules. A phylogenetic classification based upon a cladistic analysis suggests that aquatic fungi are natural members of the chromophyte group.     

PHYLOGENETIC AFFINITIES OF THE SARCINOCHRYSIDALES AND CHRYSOMERIDALES (HETEROKONTA) BASED ON ANALYSES OF MOLECULAR AND COMBINED DATA1

Small-subunit ribosomal RNA nucleotide sequences were inferred for Giraudyopsis stellifera Dangeard (Chrysomeridales), as well as for Pulvinaria sp. and Sarcinochrysis marina Geitler (Sarcinochrysidales,). Phylogenetic analyses of the molecular data indicate that the former is weakly related to the Phaeophyceae/Xanthophyceae clade, whereas the latter two have affinities to the Pelagophyceae, and the Sarcinochrysidales sensu stricto is transferred to this class. A recent study proposed that the Pelagophyceae belongs to a larger assemblage of chromophytic species characterized by reduced flagellar apparatuses. Although the flagellar apparatus characterizing the Sarcinochrysidales is reduced relative to the Chysomeridaels and some other chromophytes, it is the most complicated to be associated with “the reduced flagellar apparatus” lineage. Cladistic analyses of a traditional data set (largely ultrastructural features of the flagellar apparatus) and a combined traditional/molecular data set were used to assess the evolutionary trends of reduction in the flagellar apparatus within the heterokont chromophytes.     

Schizocladia ischiensis: a new filamentous marine chromophyte belonging to a new class,Schizocladiophyceae

A new marine filamentous chromophyte Schizocladia ischiensis sp. nov. is described from Naples, Italy, and a new class, Schizocladiophyceae, is proposed to accommodate the species based on morphology, photosynthetic pigment analysis, and rbcL and 18S rRNA gene sequences. The vegetative thallus is composed of branched filaments, 3-7 microm in diameter, containing one to two light brown parietal plastids. Cell walls are composed of layered fibers containing alginates, but lacking cellulose. Plastids are of the typical chromophyte type, containing chlorophylls a and c, and abundant fucoxanthin. Zoospores are formed by direct transformation of vegetative cells or through a process including a multinucleated cell stage. Zoospores are teardrop-shaped with a longer anterior flagellum with tubular mastigonemes and a shorter smooth posterior flagellum with a basal swelling. Flagella have a single basal plate and multi-gyred transitional helix distal to the basal plate. Each zoospore has an eyespot. Phylogenetic analyses using rbcL and 18S rDNA sequences suggest the closest phylogenetic relationship with Phaeophyceae, and then with Xanthophyceae and Phaeothamniophyceae. Nevertheless, Schizocladia differs from Phaeophyceae in some essential features (i.e. cell wall lacking cellulose and plasmodesmata, presence of flagellar transitional helix). Therefore, an independent class Schizocladiophyceae is proposed to accommodate this new taxon.     

Sequence analysis of duplicated actin genes in Lagenidium giganteum and Pythium irregulare (Oomycota)

Southern analysis of genomic DNA identified multiple-copy actin gene families in Lagenidium giganteum and Pythium irregulare (Oomycota). Polymerase chain reaction (PCR) protocols were used to amplify members of these actin gene families. Sequence analysis of genomic coding regions demonstrated five unique actin sequences in L. giganteum (Lg-Ac 1, 2, 3, 4, 5) and four unique actin sequences in P. irregulare (Pi-Acl, 2, 3, 4); none were interrupted by introns. Maximum parsimony analysis of the coding regions demonstrated a close phylogenetic relationship between oomycetes and the chromophyte alga Costaria costata. Three types of actin coding regions were identified in the chromophyte/oomycete lineage. The type 1 actin is the single-copy coding region found in C. costata. The type 2 and type 3 actins are found in the oomycetes and are the result of a gene duplication which occurred soon after the divergence of the oomycetes from the chromophyte algae. The type 2 coding regions are the single-copy sequence of Phytophthora megasperma, the Phytophthora infestans actB gene, Lg-Ac5 and Pi-Ac2. The type 3 coding regions are the single-copy sequence of Achlya bisexualis, the P. infestans actA gene, Lg-Ac1, 2, 3, 4 and Pi-Acl, 3, 4. Correspondence to: D. Bhattacharya     

Silica‐scaled chrysophytes from Abisko (Swedish Lapland)

The silica‐scaled chrysophyte flora of Swedish Lapland (near Abisko) was examined. Chrysophyte scales were found in 18 of the 32 investigated water bodies (lakes and pools). Altogether, 28 taxa from the classes Chrysophyceae and Synurophyceae were found. The most abundant species was Synura echinulata. Three species were observed for the first time in Sweden: Mallomonas maculata, M. rasilis and Spiniferomonas serrata.     

Analysis of the Cluster of Ribosomal Protein Genes in the Plastid Genome of a Unicellular Red Alga Cyanidioschyzon merolae: Translocation of the str Cluster as an Early Event in the Rhodophyte-Chromophyte Lineage of Plastid Evolution

The nucleotide sequence of a cluster of ribosomal protein genes in the plastid genome of a unicellular red alga, Cyanidioschyzon merolae, which has been supposed to be the most primitive alga, was determined. The phylogenetic tree inferred from the amino acid sequence of ribosomal proteins of two rhodophytes, a chromophyte, a glaucophyte, two chlorophytes (land plants), a cyanobacterium, and three eubacteria suggested a close relationship between the cyanobacterium Synechocystis PCC6803 and the plastids of various species in the kingdom Plantae, which is consistent with the hypothesis of the endosymbiotic origin of plastids. In this tree, the two species of rhodophytes were grouped with the chromophyte, and the glaucophyte was grouped with the chlorophytes. Analysis of the organization of the genes encoding the ribosomal proteins suggested that the translocation of the str cluster occurred early in the lineage of rhodophytes and chromophytes after these groups had been separated from chlorophytes and glaucophytes. Received: 2 June 1997 / Accepted: 15 July 1997     

EVIDENCE FOR A CLOSE RELATIONSHIP BETWEEN IOSTEPHANE AND VIGUIERA (ASTERACEAE: HELIANTHEAE)

The phylogenetic relationship of Iostephane is assessed using data from morphology, flavonoid chemistry, and chloroplast DNA and nuclear ribosomal DNA restriction fragment analysis. Morphological evidence supports placement of Iostephane in subtribe Helianthinae, but fails to clarify the placement of the genus within this assemblage. Further evidence for the placement of Iostephane in subtribe Helianthinae is provided by the presence in all species of the genus of floral flavonoids of the chalcone/aurone type, which provides a distinctive trait for the subtribe within the tribe Heliantheae. Analysis of chloroplast DNA from two species of Iostephane, I. heterophylla and I. madrensis, in comparison to Viguiera and related genera indicates that the restriction site patterns with 16 enzymes for the Iostephane species are virtually identical to one another as well as to those of Viguiera sect. Maculatae. Data from restriction fragment patterns of nuclear rDNA are concordant with the results from chloroplast DNA in suggesting a direct relationship between the two groups. The close phylogenetic relationship between Iostephane and Viguiera sect. Maculatae suggested by the DNA restriction fragment data was not suggested by any other set of data.     

Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae

The nucleotide sequence for the nuclear-encoded small subunit ribosomal RNA gene (SSU rRNA) was determined for 24 species of the Chrysophyceae sensu stricto. These sequences were aligned, using primary and secondary structure, with nine previously published sequences for the Chrysophyceae, 14 for the Synurophyceae, and five for the Eustigmatophyceae (outgroup). Data analyses were the substitution rate calibration distance method using neighbor-joining (TREECON), Kimura 2-parameter neighbor-joining method (PAUP) and the maximum parsimony method (PAUP, PHYLIP). Trees from the analyses were largely congruent, but bootstrap support was weak at many nodes. The analyses recovered clades of uniflagellate and biflagellate organisms associated with current higher level taxonomy (e.g., subclass, order). The genus Ochromonas was polyphyletic, and O. tuberculata in particular was distantly related to the other Ochromonas species in the analysis. The family Paraphysomonadaceae occupied a basal position in three of four analyses. The class Synurophyceae appeared to be embedded within the Chrysophyceae, but bootstrap support was weak (< 50%) in all analyses except the PHYLIP parsimony analysis (= 81%). It was considered premature to place the Synurophyceae back into the Chrysophyceae based upon the analysis of one gene, especially given the ultrastructural and pigment differences between the two groups, but the relationship of these two groups deserves further study.     

DISTRIBUTION OF THE MITOCHONDRIAL DEVIANT GENETIC CODE AUA FOR METHIONINE IN HETEROKONT ALGAE

The DNA sequence of the cytochrome oxidase subunit I ( COX I) gene (1059 bp), was determined in a number of heterokont algae, including five species of the Phaeophyceae [ Chorda filum (Linnaeus) Stackhouse, Colpomenia bullosa (Saunders) Yamada, Ectocarpus sp., Pseudochorda nagaii (Tokida) Inagaki, Undaria pinnatifida (Harvey) Suringar], and a member of the Raphidophyceae [ Chattonella antiqua (Hada) Ono]. The distribution of a deviant mitochondrial code, the AUA codon for methionine (AUA/Met), which was previously reported in the Xanthophyceae, was inferred from these COX I sequences. Comparative analyses of these sequences revealed that all the algae described above bear the universal genetic code, including the assignment for the AUA codon. A phylogenetic tree was constructed using the obtained sequences along with already-published COX I sequences of various heterokont algae. The clusters of the Xanthophyceae and the Phaeophyceae were resolved as sister groups with high bootstrap support, excluding a bacillariophycean species, a raphidophycean species, and three species of the Eustigmatophyceae. Taking the distribution of the deviant code and the COX I phylogenetic tree together, the genetic code change most probably occurred in an ancestor of the Xanthophyceae after it had branched off from the Phaeophyceae.