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Phylogenetic Position of the Phacotaceae Within the Chlamydophyceae As Revealed by Analysis of 18S Rdna and Rbcl Sequences

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J Mol Evol (1998) 47:420–430 © Springer-Verlag New York Inc. 1998 Phylogenetic Position of the Phacotaceae Within the Chlamydophyceae as Revealed by Analysis of 18S rDNA and rbcL Sequences D. Hepperle,1 H. Nozaki,2 S. Hohenberger,3 V.A.R. Huss,3 E. Morita,2 L. Krienitz1 1 Institute of Freshwater Ecology & Inland Fisheries, Department of Limnology of Stratified Lakes, Alte Fischerhu¨tte 2, D-16775 Neuglobsow, Germany 2 University of Tokyo, Department of Biological Sciences, Graduate School of Science, Hongo, Bunkyo, Tokyo 113, Japan 3 University of Erlangen, Institute of Botany and Pharmaceutical Biology, Staudtstr. 5, D-91058 Erlangen, Germany Received: 9 June 1997 / Accepted: 17 October 1997 Abstract. Four genera of the Phacotaceae (Phacotus, and ഛ86.6% in the rbcL gene. It showed major similari- Pteromonas, Wislouchiella, Dysmorphococcus), a family ties to the 18S rDNA of Dunaliella salina, with 95.3%, of loricated green algal flagellates within the Volvocales, and to the rbcL sequence of Chlamydomonas tetragama, were investigated by means of transmission electron mi- with 90.3% sequence homology. Additionally, the croscopy and analysis of the nuclear encoded small- Phacotaceae sensu stricto exclusively shared 10 (rbcL: 4) subunit ribosomal RNA (18S rRNA) genes and the plas- characters which were present neither in other Chlam- tid-encoded rbcL genes. Additionally, the 18S rDNA of ydomonadales nor in Dysmorphococcus globosus. Dif- Haematococcus pluvialis and the rbcL sequences of ferent phylogenetic analysis methods confirmed the hy- Chlorogonium elongatum, C. euchlorum, Dunaliella pothesis that the Phacotaceae are polyphyletic. The parva, Chloromonas serbinowii, Chlamydomonas ra- Phacotaceae sensu stricto form a stable cluster with af- diata, and C. tetragama were determined. Analysis of finities to the Dunaliellaes and possibly Haematococcus ultrastructural data justified the separation of the Phaco- pluvialis. Dysmorphococcus globosus represented an in- taceae into two groups. Phacotus, Pteromonas, and Wis- dependent lineage that is possibly related to Chlamydom- louchiella generally shared the following characters: onas moewusii and C. tetragama. egg-shaped protoplasts, a single pyrenoid with planar thylakoid double-lamellae, three-layered lorica, flagellar Key words: Phacotaceae — Volvocales — 18S rDNA channels as part of the central lorica layer, mitochondria — Phylogeny — Lorica-bearing flagellates — Green al- located in the central cytoplasm, lorica development that gae occurs in mucilaginous zoosporangia that are to be lysed, and no acid-resistant cell walls. Dysmorphococcus was clearly different in each of the characters mentioned. Direct comparison of sequences of Phacotus lenticularis, Introduction Pteromonas sp., Pteromonas protracta, and Wislouch- iella planctonica revealed DNA sequence homologies of Ettl (1983) classified the flagellated members of the ജ98.0% within the 18S gene and 93.9% within the rbcL green algae with respect to their cell walls and or- gene. D. globosus was quite different from these species, ganization into three classes: (1) Prasinophyceae— with a maximum of 92.9% homology in the 18S rRNA scale-bearing taxa (Polyblepharidales), cyst-forming Prasinophytes (Halosphaerales), and thecate taxa (Tetraselmidales); (2) Chlorophyceae—taxa without cell walls (Dunaliellales); and (3) Chlamydophyceae— Correspondence to: D. Hepperle; e-mail: [email protected] (‘‘beha¨utete’’) flagellates that have cell walls and appear 421 as unicellular (Chlamydomonadales) or multicellular perle et al. 1994; Hepperle and Krienitz 1996). This in- taxa (coenobial, ‘‘Volvocales’’). But he also mentioned dicates that the family might be polyphyletic and thus an in a previous study that Chlamydomonas seemed to be an artificial conglomerate. Although the loricae were stud- artificial genus that unified different phylogenetic lin- ied almost excessively, ultrastructural data on internal eages and had a more provisional character (Ettl 1976). morphology are scarce. This stimulated reanalyses of ul- However, this system is not consistent with analyses trastructure from different members of the Phacotaceae. based upon comparison of characteristics of the flagellar Concerning the taxonomy of the Phacotaceae it is of apparatus and molecular markers, such as 18S rDNA. interest that the genus Dysmorphococcus (Takeda 1916) Now, it is well accepted that the Prasinophytes represent was at first arranged within the ‘‘Coccomonadineae’’ at least two independent lineages of green algae and that together with Coccomonas and Pedinopera (Pascher the Tetraselmidales are to be included in the Pleurastro- 1927). At that time, Phacotus and Pteromonas were the phyceae (Steinko¨tter et al. 1994). The remaining two only members of the ‘‘Phacoteae.’’ But later the two groups, Chlamydomonadales and Volvocales, were also groups were united in a single family termed ‘‘Phacota- treated as independent lineages within the Chlorophy- ceae’’ (Bold and Starr 1953; Huber-Pestalozzi 1961; ceae by Mattox and Stewart (1984). Bourrelly 1966; Prescott 1970; Iyengar and Desikachary Studies of the nuclear-encoded small-subunit ribo- 1981). As indicated by Ettl (1983), the Phacotaceae somal RNA (18S rRNA) genes revealed that multicellu- might be divided into two groups with different lorica lar taxa (except Stephanosphaera) had a close relation- morphologies: one group is characterized by a lorica ship to some members of the Chlamydomonadales consisting of a single, uniform piece and the other by (especially to Chlamydomonas reinhardtii), whereas bivalved loricae that consist of two shell-like halves. other taxa were quite apart from these (Rausch et al. Here we present the first study on the phylogenetic relationships of the Phacotaceae based on nucleotide se- 1989; McAuley et al. 1990; Buchheim and Chapman quence and ultrastructural data from various phacotacean 1991). Analysis based on morphological and/or molecu- algae. lar data contributed to the idea that a set of coccal- organized chlorophytes also belong to the Chlamydophy- ceae, i.e., Characium vacuolatum (Wilcox et al. 1992), and Botryococcus braunii (Sawayama et al. 1995). Lewis Materials and Methods et al. (1992) compared morphological and molecular data and showed that chlorococcalean species that were char- Culture. Unialgal cultures of Pteromonas protracta (UTEX LB 647), Dysmorphococcus globosus (SAG 20-1), Wislouchiella planctonica acterized by a clockwise orientation of the basal bodies (UTEX LB 1030), Haematococcus lacustris (SAG 34-1b), Chlorogo- were also phylogenetically closely related to the nium elonagatum (IAM C-293), C. euchlorum (CCAP12/3), and Chlamydophyceae. Chlamydomonas tetragama (NIES-446) were obtained from either the The Phacotaceae were regarded as a monophyletic Culture Collection at the University of Texas (UTEX; Austin, TX, USA), the Culture Collection of Algae and Protozoa (CCAP; Cumbria, group of flagellated green algae within the Volvocales. UK), the Culture Collection of the Institute of Applied Microbiology They comprise about 70 species in 15 genera (Ettl 1983). (IAM; Tokyo, Japan), the Microbial Culture Collection, National In- The family was proposed on the presence of one single, stitute for Environmental Studies (NIES; Tsukuba, Japan), or the uniting criterion: the lorica. According to Preisig et al. Sammlung von Algenkulturen (SAG; Go¨ttingen, Germany). Phacotus (1994) loricae are considered to be cell walls fitting lenticularis (KR 91/1) was isolated by L. Krienitz from Lake Tollense and Pteromonas strains (KR 91/2, KR 91/3) derived from an oxidation loosely over the body proper of the organism and not pond in Neuglobsow (Brandenburg, Germany). All algae were cultured exhibiting defined chemical compositions. At least the in 3,000-ml batch cultures and medium 7 (Schlo¨sser 1982). organic compounds of the loricae of the Phacotaceae are supposed to be of dictyosomal origin and seem to as- Ultrastructure. Cells were fixed simultaneously in a mixture of semble on the cell surface after their excretion (Walne 1.25% glutaraldehyde, 1% osmium tetroxide, and 30 mM HEPES, pH and Dunlap 1994, 1995; Hepperle and Krienitz 1996). A 7.2, at 4°C (modified from McFadden and Melkonian 1986). After two subsequent, unknown mechanism leads to mineralization rinses in distilled water at 4°C the samples were dehydrated at room temperature in an ascending acetone series. After infiltration of the of the loricae with metallic compounds, such as calcium cells in Spurr’s low-viscosity resin:acetone (2:1) for 12 h and evapo- carbonate in the case of Phacotus (Hepperle and Krienitz ration of the acetone, the samples were transferred to pure resin for 4 1997) or iron salts in Dysmorphococcus (Porcella and h (Spurr 1969). Subsequently, the samples were centrifuged and poly- Walne 1980). This process usually results in a more or merized at 60°C for 48 h. less rigid cell wall exhibiting a species- and/or genus- specific structure and shape. Most authors consider the DNA Extraction, Polymerase Chain Reaction (PCR), and Sequenc- lorica of the Phacotaceae to be a conserved, apomorphic ing of 18S rDNA. Total DNA of cells harvested by centrifugation was characteristic (e.g., Walne and Dunlap 1994). Neverthe- obtained either by detergent treatment in 20% sodium dodecyl sulfate (SDS) or, in the case of W. planctonica, by cell fracture in a nitrogen- less, a comparison of lorica morphology and metal com- cooled mortar and extraction in CTAB at 60°C (Doyle and Doyle position reveals extreme
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  • Chloroplast Phylogenomic Analysis of Chlorophyte Green Algae Identifies a Novel Lineage Sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T

    Chloroplast Phylogenomic Analysis of Chlorophyte Green Algae Identifies a Novel Lineage Sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T

    Lemieux et al. BMC Evolutionary Biology (2015) 15:264 DOI 10.1186/s12862-015-0544-5 RESEARCHARTICLE Open Access Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T. Vincent, Aurélie Labarre, Christian Otis and Monique Turmel Abstract Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages.