Ulvophyte multicellularity: the sea lettuce genome


Sea lettuce (Ulva sp.), Jericho Beach, Vancouver, BC, February 28, 2011.

David Kirk called the Chlorophyte green algae “master colony-formers” because multicellularity has evolved so many times within this class:

Although members of most chlorophycean genera and species are unicellular flagellates, multicellular forms are present in 9 of the 11 chlorophycean orders (Melkonian 1990). Multicellularity is believed to have arisen independently in each of these orders, and in some orders more than once.

In contrast, multicellularity has probably only evolved once or twice in the probable sister group of the Chlorophyceae, the Ulvophyceae. So when numbers like 25 get thrown around for the number of times multicellularity has evolved, something like half of those times were in the green algae.

We know a lot less about how multicellularity evolved in the Ulvophyceae than we do in the volvocine algae within the Chlorophyceae. A big step forward in understanding ulvophyte multicellularity happened last week, though, with the publication of the Ulva mutabilis genome.

Ulva is a pretty amazing critter. By any reasonable standard, it is a full-blown multicellular organism, with multiple cell types, a germ-soma division of labor, and a complex life cycle including both haploid and diploid multicellular stages. But all of this is true only in the presence of certain bacteria. When it is grown axenically (i.e., in medium that is otherwise sterile), Ulva fails to develop normally, instead forming undifferentiated “calluses” more akin to bacterial colonies growing in a petri dish than to a complex seaweed:

De Clerck 2018 Fig. 1

Figure 1A&B from De Clerck et al. 2018 (slightly modified). Morphology and Anatomy of Ulva mutabilis. (A) External morphology of a blade (left) and tubular thallus (right). Both growth forms are part of the naturally occurring morphological variation (bar: 1 cm). (B) Axenically developing Ulva with a typical callus-like morphology without cell differentiation. Protrusions of the malformed exterior cell wall are visible (bar: 100 μm).

Ulva exists in the wild in two forms: either as flattened blades that are two-cells thick or as tubes one-cell thick (Figure 1A). Both forms co-occur in most clades, as well as within single species. These morphologies, however, are only established in the presence of appropriate bacterial communities. In axenic culture conditions, Ulva grows as a loose aggregate of cells with malformed cell walls (Figure 1B). Only when it is exposed to certain bacterial strains (e.g., Roseovarius and Maribacter) or grown in conditioned medium is complete morphogenesis observed. [referenced omitted]

Ulva mutabilis is the model organism within the Ulvophyceae, so a sequenced genome is a crucial resource for future research. The new paper, “Insights into the evolution of multicellularity from the sea lettuce genome,” has 36 authors from 9 countries (Belgium, USA, Germany, France, United Kingdom, Ireland, Australia, Israel, and South Africa) and is available online ahead of print. The closest thing I could find to a non-paywalled version was a ResearchGate entry, where you can request a full-text copy from the authors (I’d be shocked if they didn’t fulfill the request).

They assembled the genome from a combination of long (PacBio) and short (Illumina) reads and compared it with genomes of several other green algae and land plants.

De Clerck et al. 2018 Fig. 3

Figure 3 from De Clerck et al. 2018. Predicted Pattern of Gain and Loss of Gene Families during the Evolution of Green Algae and Land Plants. For each species, the total number of gene families, the number of orphans (genes that lack homologues in the eukaryotic data set), and the number of genes are indicated, as well as habitat and morphological characteristics. Maximum likelihood bootstrap values are indicated in black at each node. The number of gene families acquired or lost are indicated in blue along each branch in the tree.

The Ulva genome contains 98.5 million base pairs (Mbp), not drastically different from Chlamydomonas (118 Mbp), Volvox (138 Mbp), and Arabidopsis (135 Mbp), though with fewer genes. Gains and losses of gene families have been common within the green algae, as Figure 3 above shows. Among these are a couple of real surprises. First, there are relatively few transcription factors:

The evolution of a complex thallus morphology is often associated with expansions in gene families that are involved in cell signaling, transcriptional regulation, and cell adhesion. The Ulva genome encodes 251 proteins involved in transcriptional regulation—a comparatively low number for a green alga… Ulva lacks 10 families of transcription factors and two families of transcriptional regulators that are present in other green algae. Furthermore, the existing transcription-associated protein families are, on average, smaller than those in other green algae. [references and abbreviations omitted]

This is a surprise because we generally think that multicellular organisms, especially those with multiple cell types, require more complex control over gene expression, for which transcription factors are essential. In most multicellular organisms, the cells are genetically identical, even when they’re dramatically different in form and function (your liver cells have the exact same genome as your brain cells). The differences are mostly due to differential gene expression, so, the thinking goes, organisms with multiple cell types need more fine-grained control of gene expression.

The other surprise is the absence of genes in the retinoblastoma and D-type cyclin families:

Among the most remarkable gene families that have been lost are genes of the retinoblastoma (RB)/E2F pathway and associated D-type cyclins. Comparative genomic studies of volvocine algae have revealed that the co-option of the RB cell-cycle pathway is a key step towards multicellularity in this group of green algae.

Indeed, as I’ve written previously, Hanschen and colleagues showed that

When the Gonium [retinoblastoma] gene is expressed in Chlamydomonas, the normally unicellular Chlamydomonas develops multicellular colonies with cell numbers similar to those of Gonium.

Furthermore, retinoblastoma and E2F are present in the genome of Caulerpa, a much closer relative of Ulva than either Chlamydomonas or Gonium. The absence of these gene families in Ulva led De Clerck and colleagues to conclude that

…evolution toward multicellularity progressed along different trajectories in Ulva and the volvocine algae.

As Will Ratcliff has pointed out, this probably shouldn’t be a huge surprise, given that Ulva and the volvocine algae diverged on the order of 800 million years ago:

Of course, genome sequencing alone can’t tell us what genetic changes actually caused the transition from unicellular to multicellular life. That will require a research program’s worth of work, if it can be done at all. The Ulva genome has narrowed the search, though, by ruling out some possibilities (e.g. changes to the retinoblastoma sequence, expansion of transcription factor families). Perhaps more importantly, it brings Ulva research into the genomic era, and it will undoubtedly facilitate future research on this and other aspects of ulvophyte biology.


Stable links:

De Clerck, O., S.-M. Kao, K. A. Bogaert, J. Blomme, F. Foflonker, M. Kwantes, E. Vancaester, L. Vanderstraeten, E. Aydogdu, J. Boesger, G. Califano, B. Charrier, R. Clewes, A. Del Cortona, S. D’Hondt, N. Fernandez-Pozo, C. M. Gachon, M. Hanikenne, L. Lattermann, F. Leliaert, X. Liu, C. A. Maggs, Z. A. Popper, J. A. Raven, M. Van Bel, P. K. I. Wilhelmsson, D. Bhattacharya, J. C. Coates, S. A. Rensing, D. Van Der Straeten, A. Vardi, L. Sterck, K. Vandepoele, Y. Van de Peer, T. Wichard, and J. H. Bothwell. 2018. Insights into the evolution of multicellularity from the sea lettuce genome. Current Biology. DOI: 10.1016/j.cub.2018.08.015

Grosberg, R. K., and R. R. Strathmann. 2007. The evolution of multicellularity: a minor major transition? Annual Review of Ecology, Evolution, and Systematics 38:621–654. DOI: 10.1146/annurev.ecolsys.36.102403.114735

Hanschen, E. R., T. N. Marriage, P. J. Ferris, T. Hamaji, A. Toyoda, A. Fujiyama, R. Neme, H. Noguchi, Y. Minakuchi, M. Suzuki, H. Kawai-Toyooka, D. R. Smith, V. Luria, A. Karger, M. W. Kirschner, H. Sparks, J. Anderson, R. Bakaric, P. M. Durand, R. E. Michod, H. Nozaki, and B. J. S. C. Olson. 2016. The Gonium pectorale genome demostrates co-option of cell cycle regulation during the evolution of multicellularity. Nature Communications 7:11370. DOI: 10.1038/ncomms11370

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