- Research article
- Open Access
Transcriptional analysis of cell growth and morphogenesis in the unicellular green alga Micrasterias(Streptophyta), with emphasis on the role of expansin
© Vannerum et al; licensee BioMed Central Ltd. 2011
- Received: 5 May 2011
- Accepted: 25 September 2011
- Published: 25 September 2011
Streptophyte green algae share several characteristics of cell growth and cell wall formation with their relatives, the embryophytic land plants. The multilobed cell wall of Micrasterias denticulata that rebuilds symmetrically after cell division and consists of pectin and cellulose, makes this unicellular streptophyte alga an interesting model system to study the molecular controls on cell shape and cell wall formation in green plants.
Genome-wide transcript expression profiling of synchronously growing cells identified 107 genes of which the expression correlated with the growth phase. Four transcripts showed high similarity to expansins that had not been examined previously in green algae. Phylogenetic analysis suggests that these genes are most closely related to the plant EXPANSIN A family, although their domain organization is very divergent. A GFP-tagged version of the expansin-resembling protein MdEXP2 localized to the cell wall and in Golgi-derived vesicles. Overexpression phenotypes ranged from lobe elongation to loss of growth polarity and planarity. These results indicate that MdEXP2 can alter the cell wall structure and, thus, might have a function related to that of land plant expansins during cell morphogenesis.
Our study demonstrates the potential of M. denticulata as a unicellular model system, in which cell growth mechanisms have been discovered similar to those in land plants. Additionally, evidence is provided that the evolutionary origins of many cell wall components and regulatory genes in embryophytes precede the colonization of land.
- Green Fluorescence Protein
- Land Plant
- Secondary Cell Wall
- Green Fluorescence Protein Fluorescence
Although the form and function of plant cells are strongly correlated, the processes that determine the cell shape remain largely unknown. Plant cell morphogenesis is regulated in a non-cell-autonomous fashion by the surrounding tissues , hormone interference during ontogenesis, and sometimes by polyploidy as a consequence of endoreduplication [2, 3]. In contrast, in unicellular relatives of land plants, it is possible to study the endogenous controls of cell morphogenesis without the interference by interacting cells and to better understand how these mechanisms have evolved in the green lineage.
Ultimately, the plant cell morphology is determined by the composition and structure of the cell wall that governs the cell expansion direction and rate. As in land plants, the primary cell wall of M. denticulata Bréb. consists mainly of pectins [10, 11], cellulose microfibrils , hemicelluloses  and arabinogalactan proteins (AGPs) [10, 13]. The secondary cell wall owes it rigidness to cellulose microfibrils originating from rosettes organized as hexagonal arrays [14, 15], whereas mixed-linked glucan is the dominant hemicellulose .
In land plants, expansins are important regulators of turgor-driven cell wall expansion. These cell wall proteins comprise a large multigene superfamily consisting of four families (EXPA, EXPB, EXLA and EXLB) of which the evolutionary relationships are well characterized [16, 17]. They are unique in their ability to loosen the cell wall non-enzymatically by disrupting hydrogen bonds that link the cellulose and hemicellulose wall components [18–21]. Land plant expansins consist of two domains and a secretion signal. The N-terminal expansin domain 1 and the C-terminal expansin domain 2 are homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins and a domain present in a family of grass pollen allergens, identified as a putative cellulose binding site , respectively. Expansins play a role in tissue development [23, 24] and in growth of suspension-cultured cells [25, 26]. Although genes encoding expansin-like proteins have been recently identified in green algae transcriptomes , their physiological function and phylogenetic relationships with land plant expansins remain unknown.
Here, we explore the molecular basis of cell morphogenesis and cell wall formation in synchronized M. denticulata cells by means of a cDNA-amplified fragment length polymorphism (cDNA-AFLP)-based quantitative transcriptome analysis . Several cell wall-related genes, among which expansins, were identified. Examination of the expansins provided the first structural, phylogenetic and functional data on green algal homologues within this gene family.
cDNA-AFLP expression profiling
Of the 129 annotated genes, 118 clustered into six groups (designated C1a, C1b, C2, C3, C4, and C5) (Figure 2) according to the timing of their highest expression (Figure 1C,D). Except for one cluster consisting of six genes (cluster C1b; Figure 2), the expression profiles were reproducible in the two independent sampling series. The few genes not included in one of the described clusters typically showed narrow temporal expression patterns.
Based on their annotation, the TDFs were classified into 14 functional categories, named according to the Gene Ontology terminology (http://www.geneontology.org) (Figure 3; Additional file 3). The association between the functional category and the TDF clustering was not significant (χ2 test; p = 0.070). The major group with a significant hit was involved in cell wall metabolism. The second largest category corresponded to sequences sharing significant similarity to unknown or hypothetical proteins.
Of 18 TDFs with similarity to genes involved in cell wall biogenesis or cell pattern formation, the RNA samples of the second cDNA-AFLP replication series and on an independently sampled series (Additional file 1) were analyzed by real-time quantitative reverse-transcription (qRT)-PCR. In general, the expression profiles obtained by cDNA-AFLP and qRT-PCR (Additional file 4) corresponded well (Additional file 5), confirming the obtained expression results.
Genes relevant for cell pattern formation
Seven TDFs could be identified that might be relevant for cell pattern formation in M. denticulata, among which two members of the Rab GTPase cycle and two members of the SNARE cycle of membrane fusion reactions. Rab8, similar to Md1852, is known to be involved in post-Golgi transport to the plasma membrane, inducing the formation of new surface extensions and believed to be regulated by a guanine nucleotide dissociation inhibitor  possibly corresponding to Md0818. Both Md1852 and Md0818 belonged to cluster C1a and, thus, had increased mRNA levels before the onset of mitosis. This observation might be related to the determination of the basic symmetry of a M. denticulata cell before mitosis, indicated by the development of a three-lobed semicell after removal of the nucleus . In contrast, the SNARE cycle members were highly expressed in cluster C3, pointing to a role in further differentiation during the lobe stages for Md1404 (similar to plant syntaxin 32) and Md1560 (similar to a regulatory AAA-type of ATPase).
Two TDFs were identified encoding putative glycophosphatidylinositol (GPI) anchors: Md4071 and Md4341, belonging to clusters C1a, and C4, respectively. Among other properties, the function of a GPI anchor might be its dominant targeting to a specific membrane domain , possibly establishing a membrane template for morphogenesis. Md4341 turned out to be a 179-amino-acid protein containing a signal peptide and a fasciclin domain (a putative cell adhesion domain) (E-value 2.9E-07), with similarity to a fasciclin-like and an AGP-like protein from Brachypodium sylvaticum [CAJ26371.1] and Arabidopsis thaliana [AAM62616.1], respectively (Additional file 6).
Md3533 (cluster C3), similar to a very-long-chain fatty acid-condensing enzyme, might be involved in morphogenesis in accordance to the essential role in cell expansion during plant morphogenesis of Arabidopsis .
Genes involved in cell wall metabolism
Phylogenetic relationship of M. denticulataexpansin-resembling proteins
Domain organization of the M. denticulataexpansin-resembling proteins
Characteristics (domains and motifs) of the Micrasterias denticulata expansin-resembling proteins
Eight conserved cysteines
Catalytic site key residues
Four conserved tryptophan (W) residues (* structurally related residues)
2(W) 1(F*) 1(Y*)
2(W) 1(F*) 1(Y*)
HATFYG motif (A)
HFDL motif (A, B)
CDRC motif (LA)
Long carboxy terminal extension (LA)
Subcellular localization of the expansin-resembling MdEXP2and phenotypic changes due to its overexpression
Next, 26 independent transient transgenic cells were isolated and further analysed (Additional file 13). A group of cells lost the GFP-fluorescence within a few days and divided, resulting in normal daughter cells, while the majority of the cells died, possibly because of strong MdEXP2 overexpression as indicated by their bright GFP fluorescence. However, in eight independent cell lines, a range of phenotypes related to MdEXP2 overexpression during cell division and growth could be observed. Line 11 exhibited strong lobe elongation without loss of growth polarity after the first cell division (Figure 8B). The lobes were stretched and rounded instead of flattened at their tips. After the second cell division of line 11 and in all other cases (lines 6, 7, 8, 12, 13, 18, 19), the growth polarity was altered. Line 13 lost its planarity upon cell division and, thus, had the most severe phenotype. New semicells, without the characteristically lobed morphology, but almost without indentations, grew out three-dimensionally. Upon a new cell division of one of the daughter cells, the same phenotype was observed, whereas the newly formed semicells were also fused with each other (Figure 8F-I). In lines 6, 7, 8, 11 (from the second cell division onwards), 12, 18, and 19 axial but not radial elongation was impaired, resulting in semicells with a stunted polar lobe and fused lateral lobes (Figure 8C-E). Sometimes, the second division gave rise to a similar morphology (Figure 8D), but in most cases the phenotype was lost over one to two subsequent generations (Figure 8C). That all phenotypes still had the GFP signal and none of them resulted from control experiments with transgenic cells expressing only the GFP  suggests that they were related to the expression of the transgene.
Genome-wide expression analysis revealed a role for Rab and SNARE cycles in membrane fusions and for AGP-like proteins in cell pattern establishment. AGPs, differing in composition from land plants, had recently been found to be present in the growing primary cell wall of Micrasterias . Our analysis further suggests an involvement of class-III peroxidases, XTH and expansins in cell wall growth. Class-III peroxidases had been considered absent in green algae , although a (partial) mRNA occurred in the desmid Closterium . Here, a full length algal class-III peroxidase is linked to cell growth. Furthermore, despite their supposed lack of xyloglucans , XET activity was found in the streptophyte Chara and the chlorophyte Ulva . Recently, the (1→3, 1→4)-β-glucan (mixed linked glucan, MLG) has been determined as the main constituent of the secondary cell wall of Micrasterias  and in this study, the first algal XTH was identified.
The green algae Valonia (Chlorophyta) and Nitella (Streptophyta) exhibit acid-induced wall extension, but this response is seemingly not mediated by proteins [49, 50]. Contrary to the assumption of a land plant specific mechanism , four genes with significant similarity to expansins were up-regulated during cell growth of Micrasterias, in agreement with a presumed ancient evolutionary origin . Based on significant BLAST similarities with the expansin domains , global pairwise alignment and phylogeny, and structural features like the presence of a secretion signal, MdEXP2, MdEXP1, and MdEXP3 are considered expansins, but considerably diverge in gene architecture from embryophytic expansins, as indicated by both domain analysis and phylogeny. These results add to the evidence that expansins are not strongly conserved through evolution . The key residues of the GH45 domain catalytic site and the HFDL motif, which are present in land plants and Spirogyra, do not occur in Micrasterias. The HFDL motif is present in most groups of plant expansins, but is absent in a few plant EXPA and EXPB proteins . The eight N-terminal cysteines required for protein folding  and the four C-terminal tryptophans or related residues involved in cellulose binding  are conserved between Micrasterias, Spirogyra and land plants and can be considered as key characteristics of plant expansins. The GGxCGY/F and the GxxCGxCF/Y motifs in the GH45 domain are conserved as well. The only constant difference in the conserved amino acid residues in Micrasterias when compared to land plants is the occurrence of a serine residue instead of an alanine residue in the GGACGY motif of the GH45 domain. As expansins disrupt noncovalent bonding between cellulose microfibrils and matrix glucans that stick to the microfibril , we hypothesize that the characteristics of the MdEXPs might be related to the dominant MLG in the secondary cell walls of Micrasterias  instead of the (1→4)-β-glucan backbone present in dicotyledonous plants. The occurrence of MLG in lichens , fungi , green algae (Micrasterias) , horsetails , and Poales  has been suggested to result from convergent evolution , whereas the occurrence of distinct MdEXPs might be connected to two different (primary and secondary) cell wall types, implied by their different temporal expression patterns.
Based on the present expansin phylogeny, combined with current hypotheses on the evolution of the closest relatives to land plants [6, 56], expansins can fairly be assumed to have evolved before the origin of land plants. However, the unresolved relationships between Embryophytes and the streptophyte lineages Zygnematophyceae, Coleochaetophyceae and Charophyceae  hamper a solid reconstruction of expansin gene history. Assuming that the Zygnematophyceae form the closest living relatives to land plants , a possible scenario would be that expansins evolved into two lineages (EXPA and EXPB + EXL) in a common ancestor of Embryophytes and Zygnematophyceae (Figure 6B). The apparent lack of EXPB and EXL in Micrasterias and Spirogyra might be due to gene loss, early in the evolution of the Zygnematophyceae. It should be emphasized however, that the ancient relationships among expansin families are difficult to resolve. Therefore the phylogenetic positions of the green algal expansin-resembling genes should be interpreted with care, hinting at a complete divergence of the plant expansin families within the embryophytic lineage.
Distinct differences in gene architecture between Micrasterias and embryophytic expansins have raised the question whether the biochemical functions of MdEXPs and embryophytic expansins are similar. To this end, we studied functionally MdEXP2, the MdEXP with the highest expression levels during growth, through localization and overexpression. A GFP antibody detecting the MdEXP2-GFP fusion protein was used, because the sequence conservation was too low for the available plant expansin antibodies. Unfortunately, currently, because only transient genetic transformation of Micrasterias is possible , immunoelectron microscopic detection in the growing cell walls is unfeasible. Nevertheless, the ectopically produced protein was targeted to the fully-grown secondary cell wall. In addition, the phenotypic results obtained from its overexpression suggest that MdEXP2 can alter the cell wall shape, but this effect on growth cannot be excluded to result from saturation or blockage of the membrane trafficking of other essential proteins. The phenotypes were remarkably variable, whereby the phenotype severity did not seem to directly correlate with expansin abundance (as inferred from MdEXP2-GFP fluorescence intensity), as reported previously [58–62]. Although a phenotype could be observed corresponding to the expected enhanced wall extensibility due to increased expansin levels , the elongation growth impaired in most cases, but not the lateral expansion, resulting in the fusion of the lateral lobes. A number of factors might explain the reduced growth of tomato (Solanum lycopersicum) overexpressing an expansin . All together, the growth phase-specific expression, the accumulation in the cell walls, and its overexpression phenotype, allow us to to hypothesize that MdEXP2 might have a biochemical function related to that of land plant expansins.
Our study provides novel data on gene expression during morphogenesis and cell growth in the desmid Micrasterias denticulata and adds to our understanding of the evolution of genes involved in cell wall formation in green algae and land plants.
Cell walls have played crucial roles in the colonization of land by plants [63, 64]. For a detailed understanding of how cell walls have evolved, cell wall components and cell wall-related genes in land plants and their closest relatives, the streptophyte green algae need to be analyzed comprehensively. Although some cell wall components appear to be adaptations of land plants, cell wall evolution after the colonization of land is seemingly characterized by the elaboration of a pre-existing set of genes and polysaccharides rather than by substantial innovations [65–68]. The data add to the growing body of evidence that the evolutionary origins of many cell wall components and regulating genes in embryophytes antedate the colonization of land.
Culture conditions, synchronization and sampling
A clonal Micrasterias denticulata culture was grown in twofold diluted Desmidiaceae medium  at 23°C and 120-140 μmol photons.m-2.s-1 under a 14-h light/10-h dark regime.
Two independent cultures were synchronized by replacing the growth medium of a stationary culture, diluting the density, and extending the light period to 24 h. Cells were sampled from synchronized cultures for RNA extraction at five consecutive time points during growth (T1 to T5) that were chosen to include for each time point a different proportion of cells at different morphogenetic stages (bulge, lobe, and doublet stage) (Figure 1C,D). Two independent stationary cultures served as control samples. Cells were concentrated by centrifugation for 1 min at 4°C and 4000 rpm and washed with phosphate buffered saline (PBS). Cell pellets were snap-frozen in liquid nitrogen and stored at -70°C.
RNA extraction and cDNA-AFLP analysis
Total RNA was isolated from approximately 80,000 frozen cells at each time point as described  with slight modifications. Instead of β-mercaptoethanol, 2 M stock solution of the anti-RNase agent dithiothreitol was added to the extraction buffer to a final concentration of 50 mM . Cells were disrupted and homogenized in a bead mill (Retsch) (5 min at frequency 30 s-1) with silicone-carbide sharp particles (Biospec Products) after the cell pellet had been thawed and suspended in the extraction buffer. Phytopure resin (GE-Healthcare) was added during the first chloroform:isoamylalcohol extraction to eliminate mucilage contamination of the RNA . RNA samples were controlled qualitatively with the RNA 6000 Nano kit of the Bioanalyzer 2100 (Agilent Technologies) and quantified with the ND-1000 UV-Vis Spectrophotometer (Nanodrop).
Starting from 2 μg of total RNA, cDNA synthesis and cDNA-AFLP analysis with BstYI and MseI as restriction enzymes were done according to the procedures as described . For the selective amplification, BstYI + C/T + 1/MseI + 2 primer pairs were used, resulting in 128 primer combinations. The cDNA-AFLP fingerprints were visualized with an autoradiography platform (PhosphorImager 445 SI; Molecular Dynamics).
Scanned gel images were quantitatively analyzed with the AFLP-QuantarPro image analysis software (Keygene N.V.). Expression values per gene were normalized for replicate effects by subtracting the replicate mean value (Additional file 2). Average linkage hierarchical clustering with the TMeV v4 software (http://www.tm4.org) and adaptive quality-based clustering (minimum two tags in a cluster, 0.95 significance level)  of the normalized expression data were carried out.
To assess the effect of the various cell division stages (T1-T5) on the gene expression during synchronized growth, a linear regression model of the form y = μ + rep + time + ε was fitted to the data, where y represents the raw expression values, rep and time the fixed replicate and time effects, respectively, and ε the random error. For all TDFs, a F-statistic was calculated, P-values were assigned to the main term time and subsequently transformed into false discovery rates, and Q-values  (Additional file 2). Besides the TDFs with a significant (Q<0.05) differential expression across the five time points, TDFs that were clearly absent in the stationary cultures but present during the synchronized growth, were excised from the dried gels, irrespective the significance of their differential expression across the five stages, followed by amplification and subsequent sequencing .
The TDFs were designated by Md (for M. denticulata) followed by a number corresponding to the AFLP fragment. After mutual alignment of the sequences, only the longest one of a group of identical sequences was retained, except when the TDFs displayed different expression profiles. Each sequence was identified by a similarity search against the public databases with the Blast2GO v1.7.2 program (http://www.Blast2GO.de) . In addition to hits displaying an E-value < 1.E-03, hits with E-values between 1.E + 00 and 1.E-03 and a similarity > 50% were retained for further analysis.
Real-time qRT-PCR assay
Primers (Additional file 14) were designed with the Beacon Designer 7.0 (PREMIER Biosoft International) and the Oligo PerfectTM Designer (Invitrogen). Isolated RNA was treated with DNaseI (GE-Healthcare). An aliquot of 1 μg of total RNA from each sample was used for cDNA synthesis. The reverse transcription was carried out with oligo-dT primers and the SuperscriptTM II reverse transcriptase (Invitrogen) according to the manufacturer's instructions.
A set of reference genes was selected, based on their constitutive expression pattern during morphogenesis, to serve as a normalization factor in quantitative reverse-transcription-(qRT)-PCR analysis. Their expression stability (M) was analyzed with the geNormTM program . Among 10 constitutively expressed TDFs, Md0789 (similar to a reticulon of Arabidopsis thaliana) and Md1473 (similar to peroxiredoxin 6 of Norway rat [Rattus norvegicus]) (M value = 0.421 and 0.489, respectively) were the two most stably expressed genes, followed by Md0386 (similar to the unknown gene of A. thaliana at5g13390 t22n19_40). To determine the number of internal control genes necessary for reliable data normalization, the pairwise variation value between two sequential normalization factors V2/3 was calculated with geNormTM and turned out to be 0.151 under our experimental conditions, slightly higher than the cut-off value of 0.15. The inclusion of a fourth internal control gene resulted in an increase of the pairwise variation, yielding a V3/4 value of 0.129. As a result, the use of the two or three most stably expressed genes was considered to be sufficient for reliable data normalization . PCR fragments were amplified in triplicate on the LightcyclerTM 480 (Roche Applied Science) platform with SYBRTM Green QPCR Master Mix (Stratagene), according to the manufacturer's instructions with cycling conditions of 10 min preincubation at 95°C and 45 cycles at 95°C for 10 s, 58°C for 15 s, and 72°C for 15 s. Amplicon dissociation curves were recorded by heating from 65°C to 95°C. qBaseTM  was used for relative quantification.
RACE PCRs, protein domain identification, sequence alignment and phylogenetic analyses
The ends of the cDNAs were obtained by rapid amplification of cDNA ends (RACE) PCRs with plasmid DNA from a cDNA library of growth-synchronized M. denticulata (purchased from Invitrogen) as template. For MdEXP1, MdEXP3, and Md0434 only 5' RACE PCR was done, because the TDF contained the stopcodon and a part of the 3' untranslated region. For Md4341, MdXTH1, MdEXP2, and MdEXP4 both 5' RACE and 3' RACE were necessary. Gene-specific primers were designed with the eprimer3 program  and used in combination with vector-specific (pDONR222.1) primers (Additional file 15) in a PCR consisting of 1 min pre-incubation at 95°C and 30 cycles at 95°C for 30 s, 54°C for 30 s and 72°C for 2 min 30 s, followed by 1 cycle at 72°C for 5 min.
Protein domains in the ORF sequences were identified with the SMART tool (http://smart.embl-heidelberg.de/) [79, 80]. Signal sequences were confirmed with the SignalP 3.0 Server (http://www.cbs.dtu.dk/services/SignalP) [81, 82] and iPSORT prediction (http://ipsort.hgc.jp/) .
Similar sequences were retrieved from GenBank (http://www.ncbi.nlm.nih.gov) using protein BLAST and tblastx  (Additional file 16). The sequences were aligned using MUSCLE . To remove signal peptides and C-terminal extensions, the alignment was trimmed from a conserved tryptophan near the N-terminus to a conserved phenylalanine near the C-terminus .
Two sets of alignments were considered for the phylogenetic analyses. The first dataset consisted of the four M. denticulata expansin-resembling proteins (MdEXPs), 26 land plant expansins representing the 17 orthologous clades within the four land plant expansin families , and six EST sequences of the streptophyte green alga Spirogyra pratensis that showed significant similarity to land plant expansins . Five expansin-like sequences of the social amoeba, Dictyostelium discoideum, were selected as outgroup based on their inferred relationship with land plant expansins [16, 86]. This alignment was 227 amino acids long (Additional file 17). The second dataset included all sequences of the first alignment plus nine putative expansin genes found in four species of Chlorophyta (the sister clade of the Streptophyta) (322 amino acids long; Additional file 18) and was used to assess the phylogenetic position of other putative expansin sequences of green algae.
Models of protein evolution were selected with ProtTest 1.4 . Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) were analyzed under a WAG model of amino acid substitution with among site rate heterogeneity (gamma distribution with eight categories) for all datasets with PhyML v2.4.4  and non-parametric bootstrapping (1000 replicates) to assess statistical support of internal branches with MrBayes 3.1.2 , respectively. Two parallel runs, each consisting of four incrementally heated chains were run for 2 x106 generations, sampling every 1000 generations. Convergence of log-likelihoods was assessed in Tracer v1.4 . A burn-in sample of 500 trees (well beyond the point at which convergence of parameter estimates had taken place) was removed before the majority rule consensus trees were constructed.
Overexpression of MdEXP2and microscopy
The ORF of MdEXP2 was cloned into the SpeI restriction site (ACTAGT) of the vector pSA405A under the control of the chlorophyll a/b-binding protein encoding gene of the desmid Closterium and was C-terminally fused to the green fluorescence protein gene (GFP) . Primers were: forward primer 5'-ATGACTAGTATGAAAATCGGCATAATCCA-3' and reverse primer 5'-GGAACTAGTTAGGCACCCATTAACGGC-3'. The PCR was 2 min preincubation at 94°C and 5 cycles at 94°C for 45 s, 45°C for 45 s, and 68°C for 3 min, followed by 30 cycles at 94°C for 45 s, 55°C for 45 s, and 68°C for 2 min, and by 1 cycle at 72°C for 5 min. The recombined plasmid was introduced into M. denticulata by microparticle bombardment .
For confocal microscopy, a 100M microscope (Zeiss) was used, equipped with the LSM510 software version 3.2. Samples were scanned with a 20x (numerical aperture of 0.5) and a 63x water corrected objective (numerical aperture of 1.2). GFP fluorescence was visualized with argon laser illumination at 488 nm and a 500 to 530 nm band emission filter.
For transmission electron microscopy (TEM), a GFP antibody (Rb, (ab6556) Abcam) compatible protocol was followed to prepare the samples. MdEXP2-GFP-overexpressing M. denticulata cells were embedded in a yeast paste in a membrane carrier (Leica) and frozen immediately in a high-pressure freezer (EM PACT; Leica Microsystems). Freeze substitution was carried out in a Leica EM AFS instrument. Samples were infiltrated at 4°C stepwise in LR-White, hard grade (London Resin Company Ltd.) and embedded in capsules. Ultrathin sections of gold interference color were cut with an EM UC6 ultramicrotome (Leica) and collected on formvar-coated copper mesh grids. Grids were floated on blocking solution followed by incubation in a 1:25 and 1:10 dilution (in 1% bovine serum albumin in PBS) of primary antibodies (GFP antibody, (Rb, (ab6556) Abcam) for 60 min. The grids were labelled with protein A-10-nm gold (PAG10nm) (Cell Biology Department, Utrecht University). Control experiments consisted of treating sections with PAG10nm alone. Sections were post-stained in an automatic contrasting instrument (EM AC20; Leica Microsystems GmbH) for 30 min in uranyl acetate at 20°C and for 7 min in lead stain at 20°C. Grids were viewed with a 1010 transmission electron microscope (JEOL) operating at 80 kV.
Newly obtained sequence data were deposited in GenBank; the transcript derived fragments under accession numbers HE578289 to HE578716, the reference genes under accession numbers HE580226 to HE580228, and the open reading frames under accession numbers HE578717 to HE578726.
The authors thank Debbie Rombaut and Sofie D'hondt for assistance with the cDNA-AFLP analysis, Andy Vierstraete and Wilson Ardilez-Diaz for sequencing, Filip Waumans for constructing a database for the sequences identified in this study, Klaas Vandepoele for help with bioinformatics, Mansour Karimi for cloning advice, Ellen Cocquyt for phylogenetic advice, Daniel Cosgrove for nomenclatural advice, and Martine De Cock for help in preparing the manuscript. This work was supported by the Interuniversity Attraction Poles Programme (UIAP VI/33), initiated by the Belgian State, Science Policy Office, the Research Foundation-Flanders (postdoctoral fellowship grants to F.L. and L.D.V.), and the Agency for Innovation by Science and Technology in Flanders ("Strategisch Basisonderzoek" project SBO040093 and predoctoral fellowships to K.V., M.J.J.H., and J.G.).
- Dupuy L, Mackenzie J, Haseloff J: Coordination of plant cell division and expansion in a simple morphogenetic system. Proc Natl Acad Sci USA. 2010, 107: 2711-2716. 10.1073/pnas.0906322107.PubMedPubMed CentralView ArticleGoogle Scholar
- Yang Z, Fu Y: ROP/RAC GTPase signaling. Curr Opin Plant Biol. 2007, 10: 490-494. 10.1016/j.pbi.2007.07.005.PubMedPubMed CentralView ArticleGoogle Scholar
- Kryvych S, Nikiforova V, Herzog M, Perezza D, Fisahn J: Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level. Plant Physiol Biochem. 2008, 46: 160-173. 10.1016/j.plaphy.2007.11.001.PubMedView ArticleGoogle Scholar
- Karol KG, McCourt RM, Cimino MT, Delwiche CF: The closest living relatives of land plants. Science. 2001, 294: 2351-2353. 10.1126/science.1065156.PubMedView ArticleGoogle Scholar
- Turmel M, Pombert JF, Charlebois P, Otis C, Lemieux C: The green algal ancestry of land plants as revealed by the chloroplast genome. Int J Plant Sci. 2007, 168: 679-689. 10.1086/513470.View ArticleGoogle Scholar
- Rodríguez-Ezpeleta N, Philippe H, Brinkmann H, Becker B, Melkonian M: Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta. Mol Biol Evol. 2007, 24: 723-731.PubMedView ArticleGoogle Scholar
- Finet C, Timme RE, Delwiche CF, Marlétaz F: Multigene phylogeny of the green lineage reveals the origin and diversification of land plants. Curr Biol. 2010, 20: 2217-2222. 10.1016/j.cub.2010.11.035.PubMedView ArticleGoogle Scholar
- Wodniok S, Brinkmann H, Glockner G, Heidel A, et al: Origin of land plants: Do conjugating green algae hold the key?. BMC Evol Biol. 2011, 11: 104-10.1186/1471-2148-11-104.PubMedPubMed CentralView ArticleGoogle Scholar
- Meindl U: Micrasterias cells as a model system for research on morphogenesis. Microbiol Rev. 1993, 57: 415-433.PubMedPubMed CentralGoogle Scholar
- Lütz-Meindl U, Brosch-Salomon S: Cell wall secretion in the green alga Micrasterias. J Microsc. 2000, 198: 208-217. 10.1046/j.1365-2818.2000.00699.x.PubMedView ArticleGoogle Scholar
- Eder M, Lütz-Meindl U: Pectin-like carbohydrates in the green alga Micrasterias characterized by cytochemi cal analysis and energy filtering TEM. J Microsc. 2008, 231: 201-214. 10.1111/j.1365-2818.2008.02036.x.PubMedView ArticleGoogle Scholar
- Giddings TH, Brower DL, Staehelin LA: Visualization of particle complexes in the plasma membrane of Micrasterias denticulata associated with the formation of cellulose fibrils in primary and secondary cell walls. J Cell Biol. 1980, 84: 327-339. 10.1083/jcb.84.2.327.PubMedView ArticleGoogle Scholar
- Eder M, Tenhaken R, Driouich A, Lütz-Meindl U: Occurrence and characterization of arabinogalactan-like proteins and hemicelluloses in Micrasterias (Streptophyta). J Phycol. 2008, 44: 1221-1234. 10.1111/j.1529-8817.2008.00576.x.View ArticleGoogle Scholar
- Kim NH, Herth W, Vuong R, Chanzy H: The cellulose system in the cell wall of Micrasterias. J Struct Biol. 1996, 117: 195-203. 10.1006/jsbi.1996.0083.PubMedView ArticleGoogle Scholar
- Nakashima J, Heathman A, Brown RM: Antibodies against a Gossypium hirsutum recombinant cellulose synthase (Ces A) specifically label cellulose synthase in Micrasterias denticulata. Cellulose. 2006, 13: 181-190. 10.1007/s10570-006-9059-y.View ArticleGoogle Scholar
- Li Y, Darley CP, Ongaro V, Fleming A, Schipper O, Baldauf SL, McQueen-Mason SJ: Plant expansins are a complex multigene family with an ancient evolutionary origin. Plant Physiol. 2002, 128: 854-864. 10.1104/pp.010658.PubMedPubMed CentralView ArticleGoogle Scholar
- Carey RE, Cosgrove DJ: Portrait of the expansin superfamily in Physcomitrella patens: comparisons with angiosperm expansins. Ann Bot. 2007, 99: 1131-1141. 10.1093/aob/mcm044.PubMedPubMed CentralView ArticleGoogle Scholar
- McQueen-Mason S, Durachko DM, Cosgrove DJ: Two endogenous proteins that induce cell wall extension in plants. Plant Cell. 1992, 4: 1425-1433.PubMedPubMed CentralView ArticleGoogle Scholar
- McQueen-Mason SJ, Cosgrove DJ: Expansin mode of action on cell walls: Analysis of wall hydrolysis, stress relaxation, and binding. Plant Physiol. 1995, 107: 87-100.PubMedPubMed CentralGoogle Scholar
- Cosgrove DJ: Expansive growth of plant cell walls. Plant Physiol Biochem. 2000, 38: 109-124. 10.1016/S0981-9428(00)00164-9.PubMedView ArticleGoogle Scholar
- Cosgrove DJ: Loosening of plant cell walls by expansins. Nature. 2000, 407: 321-326. 10.1038/35030000.PubMedView ArticleGoogle Scholar
- Sampedro J, Cosgrove DJ: The expansin superfamily. Genome Biol. 2005, 6: 242-10.1186/gb-2005-6-12-242.PubMedPubMed CentralView ArticleGoogle Scholar
- Pien S, Wyrzykowska J, McQueen-Mason S, Smart C, Fleming A: Local expression of expansin induces the entire process of leaf development and modifies leaf shape. Proc Natl Acad Sci USA. 2001, 98: 11812-11817. 10.1073/pnas.191380498.PubMedPubMed CentralView ArticleGoogle Scholar
- Cho HT, Cosgrove DJ: Regulation of root hair initiation and expansin gene expression in Arabidopsis. Plant Cell. 2002, 14: 3237-3253. 10.1105/tpc.006437.PubMedPubMed CentralView ArticleGoogle Scholar
- Link BM, Cosgrove DJ: Acid-growth response and α-expansins in suspension cultures of Bright Yellow 2 tobacco. Plant Physiol. 1998, 118: 907-916. 10.1104/pp.118.3.907.PubMedPubMed CentralView ArticleGoogle Scholar
- Wang CX, Wang L, McQueen-Mason SJ, Pritchard J, Thomas CR: pH and expansin action on single suspension-cultured tomato (Lycopersicon esculentum) cells. J Plant Res. 2008, 121: 527-534. 10.1007/s10265-008-0176-6.PubMedView ArticleGoogle Scholar
- Timme RE, Delwiche CF: Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. BMC Plant Biol. 2010, 10: 96-10.1186/1471-2229-10-96.PubMedPubMed CentralView ArticleGoogle Scholar
- Vuylsteke M, Peleman JD, van Eijk MJT: AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protocols. 2007, 2: 1399-1413. 10.1038/nprot.2007.174.PubMedView ArticleGoogle Scholar
- Milioni D, Sado PE, Stacey NJ, Roberts K, McCann MC: Early gene expression associated with the commitment and differentiation of a plant tracheary element is revealed by cDNA-amplified fragment length polymorphism analysis. Plant Cell. 2002, 14: 2813-2824. 10.1105/tpc.005231.PubMedPubMed CentralView ArticleGoogle Scholar
- Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inzé D, Zabeau M: Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics. 2003, 269: 173-179.PubMedGoogle Scholar
- Schwartz SL, Cao C, Pylypenko O, Rak A, Wandinger-Ness A: Rab GTPases at a glance. J Cell Sci. 2007, 120: 3905-3910. 10.1242/jcs.015909. [Err. J Cell Sci 121, 246 2008)].PubMedView ArticleGoogle Scholar
- Kallio P, Heikkilä H: On the effect of elimination of nuclear control in Micrasterias. Plant Cells. Edited by: Bonotto S, Goutier R, Kirchmann K, Maisin JR. 1972, New York, Academic Press, 167-192.Google Scholar
- Takos AM, Dry IB, Soole KL: Detection of glycosyl-phosphatidylinositol-anchored proteins on the surface of Nicotiana tabacum protoplasts. FEBS Lett. 1997, 405: 1-4. 10.1016/S0014-5793(97)00064-1.PubMedView ArticleGoogle Scholar
- Zheng H, Rowland O, Kunst L: Disruptions of the Arabidopsis enoyl-CoA reductase gene reveal an essential role for very-long-chain fatty acid synthesis in cell expansion during plant morphogenesis. Plant Cell. 2005, 17: 1467-1481. 10.1105/tpc.104.030155.PubMedPubMed CentralView ArticleGoogle Scholar
- Vannerum K, Abe J, Sekimoto H, Inzé D, Vyverman W: Intracellular localization of an endogenous cellulose synthase of Micrasterias denticulata (Demidiales, Chlorophyta) by means of transient genetic transformation. J Phycol. 2010, 46: 839-845. 10.1111/j.1529-8817.2010.00867.x.View ArticleGoogle Scholar
- Oertel A, Aichinger N, Hochreiter R, Thalhamer J, Lütz-Meindl U: Analysis of mucilage secretion and excretion in Micrasterias (Chlorophyta) by means of immunoelectron microscopy and digital time lapse video microscopy. J Phycol. 2004, 40: 711-720. 10.1111/j.1529-8817.2004.03222.x.View ArticleGoogle Scholar
- Henrissat B, Coutinho PM, Davies GJ: A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol. 2001, 47: 55-72. 10.1023/A:1010667012056.PubMedView ArticleGoogle Scholar
- Nishitani K: The role of endoxyloglucan transferase in the organization of plant cell walls. Int Rev Cytol. 1997, 173: 157-206.PubMedView ArticleGoogle Scholar
- Shakin-Eshleman SH, Spitalnik SL, Kasturi L: The amino acid at the X position of an Asn-X-Ser sequon is an important determinant of N-linked core-glycosylation efficiency. J Biol Chem. 1996, 271: 6363-6366. 10.1074/jbc.271.11.6363.PubMedView ArticleGoogle Scholar
- Passardi F, Longet D, Penel C, Dunand C: The class III peroxidase multigenic family in rice and its evolution in land plants. Phytochemistry. 2004, 65: 1879-1893. 10.1016/j.phytochem.2004.06.023.PubMedView ArticleGoogle Scholar
- Brook AJ: The Biology of Desmids. Oxford, Blackwell Scientific; 1981,Botanical Monographs, Vol. 16.Google Scholar
- Toone EJ: Structure and energetics of protein-carbohydrate complexes. Curr Opin Struct Biol. 1994, 4: 719-728. 10.1016/S0959-440X(94)90170-8.View ArticleGoogle Scholar
- Wu Y, Meeley RB, Cosgrove DJ: Analysis and expression of the α-expansin and β-expansin gene families in maize. Plant Physiol. 2001, 126: 222-232. 10.1104/pp.126.1.222.PubMedPubMed CentralView ArticleGoogle Scholar
- Ward WW: Biochemical and physical properties of green fluorescentprotein. In Green Fluorescent Protein: Properties, Applications and Protocols.Edited by: Chalfie M, Kain SR. New York, Wiley; 2005:39-66, Methods ofBiochemical Analysis, Vol. 47.View ArticleGoogle Scholar
- Passardi F, Penel C, Dunand C: Performing the paradoxical: how plant peroxidases modify the cell wall. Trends Plant Sci. 2004, 9: 534-540. 10.1016/j.tplants.2004.09.002.PubMedView ArticleGoogle Scholar
- Sekimoto H, Tanabe Y, Takizawa M, Ito N, Fukumoto Rh, Ito M: Expressed sequence tags from the Closterium peracerosum-strigosum-littorale complex, a unicellular charophycean alga, in the sexual reproduction process. DNA Res. 2003, 10: 147-153. 10.1093/dnares/10.4.147.PubMedView ArticleGoogle Scholar
- Popper ZA, Fry SC: Primary cell wall composition of bryophytes and charophytes. Ann Bot. 2003, 91: 1-12. 10.1093/aob/mcg013.PubMedPubMed CentralView ArticleGoogle Scholar
- Van Sandt VST, Stieperaere H, Guisez Y, Verbelen JP, Vissenberg K: XET activity is found near sites of growth and cell elongation in bryophytes and some green algae: new insights into the evolution of primary cell wall elongation. Ann Bot. 2007, 99: 39-51. 10.1093/aob/mcl232.PubMedPubMed CentralView ArticleGoogle Scholar
- Taiz L: Plant cell expansion regulation of cell wall mechanical properties. Annu Rev Plant Physiol. 1984, 35: 585-657. 10.1146/annurev.pp.35.060184.003101.View ArticleGoogle Scholar
- Tepfer M, Cleland RE: A comparison of acid-induced cell wall loosening in Valonia ventricosa and in oat coleoptiles. Plant Physiol. 1979, 63: 898-902. 10.1104/pp.63.5.898.PubMedPubMed CentralView ArticleGoogle Scholar
- Olafsdottir ES, Ingólfsdottir K: Polysaccharides from lichens: structural characteristics and biological activity. Planta Med. 2001, 67: 199-208. 10.1055/s-2001-12012.PubMedView ArticleGoogle Scholar
- Pettolino F, Sasaki I, Turbic A, Wilson SM, Bacic A, Hrmova M, Fincher GB: Hyphal cell walls from the plant pathogen Rhynchosporium secalis contain (1,3/1,6)-β-D-glucans, galacto- and rhamnomannans, (1,3;1,4)-β-D-glucans and chitin. FEBS J. 2009, 276: 3698-3709. 10.1111/j.1742-4658.2009.07086.x.PubMedView ArticleGoogle Scholar
- Fry SC, Nesselrode BHWA, Miller JG, Mewburn BR: Mixed-linkage (1→3,1→4)-β-D-glucan is a major hemicellulose of Equisetum (horsetail) cell walls. New Phytol. 2008, 179: 104-115. 10.1111/j.1469-8137.2008.02435.x.PubMedView ArticleGoogle Scholar
- Trethewey JAK, Campbell LM, Harris PJ: (1℮3),(1→4)-β-D-glucans in the cell walls of the Poales (sensu lato): an immunogold labeling study using a monoclonal antibody. Am J Bot. 2005, 92: 1660-1674. 10.3732/ajb.92.10.1660.PubMedView ArticleGoogle Scholar
- Popper ZA, Tuohy MG: Beyond the green: understanding the evolutionary puzzle of plant and algal cell walls. Plant Physiol. 2010, 153: 373-383. 10.1104/pp.110.158055.PubMedPubMed CentralView ArticleGoogle Scholar
- Lemieux C, Otis C, Turmel M: A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol. 2007, 5: 2-10.1186/1741-7007-5-2.PubMedPubMed CentralView ArticleGoogle Scholar
- Leliaert F, Verbruggen H, Zechman FW: Into the deep: new discoveries at the base of the green plant phylogeny. BioEssays. 2011, 33: 683-692. 10.1002/bies.201100035.PubMedView ArticleGoogle Scholar
- Caderas D, Muster M, Vogler H, Mandel T, Rose JKC, McQueen-Mason S, Kuhlemeier C: Limited correlation between expansin gene expression and elongation growth rate. Plant Physiol. 2000, 123: 1399-1413. 10.1104/pp.123.4.1399.PubMedPubMed CentralView ArticleGoogle Scholar
- Rochange SF, Wenzel CL, McQueen-Mason SJ: Impaired growth in transgenic plants over-expressing an expansin isoform. Plant Mol Biol. 2001, 46: 581-589. 10.1023/A:1010650217100.PubMedView ArticleGoogle Scholar
- Lee Y, Kende H: Expression of β-expansins is correlated with internodal elongation in deepwater rice. Plant Physiol. 2001, 127: 645-654. 10.1104/pp.010345.PubMedPubMed CentralView ArticleGoogle Scholar
- Choi D, Lee Y, Cho HT, Kende H: Regulation of expansin gene expression affects growth and development in transgenic rice plants. Plant Cell. 2003, 15: 1386-1398. 10.1105/tpc.011965.PubMedPubMed CentralView ArticleGoogle Scholar
- Obembe OO, Jacobsen E, Visser R, Vincken JP: Expression of an expansin carbohydrate-binding module affects xylem and phloem formation. Afr J Biotechnol. 2007, 6: 1608-1616.Google Scholar
- Kenrick P, Crane PR: The origin and early evolution of plants on land. Nature. 1997, 389: 33-39. 10.1038/37918.View ArticleGoogle Scholar
- Graham LE, Cook ME, Busse JS: The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc Natl Acad Sci USA. 2000, 97: 4535-4540. 10.1073/pnas.97.9.4535.PubMedPubMed CentralView ArticleGoogle Scholar
- Popper ZA, Tuohy MG: Beyond the green: Understanding the evolutionary puzzle of plant and algal cell walls. Plant Physiol. 2010, 153: 73-383.View ArticleGoogle Scholar
- Sørensen I, Domozych D, Willats WGT: How have plant cell walls evolved?. Plant Physiol. 2010, 153: 366-372. 10.1104/pp.110.154427.PubMedPubMed CentralView ArticleGoogle Scholar
- Popper ZA, Michel G, Hervé C, Domozych DS, Willats WGT, Tuohy MG, Kloareg B, Stengel DB: Evolution and diversity of plant cell walls: From algae to flowering plants. Annu Rev Plant Biol. 2011, 62: 567-590. 10.1146/annurev-arplant-042110-103809.PubMedView ArticleGoogle Scholar
- Sørensen I, Pettolino FA, Bacic A, Ralph J, Lu F, O'Neill MA, Fei Z, Rose JKC, Domozych DS, Willats WGT: The Charophycean green algae provide insights into the early origins of plant cell walls. The Plant Journal. 2011Google Scholar
- Schlösser UG: Sammlung von Algenkulturen. Ber Dtsch Bot Ges. 1982, 95: 181-276.Google Scholar
- Chang S, Puryear J, Cairney J: A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep. 1993, 11: 113-116. 10.1007/BF02670468.View ArticleGoogle Scholar
- Pearson G, Lago-Leston A, Valente M, Serrão E: Simple and rapid RNA extraction from freeze-dried tissue of brown algae and seagrasses. Eur J Phycol. 2006, 41: 97-104. 10.1080/09670260500505011.View ArticleGoogle Scholar
- Kiefer E, Heller W, Ernst D: A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol Biol Rep. 2000, 18: 33-39. 10.1007/BF02825291.View ArticleGoogle Scholar
- De Smet F, Mathys J, Marchal K, Thijs G, De Moor B, Moreau Y: Adaptive quality-based clustering of gene expression profiles. Bioinformatics. 2002, 18: 735-746. 10.1093/bioinformatics/18.5.735.PubMedView ArticleGoogle Scholar
- Storey JD, Tibshirani R: Statistical significance for genome wide studies. Proc Natl Acad Sci USA. 2003, 100: 9440-9445. 10.1073/pnas.1530509100.PubMedPubMed CentralView ArticleGoogle Scholar
- Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.PubMedView ArticleGoogle Scholar
- Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3: research 0034.1-0034.11Google Scholar
- Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J: qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007, 8: R19.1-R19.14.View ArticleGoogle Scholar
- Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16: 276-277. 10.1016/S0168-9525(00)02024-2.PubMedView ArticleGoogle Scholar
- Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA. 1998, 95: 5857-5864. 10.1073/pnas.95.11.5857.PubMedPubMed CentralView ArticleGoogle Scholar
- Letunic I, Doerks T, Bork P: SMART 6: recent updates and new developments. Nucleic Acids Res. 2009, 37: D229-D232. 10.1093/nar/gkn808.PubMedPubMed CentralView ArticleGoogle Scholar
- Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997, 10: 1-6. 10.1093/protein/10.1.1.PubMedView ArticleGoogle Scholar
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340: 783-795. 10.1016/j.jmb.2004.05.028.PubMedView ArticleGoogle Scholar
- Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S: Extensive feature detection of N-terminal protein sorting signals. Bioinformatics. 2002, 18: 298-305. 10.1093/bioinformatics/18.2.298.PubMedView ArticleGoogle Scholar
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMedPubMed CentralView ArticleGoogle Scholar
- Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.PubMedPubMed CentralView ArticleGoogle Scholar
- Ogasawara S, Shimada N, Kawata T: Role of an expansin-like molecule in Dictyostelium morphogenesis and regulation of its gene expression by the signal transducer and activator of transcription protein dd-STATa. Dev Growth Differ. 2009, 51: 109-122. 10.1111/j.1440-169X.2009.01086.x.PubMedView ArticleGoogle Scholar
- Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005, 21: 2104-2105. 10.1093/bioinformatics/bti263.PubMedView ArticleGoogle Scholar
- Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520.PubMedView ArticleGoogle Scholar
- Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.PubMedView ArticleGoogle Scholar
- Rambaut A, Drummond AJ: Tracer v1.4. 2007, [http://beast.bio.ed.ac.uk/]Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.