The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity

The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.

M ulticellular organisms have independently evolved numerous times throughout the tree of life including plants, animals, fungi, cyanobacteria, amoeba, brown algae, red algae and green algae 1,2 . In animals, multicellularity emerged 600-950 million years ago (Myr ago) correlating with a large expansion of genes encoding transcription factors, signalling pathways, and cell adhesion genes that were co-opted from their unicellular ancestors 3,4 Similarly, multicellular, terrestrial plants emerged B750 Myr ago correlating with an expansion of many signalling pathways present in their unicellular relatives 5,6 . However, because most multicellular lineages have long diverged from their unicellular relatives, the genomic signature of the transition to multicellularity has been obscured, and consequently this evolutionary process remains enigmatic.
The volvocine green algae are a unique model system for the evolution of multicellularity because the unicellular ancestry is clear, the emergence of multicellularity occurred B230 Myr ago, and species exhibit a stepwise increase in morphological complexity ranging from undifferentiated colonies to differentiated multicellular species 7,8 (Fig. 1, Supplementary Figs 1,2). Unicellular Chlamydomonas reinhardtii is thought to resemble the unicellular ancestor of multicellular volvocines, including undifferentiated Gonium pectorale and differentiated Volvox carteri (Fig. 1).
Chlamydomonas undergoes a variant cell cycle ( Supplementary  Fig. 2), regulated by homologues of the retinoblastoma cell cycle pathway, termed multiple-fission where it divides by a series of rapid cell divisions producing individual daughter cells [9][10][11] . Gonium typically forms 8-or 16-celled undifferentiated colonies, where each constituent cell resembles a Chlamydomonas cell (Fig. 1). Gonium also undergoes multiple fission forming daughter colonies by keeping cells attached after multiple-fission, suggesting either cell cycle regulation 12 , or cell-cell adhesion has been modified to promote multicellularity. In Gonium, like Chlamydomonas, growth and cell division are uncoupled 13,14 . Asexual juvenile Gonium colonies grow (without cell division) into adults. After cell division through multiple-fission, juvenile colonies hatch forming 8 or 16 daughter colonies of 8 or 16 cells ( Supplementary Fig. 2). Volvox contains approximately 2,000 small, terminally differentiated, somatic cells on the surface of the spheroid and approximately 16 large reproductive cells embedded in extracellular matrix (ECM) inside the spheroid (Fig. 1). Volvox also has modified multiple fission where germ-soma separation is established after an asymmetric cell division 8,14 .
The transition to multicellularity in the Volvocales was thought to involve at least 12 steps (Supplementary Fig. 1) 15,16 though the genetic basis of these steps remains enigmatic. Genomic comparison of the extremes of morphological complexity, Chlamydomonas and Volvox, suggests few genetic changes are required 17 , but it is unclear how and when the genes important for multicellularity evolved during these 12 steps 14 .
By sequencing the genome of the undifferentiated, chlorophycean Gonium pectorale, a species without a differentiated ancestor 16 , we find co-option of cell cycle regulation, which occurred during the initial transition to cell groups, as the genetic basis for the evolution of multicellularity. The cell cycle regulation found in undifferentiated Gonium, co-opted in a multicellular context and shared with germ-soma-differentiated Volvox, indicates group-level adaptations in undifferentiated colonies. The early co-option of cell cycle regulation for group-level life cycle and reproduction is a critical and formative step in the evolution of multicellularity.

Results
Genomic comparisons of volvocine algae. At the genomic level, the genomes of Chlamydomonas, Gonium and Volvox are similar, though various measures of genome compactness correlate with cell number, consistent with a long-term increase in organismal size 18,19 . Chlamydomonas and Gonium have similar GC content near 64%, while Volvox has 56% GC (Table 1). Otherwise, Chlamydomonas, Gonium and Volvox have decreasing gene densities of 159.6, 120.9 and 113.7 genes per megabase, with an increasing average intron length of 279, 349 and 500 base pairs, respectively. Although intron length increases with organismal complexity, the number of introns per gene (Chlamydomonas, 7.46; Gonium, 6.5; Volvox 6.8, Table 1) does not. GC content, intron length and gene density correlate with morphological complexity.
We next examined genome-wide evolution in all three species to better understand the genetic basis for the evolution of multicellularity. A prediction of lineage-specific genes 20 shows few genes correlate with the evolution of multicellularity in the Volvocales (phylostratum 7; PS7) with a maximum of 180-357 genes (Fig. 2a). This suggests that the evolution of multicellularity does not rely upon the evolution of de novo genes. Though gene regulation may be important during multicellular innovation, the diversity and abundance of transcription factors is similar in Chlamydomonas, Gonium and Volvox (Fig. 2b Supplementary Fig. 3). Although enrichment of transcription factors can correlate with the evolution of multicellularity 3 , this is not always the case 21 ; we found that Gonium and Volvox have fewer transcription factors than in Chlamydomonas (Fig. 2b) Supplementary Fig. 3). Using all published chlorophyte green algae genomes, we constructed Markov-based gene families (Chlamydomonas, 73%; Gonium, 73%; Volvox, 70% of genes in gene families of size greater than one). Compared with 2,844 net gene families gained, which correlate with the origin of the Chlorophyceae, a phylogenetic analysis of these gene families suggests little protein innovation (110 net gene families) during the evolution of multicellularity (Fig. 2c). These same green algae genomes allowed analysis into Pfam domain innovation, which may correlate with the evolution of multicellularity. We found innovation of only nine Pfam domains correlating with the evolution of multicellularity (Fig. 2d Fig. 4). Interestingly, there is an excess of species-specific genes (Fig. 2a,c) and Pfam domains (Fig. 2d) compared with multicellularity-correlated genes and Pfam domains, suggesting that species-specific adaptations are more numerous than changes correlating with the evolution of multicellularity. We observe more evidence of species-specific, rather than multicellular-specific, protein innovations, suggesting species-specific adaptation (Fig. 2a,c,d, Supplementary Tables 5-8) rather than genome-wide differences correlating with the evolution of multicellularity. The evolution of multicellularity in the volvocine algae does not require large-scale genomic innovation.
Co-option of cell cycle regulation for multicellularity. Notably, we observe that the genetic innovation correlating with multicellularity, shared between Gonium and Volvox, evolved through co-option of existing developmental programs of cell cycle control. Volvocine algae have a common multiple-fission life cycle, with variation in timing and number of divisions ( Supplementary Fig. 1 Table 9) 9,10 , in which cyclin-dependent kinases (CDKs) bind cyclin proteins to phosphorylate and regulate retinoblastoma (RB or MAT3 in the Volvocales), which in turn de-represses the cell cycle (Fig. 3a).   Although most of these regulators are nearly identical in Chlamydomonas, Gonium and Volvox (Fig. 3b,e), there are two notable differences. First, Volvox has a four gene expansion of cyclin D1 genes (Fig. 3c) 17 . As Volvox has tissue differentiation, these cyclin D1 genes may have been important for tissue development as is the case in metazoans and land plants 22,23 , supported by the fact that RB has moved into the mating locus of Gonium and Volvox and is differentially expressed between mating loci ( Fig. 3d) 24,25 . However, the tandem array expansion of the cyclin D1 genes is also found in Gonium (Fig. 3c), where cyclin D genes display elevated dN/dS ratios compared with other cell cycle regulators ( Supplementary Fig. 8), suggesting the function of these cyclin Ds may be important for the transition to undifferentiated colonies, rather than tissue differentiation. Second, there is modification of the RB gene in Gonium and Volvox (Fig. 3d, Supplementary Figs 5-7). Protein dimers of cyclins and CDKs primarily regulate RB by phosphorylating serine or threonine residues, which is thought to regulate RB binding of chromatin via E2F/DP transcription factors 11,26,27 . Recently it has been shown in human cells that cyclin D and CDK4/6 regulate monophosphorylation of RB proteins for G 1 phase-specific RB functions 27 . If similar in Gonium, this would suggest a role of the expanded cyclin D1 genes for regulating RB to express multicellularity-related genes during G 1 phase. If the expanded cyclin D1 proteins found in Gonium regulate multicellular cell cycle changes, modification of cyclin D-CDK phosphorylation sites in RB is predicted. Indeed, the linker of the E2F/DP binding pocket of RB is shorter in Gonium and Volvox compared with Chlamydomonas (Fig. 3d, Supplementary Figs 5 and 6), potentially altering how RB binds to chromatin via E2F/ DP. In addition, phosphorylation sites between the E2F/DP pocket region (RB-A and RB-B domains) and the conserved carboxy (C)-terminal domain are absent in Gonium and Volvox RB proteins (Fig. 3d). Interestingly, in animals the C terminus of RB is intertwined with E2F/DP and changes in the phosphorylation by cyclin-CDK complexes could also alter E2F/DP binding 28 . As these phosphorylation sites are absent in Gonium and Volvox RB proteins (Fig. 3d), this suggests that RB co-option for multicellularity may result in differences in locusspecific temporal expression of genes important for multicellularity during G 1 , such as cell-cell adhesion genes. Given the role the RB pathway plays in regulating the cell cycle in Chlamydomonas, its early modification found in Gonium, and its co-option for complex morphology in Volvox, RB pathway regulation might be a key step towards multicellularity in the volvocine algae.
To test whether RB modifications present in Gonium and Volvox (compared with Chlamydomonas) are unrelated to, cause or are a consequence of multicellularity, we expressed the Chlamydomonas 11 and Gonium RB genes in a Chlamydomonas strain lacking its RB gene (rb, mat3-4 strain, Fig. 4a) 9,11 using the promoter and terminator from the Chlamydomonas RB gene to ensure expression near wild-type levels (Fig. 4b,c) 11 . The Chlamydomonas RB gene rescues the small cell size defect in the rb mutant (HA-CrRB::rb, Fig. 4a), while the Gonium RB gene rescues the cell size defect and causes the Chlamydomonas rb mutant to become non-palmelloid colonial, ranging from 2 to 16 normal-sized cells (HA-GpRB::rb, Fig. 4a). Crossing RB gain-of-function transformed Chlamydomonas strain to a Chlamydomonas strain lacking DP1, a gene that dimerizes with E2F to anchor RB to chromatin 11 , results in suppression of the colonial phenotype and large-sized cells (HA-GpRB::rb::dp1, Fig. 4a) consistent with the phenotype of the Chlamydomonas dp1 mutant itself 10 . This demonstrates that the Gonium RB gene causes colonial multicellularity (Fig. 4a) through the RB pathway (Fig. 3a)   regulates the expression of cell cycle related genes in Gonium and Volvox are important for co-option of these RB targeted genes for multicellularity (Figs 3 and 4). This gain-of-function demonstrates a causal link between cell cycle regulation and the group level during the evolution of multicellularity, emphasizing that multicellularity can evolve by co-option and modification of regulatory genes rather than extensive genomic differences or innovation.
Volvox innovations for morphological complexity. In Volvox, somatic differentiation is causally regulated by the regA gene cluster, a set of putative DNA-binding transcription factors thought to regulate chloroplast biogenesis [29][30][31] . The regA gene cluster is absent in Chlamydomonas and Gonium (Fig. 5a,b), but is present in diverse Volvox ferrisii and Volvox gigas 32 , suggesting early evolution and co-option of this cluster shortly after the split of Gonium and Volvox lineages (Fig. 1) 32 . Interestingly, if the absence of regA in Gonium is indicative of the absence of regA in Astrephomene, with an independent evolution of somatic cells ( Fig. 1) 16 , Astrephomene may determine somatic cell fate through a different pathway than Volvox suggesting multiple evolutionary pathways and subsequent evolutionary consequences during the evolution of multicellularity. Indeed, undifferentiated multicellularity evolved once in the Volvocales 16 , while additional morphological complexity (for example, cellular differentiation and large Volvox body size) has repeatedly evolved, suggesting a relative ease to gain and lose additional complexity. We investigated proteins related to morphological complexity, pherophorins and matrix metalloprotease (MMP) proteins, in the volvocine algae 17 . These proteins are hypothesized to produce ECM and break up cell wall components during reproduction in Gonium and other Volvocales 15,33,34 . While Chlamydomonas contains no ECM and Gonium contains little ECM, a Volvox spheroid is largely composed of ECM (Fig. 1). Pherophorin and MMP gene families are expanded in Volvox relative to Chlamydomonas (Fig. 5c) 17 . We found the expansion of pherophorins and MMP genes in Volvox (Fig. 5c, Supplementary  Data 2 and 3) is not present in Gonium, though some speciesspecific expansion of MMP genes has occurred (Supplementary Data 2 and 3). While some expansion of ECM gene families in Gonium was expected 14 to direct the cell wall layer synthesis of a Gonium colony, this layer may instead be directed through differential gene expression. Pherophorin, MMP expansion and cellular differentiation correlate with expanded organismal size rather than the origin of multicellularity, suggesting a subsequent step in the evolution of multicellularity.

Discussion
We have investigated the evolution of multicellularity in the volvocine algae by sequencing the genome of the undifferentiated Gonium. Despite morphological differences, it was known that the Chlamydomonas and Volvox genomes are strikingly similar, suggesting that multicellularity required few genetic innovations 17,35 . However, these two genomes, positioned at the extremes of volvocine morphology, were unable to resolve the tempo and mode 36 of the evolutionary transition to multicellularity.
The evolution of multicellularity in the volvocine algae is thought to involve 12 morphological innovations ( Supplementary  Fig. 1) 15 . Five of these steps correlate with the evolution of cell groups 7 , a period of rapid evolutionary change (tempo). This view emphasizes the importance, and subsequent modification, of innovations correlating with undifferentiated colonies (mode). Finding support for this view, we have generalized these 12 steps into three major phases (Fig. 6): the evolution of cell cycle regulation to form cooperative groups via cell-cell adhesion, the Chlamydomonas and Volvox, we can now identify the genetic pathways associated with each of these steps. The evolution of undifferentiated colonies correlates with RB cell cycle regulatory pathway evolution (Figs 3 and 4), which is further modified as complexity increases in the Volvocales 24 . Increased organismal size toward Volvox correlates with an expansion of pherophorins and MMPs (Fig. 5c). Finally the evolution of the regA gene cluster underlies somatic differentiation (Fig. 5a,b). Future sequencing of additional Volvocales genomes should clarify the evolutionary steps required for the evolution of germ and soma. Our threephase model for the emergence of multicellularity, supported by the genetic pathways important for their evolution, changes our understanding of the tempo and mode of multicellular evolution previously obscured in other taxa such as plants, fungi and animals due to genomic divergence (Fig. 6). Interestingly, an emerging theme throughout the evolution of multicellularity is that the genetic basis for the evolutionary transition emerges much earlier than anticipated 3,6,32 . In plants and animals, RB proteins are important for regulating both cell proliferation and differentiation by highly complex locus interactions with chromatin and chromatin remodelling factors 37,38 . Our finding that the RB pathway was co-opted early for multicellularity in undifferentiated colonies suggests that the template for subsequent evolutionary innovations in developmental programs was laid out during the transition to undifferentiated multicellularity via RB and cell cycle modifications, rather than with emergence of germ and somatic cellular differentiation. Interestingly, RB has been further coopted for a role in sexual differentiation in Volvox, where there are male-and female-specific isoforms of RB 24 . This suggests that the evolution of multicellular cell cycle regulation was a critical step for the evolution of multicellularity. By comparing the genomes of these three volvocine green algae, we have determined that the mechanism of multicellular evolution is primarily cooption and regulatory modification of existing genetic pathways 39 . Gene duplication forms the basis of subsequent multicellular innovations.
The genomic age is illuminating the genetic pathways that are important for the evolution of multicellularity in other organisms where genes such as cadherins and integrins in animals 3,4 and cell wall biogenesis genes in plants 6 . These are roughly analogous to     metalloproteases and pherophorins in the volvocine algae highlighting convergences on similar genetic innovations for multicellularity. The substantial innovation and expansion of transcription factors and signalling networks found in animals and plants 3,6 is not present in the volvocine algae. However, the volvocine algae demonstrate the critical role of transcriptional regulation of the cell cycle by RB for the formation of undifferentiated colonies. RB proteins regulate the cell cycle of most eukaryotes 11,26 , and are tumour suppressors in humans 26 , suggesting a broader role for RB and cell cycle regulation during the evolution of multicellularity.
The implications of these findings are greater than simply identifying when genes evolved during the evolution of multicellularity. Theoretical work has emphasized the need for greater understanding of the origin of an integrated group life cycle during the evolution of multicellularity 12,[40][41][42] . The field has been concerned with the evolution of germ-soma division of labour as the defining step in the evolution of multicellularity 40,43-45 ; indeed, a recent review of animal multicellularity 45 does not mention the importance of cell cycle regulation and group formation. The Gonium genome reflects the early evolution of cell cycle regulation (Figs 3 and 4) in undifferentiated groups, conserved and modified in differentiated Volvox, that is indicative of the emergence of colony level adaptations. We highlight an early and formative step, the co-option and expansion of cell cycle regulation, as important for the evolution of cooperative groups and impacting the evolution of more complicated body plans; one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.
For next-generation sequencing and construction of a fosmid library, total DNA was extracted. Sequencing libraries were prepared using the GS FLX Titanium Rapid Library Preparation Kit (F. Hoffmann-La Roche, Basel, Switzerland) and the TruSeq DNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA) and were run on both GS FLX (F. Hoffmann-La Roche) and MiSeq (Illumina Inc.) machines. Newbler v2.6 was used to assemble the GS FLX reads. A fosmid library was constructed in-house using vector pKS300. The fosmid library (23,424 clones) and BAC library (18,048 clones, Genome Institute (CUGI), Clemson University, Clemson, SC, USA) were end-sequenced using a BigDye terminator kit v3 (Life Technologies, Carlsbad, CA, USA) analysed on automated ABI3730 capillary sequencers (Life Technologies).
Evidence-based gene prediction. Introns hint file generation was done through a two-step, iterative mapping approach using Bowtie/Tophat command lines and custom Perl scripts written by Mario Stanke as part of AUGUSTUS 46 , (available at: http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n= IncorporatingRNAseq.Tophat). AUGUSTUS version 2.6.1 was selected because its algorithm has been successfully tuned to predict genes in Chlamydomonas and Volvox genomes, which contain high GC content 46 . Reads were first mapped to the genome assembly with Tophat version 2.0.2 (ref. 47) and the raw alignments were filtered to create an initial (intron) hints file, which was subsequently provided to AUGUSTUS during gene prediction. An exon-exon junction database was generated from the initial AUGUSTUS prediction via a Perl script. The twicemapped reads (once to the genome and once to the exon-exon sequences) were then merged, filtered and a final intron hints file was created. From this, the final gene prediction with AUGUSTUS was performed.
Pfam domain analysis. Diversity and abundance of Pfam domains was determined for all published green algae genomes. Chlorophyte genomes including Bathycoccus prasinos 48  Analysis of transcription-associated proteins. Transcription-associated proteins (TAPs) include transcription factors (enhance or repress transcription) and transcription regulators (proteins which indirectly regulate transcription such as scaffold proteins, histone modification or DNA methylation). We combined three TAP classification rules for plants; PlantTFDB 54 , PlnTFDB 55 and PlanTAPDB 56 to make a set of classification rules for 96 TAP families. Conflicts between the three sets of rules were manually resolved using the rule that included more genes as transcription-associated proteins.
Each transcription family includes at least one, up to three, mandatory domains. Families may include up to six forbidden domains (that is, a gene G cannot be in family F if domain D is present); not all families have defined forbidden domains. All mandatory and forbidden domains were represented by a full-length, global, Hidden Markov Model (HMM). Available HMMs were retrieved from Pfam_ls database 57,58 . When HMMs were not available from the Pfam_ls database, custom HMMs were made using multiple sequence alignments from PlnTFDB 55 and the HMM was calculated using HMMER version 3.0 (ref. 59) using 'hmmbuild' with default parameters and 'hmmcalibrate-seed 0 0 .
Gathering cutoff thresholds (GA) for the custom HMMs were set as the lowest score of a true positive hit using a 'hmmscan' search against several complete Chlorophyte genomes. Chlorophyte genomes including Bathycoccus prasinos 48 Fig. 3). Subsequent hits were classified into a TAP family. Conflicts between multiple TAP families were resolved by assigning the gene to the TAP family with the highest score (Supplementary Table 1).
Construction of protein families. Protein families were created using OrthoMCL 60 with a variety of inflation values ranging from 1.2 to 4.0 in steps of 0.1 ( Supplementary Figs 16-17 17 . This analysis was repeated for both Volvox version 1 and Volvox version 2. The inflation value of 1.9 was used for both analyses for consistency and was chosen to have relatively large, coarser grained clusters that were robust to higher inflation values ( Supplementary Figs 16-19). To avoid bias introduced by not including all genes for each species, genes not assigned to a gene family (singletons) were assigned to single gene families and included in all subsequent phylogenetic gene family analyses.
A species tree was calculated by extracting OrthoMCL gene families containing only one copy in each species, for a total of 1,457 genes. The OrthoMCL run with an inflation value of 1.5 was chosen to use larger, coarser grained clusters, thus increasing the likelihood of capturing true 1:1:1 orthologues. This species tree included Volvox carteri version 2. These genes were independently aligned using A rapid bootstrapping analysis to search for the best-scoring ML tree was run with 100 bootstraps. The resulting species tree is consistent with previous results 16,51,[63][64][65] and had 100 bootstrap support at every node ( Supplementary  Fig. 20). This result is also consistent with numerous morphological characteristics supporting a closer relationship of Gonium and Volvox 66 .
Gene family evolution within the volvocine algae was analysed using Count version 10.04 (ref. 67) to perform several parsimony analyses including symmetric Wagner parsimony (each gene family may be gained or expanded multiple times and the gain penalty is equal to the loss penalty) and asymmetric Wagner parsimony (each gene family may be gained or expanded multiple times and the gain penalty is two times higher than the loss penalty). This analysis was repeated for both Volvox version 1 and version 2 genomes (Supplementary Tables 5-8).
dN/dS analysis. During our OrthoMCL construction of protein gene families, we identified 6,154 clusters with exactly one copy in Chlamydomonas (version 5.3), Gonium and Volvox (version 2). The number of genes from other unicellular (non-Chlamydomonas) Chlorophyte species was ignored. This criteria is relatively strict as it does not include any genes with a duplicate in any species (copy number greater than one in any species) or any genes which are not essential (no copy present in any species) resulting in 1:1:1 orthologues. Given the relatively high gene duplication rates in volvocine algae (data not shown), these strict criteria support an interpretation of 1:1:1 orthology. Genome-wide pairwise comparisons of dN, dS and dN/dS were calculated (Supplementary Fig. 21; Supplementary Table 11) using PAML and codeml (ML analysis 68 ) based on nucleotide translation based alignments (proteins were aligned using MUSCLE 61 ).
Prediction of lineage-specific genes. The phylostratigraphy method 20 assumes Dollo's parsimony (that is, it is more likely that a gene observed in two distant clades was present in the common ancestor and multiple independent gains are not possible). This provides an entry point for testing evolutionary hypotheses related to the age of genes and to quantify how much gene-level innovation has occurred along each phylogenetic branch. Old genes are classified in low phylostrata (present in distant species, PS1-PS7) and young genes are classified in higher phylostrata (for example, genus-or species-specific genes, PS8-PS9). The resolution of each phylostratum strictly depends on the availability of reliable outgroups (the availability of reliable genomic outgroups is relatively low in Chlorophyte algae). The phylogenetic classes were defined from those in each NCBI Taxonomy entry for Chlamydomonas, Gonium and Volvox, resulting in nine expected phylostrata for each species. All proteins were subjected to a BLASTP search with an E-value threshold of 0.001 against the NCBI nr database. Placement in phylostrata was derived from the taxonomic information of these hits for each protein, using the most distant hit, and following Dollo's parsimony.
Phylogenetic analyses. Unless otherwise stated, all phylogenetic analyses were performed using a custom pipeline of SATe version 2.2.7 (ref. 69) coupled with RAxML version 8 (ref. 62). Full gene protein sequences were passed to SATe using a FASTTREE tree estimation with a RAxML search after tree formation with a maximum limit of 10 iterations and the 'longest' decomposition strategy. Bootstraps were made on the SATe output alignment and tree using RAxML with automatic model selection, a rapid hill climbing algorithm ( À f d) and 100 bootstrap partitions. Bipartition information ( À f a) was obtained using the SATe output tree and RAxML bootstraps.
Chlamydomonas strains culture conditions. Wild-type Chlamydomonas reinhardtii 6145 and 21gr, and HA-CrRB (HA-MAT3::mat3-4, here referred to as HA-CrRB::rb), mat3-4 (here referred to as rb), and dp1 have been previously described [9][10][11] . Briefly, wild-type strains 6145 (MT À ) and 21gr (MT þ ) are mating pairs that have been back crossed to eliminate the y1 mutation in 6145 (ref. 10). The RB knockout strain has been previously characterized as a null allele, and the knockout mutation is the rb allele 9,11 . The rb mutation can be complemented by a amino (N)-terminally tagged version of the gene that behaves identical to wild type. Previously, a knockout mutation in the Chlamydomonas DP1 gene, dp1, was identified and characterized 10,11 . All the strains were maintained on TAP plates. For phenotype analysis, the strains were grown in high salt media (HSM) synchronously under 14 h of 150 mE of light, samples were fixed hourly and examined by light microscopy 10,11 .
Cloning of Gonium pectorale RB and transformation into rb. A 3X haemagluttin (HA) tagged copy of the Gonium pectorale RB gene was cloned using InFusion Cloning (Clontech) to be driven by the Chlamydomonas RB promoter and terminator that includes a AphVIII selectable marker for Chlamydomonas transformation (Fig. 4, (ref. 11)). Gonium pectorale genomic DNA from K4F3 was used as a template and the genomic region of RB was amplified without its ATG start codon using the primers 5 0 -CAGATTACGCTACTAGATCTGCCGAAGCTG AACGTTTTACTGCG-3 0 , and 5 0 -CTCCGGCCGCGGTGCCTAATTTGCG CCGTACCGCCGGA-3 0 . These primers overlap with the 3X HA tag and 3 0 terminator from the previously created HA-CrRB transformation clone that complements the rb mutation 11 . The HA-CrRB plasmid was amplified by inverse PCR with 5 0 -TCTAGTAGCGTAATCTGGAACGTCATATGGATAGG-3 0 and 5 0 -GCACCGCGGCCGGAGGT-3 0 primers. PCR products were gel purified with a QiaQuick gel extraction kit (Qiagen). Purified PCR fragments were fused by InFusion (Clontech) cloning based on overlaps in the amplified sequences and transformed into chemically competent DH5-apha cells, after which the clone was confirmed by sequencing.
Transformation of Chlamydomonas reinhardtii. The rb strain was transformed with glass beads 11 , with the HA-GpRB clone (above) and as a control with HA-CrRB and pSI103 (AphVIII selectable marker only) and selected on TAP plates supplemented with 20 mg ml À 1 paromycin 11 . Candidate strains were screened by growth morphology 10,11 , and then screened for expression by immunoblotting with an anti-HA antibody (Roche 3F10, high affinity 11 ). Four independent strains expressing the HA-GpRB, and five independent strains expressing HA-CrRB were created. Control complementation of the rb mutation with HA-CrRB occurred at rates similar to previous results 11 . The presence of the rb mutation was confirmed by replica plating on TAP plates supplemented with 10 mg ml À 1 emetine 9,11 .
Immunoblotting HA-GpRB and HA-CrRB strains complementing rb. Whole-cell lysates from strains were prepared, separated and immunoblotted 11 . Briefly, the anti-HA antibody used for detection of HA-GpRB and HA-CrRB was an anti-HA high affinity monoclonal antibody (clone 3F10, Roche) and anti-alpha-tubulin monoclonal antibody (Sigma), as previously described 11 . The expression levels of RB in HA-CrRB strains have been previously shown to be similar to wild-type Chlamydomonas expression levels 11 . The expression levels of RB in HA-GpRB are similar, if not slightly below, the expression levels of HA-CrRB, suggesting that overexpression of RB is not causing the observed colonial phenotype, but rather modification to the Gonium RB gene.
Measurement of cell or colony size distribution. The size of cells and groups of cells was measured with a Moxi Z automated cell sizer/counter using type 'S' cassettes (ORFLO Technologies). Sizing is based on the Coulter principle used previously with Chlamydomonas reinhardtii 10,11 .