Phylogeny of the colonial green flagellates: a study of 18S and 26S rRNA sequence data

Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae)

In the green algal order Volvocales (Chlorophyceae), flagellate colonial forms have evolved at least four times. One of these colonial lineages, Tetrabaenaceae-Goniaceae-Volvocaceae (TGV), which belongs to the clade Reinhardtinia, is closely related to several unicellular chlamydomonads in the genera Chlamydomonas and Vitreochlamys. However, the unicellular sister of TGV has not been specified. Here, the largest ever 18S rRNA phylogenetic tree of Reinhardtinia was constructed including several newly isolated chlamydomonads, and a clade (core-Reinhardtinia) including 32 unicellular lineages and three colonial families were recognized. Interrelationships within core-Reinhardtinia were barely resolved in the tree, and therefore combined 18S-atpB-psaA-psaB-psbC-rbcL gene phylogenetic analyses were performed with selected representatives of 29 of the 32 unicellular lineages and three colonial families. The 29 unicellular lineages were clustered into five metaclades and an unassigned lineage; the metaclade that includes Chlamydomonas pila was resolved, with moderate support, as the sister clade to TGV. To examine possible biases from specific gene(s), long-branch taxa, and the heterogeneous base composition, phylogenetic analyses using several smaller data sets were also performed. Light microscopy of C. pila and its relatives indicated that any early steps towards colony evolution appeared after divergence of TGV from the C. pila lineage.

Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life

BACKGROUND

Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.

METHODOLOGY/PRINCIPAL FINDINGS

Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.

CONCLUSIONS/SIGNIFICANCE

Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.

Swapped green algal promoters: aphVIII-based gene constructs with Chlamydomonas flanking sequences work as dominant selectable markers in Volvox and vice versa

Production of transgenic organisms is a well-established, versatile course of action in molecular biology. Genetic engineering often requires heterologous, dominant antibiotic resistance genes that have been used as selectable markers in many species. However, as heterologous 5' and 3' flanking sequences often result in very low expression rates, endogenous flanking sequences, especially promoters, are mostly required and are easily obtained in model organisms, but it is much more complicated and time-consuming to get appropriate sequences from less common organisms. In this paper, we show that aminoglycoside 3'-phosphotransferase gene (aphVIII) based constructs with 3' and 5' untranslated flanking sequences (including promoters) from the multicellular green alga Volvox work in the unicellular green alga Chlamydomonas and flanking sequences from Chlamydomonas work in Volvox, at least if a low expression rate is compensated by an enforced high gene dosage. This strategy might be useful for all investigators that intend to transform species in which genomic sequences are not available, but sequences from related organisms exist.

The pherophorins: common, versatile building blocks in the evolution of extracellular matrix architecture in Volvocales

Green algae of the order Volvocales provide an unrivalled opportunity for exploring the transition from unicellularity to multicellularity. They range from unicells, like Chlamydomonas, through homocytic colonial forms with increasing cooperation of individual cells, like Gonium or Pandorina, to heterocytic multicellular forms with different cell types and a complete division of labour, like Volvox. A fundamental requirement for the evolution of multicellularity is the development of a complex, multifunctional extracellular matrix (ECM). The ECM has many functions, which can change under developmental control or as a result of environmental factors. Here molecular data from 15 novel proteins are presented. These proteins have been identified in Chlamydomonas reinhardtii, Gonium pectorale, Pandorina morum and Volvox carteri, and all belong to a single protein family, the pherophorins. Pherophorin-V1 is shown to be a glycoprotein localized to the 'cellular zone' of the V. carteri ECM. Pherophorin-V1 and -V2 mRNAs are strongly induced not only by the sex inducer, which triggers sexual development at extremely low concentrations, but also by mechanical wounding. Like the extensins of higher plants, which are also developmentally controlled or sometimes inducible by wounding, the pherophorins contain a (hydroxy-)proline-rich (HR) rod-like domain and are abundant within the extracellular compartment. In contrast to most extensins, pherophorins have additional globular A and B domains on both ends of the HR domains. Therefore pherophorins most closely resemble a particular class of higher plant extensin, the solanaceous lectins (e.g. potato lectin), suggesting multivalent carbohydrate-binding functions are present within the A and B domains and are responsible for cross-linking. Our results suggest that pherophorins are used as the building blocks for the extracellular scaffold throughout the Volvocales, with the characteristic mesh sizes in different ECM structures being a result of the highly diverse extensions of the HR domains. Pherophorins have therefore been a versatile element during the evolution of ECM architecture in these green algae.

A twelve-step program for evolving multicellularity and a division of labor

The volvocine algae provide an unrivalled opportunity to explore details of an evolutionary pathway leading from a unicellular ancestor to multicellular organisms with a division of labor between different cell types. Members of this monophyletic group of green flagellates range in complexity from unicellular Chlamydomonas through a series of extant organisms of intermediate size and complexity to Volvox, a genus of spherical organisms that have thousands of cells and a germ-soma division of labor. It is estimated that these organisms all shared a common ancestor about 50 +/- 20 MYA. Here we outline twelve important ways in which the developmental repertoire of an ancestral unicell similar to modern C. reinhardtii was modified to produce first a small colonial organism like Gonium that was capable of swimming directionally, then a sequence of larger organisms (such as Pandorina, Eudorina and Pleodorina) in which there was an increasing tendency to differentiate two cell types, and eventually Volvox carteri with its complete germ-soma division of labor.

Green algae and the origin of land plants

Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled.

Evolution of multicellularity in the volvocine algae

Recent studies reveal that relationships among the volvocine algae are more complex than was previously believed. Nevertheless, this group still appears to provide an unrivaled opportunity to analyze an evolutionary pathway leading from unicellularity (Chlamydomonas) to multicellularity with division of labor (Volvox). Significant progress in this regard was made in the past year when two genes playing key roles in Volvox cellular differentiation were cloned, and clues were uncovered regarding their mechanisms of action.

Phylogenetic analysis of "Volvocacae" for comparative genetic studies

Sequence analysis based on multiple isolates representing essentially all genera and species of the classic family Volvocaeae has clarified their phylogenetic relationships. Cloned internal transcribed spacer sequences (ITS-1 and ITS-2, flanking the 5.8S gene of the nuclear ribosomal gene cistrons) were aligned, guided by ITS transcript secondary structural features, and subjected to parsimony and neighbor joining distance analysis. Results confirm the notion of a single common ancestor, and Chlamydomonas reinharditii alone among all sequenced green unicells is most similar. Interbreeding isolates were nearest neighbors on the evolutionary tree in all cases. Some taxa, at whatever level, prove to be clades by sequence comparisons, but others provide striking exceptions. The morphological species Pandorina morum, known to be widespread and diverse in mating pairs, was found to encompass all of the isolates of the four species of Volvulina. Platydorina appears to have originated early and not to fall within the genus Eudorina, with which it can sometimes be confused by morphology. The four species of Pleodorina appear variously associated with Eudorina examples. Although the species of Volvox are each clades, the genus Volvox is not. The conclusions confirm and extend prior, more limited, studies on nuclear SSU and LSU rDNA genes and plastid-encoded rbcL and atpB. The phylogenetic tree suggests which classical taxonomic characters are most misleading and provides a framework for molecular studies of the cell cycle-related and other alterations that have engendered diversity in both vegetative and sexual colony patterns in this classical family.

Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness

The determination of the secondary structure of the internal transcribed spacer (ITS) regions separating nuclear ribosomal RNA genes of Chlorophytes has improved the fidelity of alignment of nuclear ribosomal ITS sequences from related organisms. Application of this information to sequences from green algae and plants suggested that a subset of the ITS-2 positions is relatively conserved. Organisms that can mate are identical at all of these 116 positions, or differ by at most, one nucleotide change. Here we sequenced and compared the ITS-1 and ITS-2 of 40 green flagellates in search of the nearest relative to Chlamydomonas reinhardtii. The analysis clearly revealed one unique candidate, C. incerta. Several ancillary benefits of the analysis included the identification of mislabelled cultures, the resolution of confusion concerning C. smithii, the discovery of misidentified sequences in GenBank derived from a green algal contaminant, and an overview of evolutionary relationships among the Volvocales, which is congruent with that derived from rDNA gene sequence comparisons but improves upon its resolution. The study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequences, are most useful in systematic and other studies.

Volvox carteri alpha 2- and beta 2-tubulin-encoding genes: regulatory signals and transcription

Microtubules (MT) carry out several specialized morphogenetic functions in the multicellular green alga Volvox carteri (Vc), in addition to functions also executed in its closest unicellular relative, Chlamydomonas reinhardtii (Cr). To find out if these differences in morphogenetic complexity are reflected in tubulin (Tub) differences, we have compared the Vc alpha tub and beta tub genes with their Cr counterparts. The Vc genome contains two alpha tub and two beta tub genes. We report here the sequences of the alpha 2tub and beta 2tub genes, and thus complete the set of four tub sequences. The two alpha tub and two beta tub genes code for identical 451 (alpha) and 443 (beta) amino acid (aa) polypeptides; they differ from the Cr homologs in two (alpha) and one (beta) residues, respectively. Silent nucleotide (nt) exchanges between sibling genes are much more frequent in Vc than in Cr (12 vs. 2%), probably owing to a more stringent codon bias in the latter alga. Transcription of alpha 2tub and beta 2tub starts with an A, 26 bp (alpha 2) or 25 bp (beta 2) downstream from the TATA box. A 16-bp promoter element upstream and a G + C-rich sequence downstream from the TATA box are conserved in all tub of both species. Moreover, a 28-bp element of conserved sequence, and hence of possible functional significance, was found at similar locations in the 5' untranslated region (UTR) of all four alpha tub. A conserved TGTAA downstream from the translation stop codon represents the algal poly(A)-addition signal (in both Vc and Cr).(ABSTRACT TRUNCATED AT 250 WORDS)

Domain conservation in several volvocalean cell wall proteins

Based on our previous work demonstrating that (SerPro)x epitopes are common to extensin-like cell wall proteins in Chlamydomonas' reinhardtii, we looked for similar proteins in the distantly related species C. eugametos. Using a polyclonal antiserum against a (SerPro)10 oligopeptide, we found distinct sets of stage-specific polypeptides immunoprecipitated from in vitro translations of C. eugametos RNA. Screening of a C. eugametos cDNA expression library with the antiserum led to the isolation of a cDNA (WP6) encoding a (SerPro)x-rich multidomain wall protein. Analysis of a similarly selected cDNA (VSP-3) from a C. reinhardtii cDNA expression library revealed that it also coded for a (SerPro)x-rich multidomain wall protein. The C-terminal rod domains of VSP-3 and WP6 are highly homologous, while the N-terminal domains are dissimilar; however, the N-terminal domain of VSP-3 is homologous to the globular domain of a cell wall protein from Volvox carteri. Exon shuffling might be responsible for this example of domain conservation over 350 million years of volvocalean cell wall protein evolution.

Perspectives on future applications of experimental biology to evolution

The first three decades of the subdiscipline of biology known as "molecular evolution" have generated large amounts of new information that illuminate the nature of evolutionary pattern and process. Major progress has been made in identifying primary sequence variation in genes and their protein products, initially from biochemically tractable systems (from large or culturable organisms and from highly-reiterated genes or highly-expressed gene products). In the 1980s, these techniques that had been limited to specialists, to relatively few representatives of the diversity of life, and to a small number of those organisms' genes, were extended through advances in molecular genetics and biochemistry, resulting in an explosion of molecular information and a proliferation of molecular trees. Studies of variation in molecular characters also were rarely linked with studies of anatomical, behavioral or ecological diversity. More sophisticated molecular genetic and biochemical techniques, currently being applied to long-standing questions in cell and developmental biology in model systems, should be applicable to more diverse lineages in the next decade. Molecular trees produced from one or more "housekeeping genes" can identify key lineages (species, populations, genomes or gene families) which, by comparison to model systems, may illuminate important aspects of higher level variability. Thus, the next phase of research in the field of molecular evolution should see greater linkage between studies of simple molecular and more complex developmental characters, and increased functional testing of genes and gene products in an evolutionary context. This review highlights some comparative experimental approaches that I believe will be most effective in extending our understanding of molecular evolution and better linking the field to other areas of science in the next few years.

Flagellar, cellular and organismal polarity in Volvox carteri

It has previously been shown that the flagellar apparatus of the mature Volvox carteri somatic cell lacks the 180° rotational symmetry typical of most unicellular green algae. This asymmetry has been postulated to be the result of rotation of each half of the flagellar apparatus. Here it is shown that V. carteri axonemes contain polarity markers that are similar to those found in Chlamydomonas, except that in V. carteri the number one doublets do not face each other as they do in Chlamydomonas but are oriented in parallel and at approximately right angles to the line that connects the flagella. Thus, the rotational orientations of the axonemes are consistent with the postulate that the flagella of V. carteri have rotated in opposite directions, as was predicted earlier from the positions of the basal fibers and microtubular rootlets. Moreover, high-speed cinephotomicrographic analysis shows that the V. carteri flagellar effective strokes are also oriented in approximately the same direction, and in parallel planes. These results suggest that the direction of the effective stroke in both Chlamydomonas and Volvox is fixed, and that rotation of the axoneme is the cause of the differences in flagellar motility observed between Chlamydomonas and Volvox. These differences are probably essential for effective organismal motility. Cellular polarity of V. carteri can be related to that of Chlamydomonas after taking into account the developmental reorientation of flagellar apparatus components. This reorientation also results in the movement of the eyespot from a position nearer one of the flagellar bases to a position approximately equidistant between them. By analogy to Chlamydomonas, the anti side of the V. carteri somatic cell faces the spheroid anterior, the syn side faces the spheroid posterior. The cis side of the cell is to the cell's left (the right to an outside observer), although it cannot be described solely on the basis of eyespot position as it can in Chlamydomonas, while the trans side is to the cell's right. It follows that if the direction of the effective flagellar stroke is specified by structural features, then effective organismal motility in V. carteri, will be accomplished only if the cells are held in the proper orientation with respect to one another. The simplest arrangement that will yield both progression and rotation in ovoid or spherical colonies composed of biflagellate isokont cells is one in which the cells are arranged with rotational symmetry about the anterior-posterior axis of the spheroid. Analysis of the polarity of somatic cells from throughout the spheroid shows that it is constructed with just such symmetry. This symmetry probably originates with the very first divisions.

Green algae and the evolution of land plants: inferences from nuclear-encoded rRNA gene sequences

Phylogenetic analysis of 381 informative sites in partial sequences of nuclear-encoded large and small subunit ribosomal RNAs from 38 chlorophyll a- and b-containing plants (Chlorobionta sensu Bremer) including tracheophytes, bryophytes, charophytes and chlorophytes, supports the hypotheses of: (1) monophyly of the green plants (excluding Euglenophyta); (2) monophyly of the embryophytes; (3) non-monophyly of the bryophytes; (4) monophyly of the tracheophytes; and (5) a single origin of embryophytes from charophycean green algae. The Charales and Klebsormidium appear to be the green algae most closely related to the land plants. The unexpected basal divergence of Coleochaete and the apparent non-monophyly of the Zygnematales are not robustly supported and, thus, are interpreted to be sources of new questions, rather than new phylogenetic hypotheses.