What is a plant? (part 2)

Plants are eukaryotes.  'Eu' from the Greek for true and 'karyote' for nut, meaning the nucleus.  Eukaryotes have cells with a nucleus containing their genome in the form of DNA organised in chromosomes.  Eukaryotes, all the plants, animals and other living things, except bacteria and archaea, are thought to have evolved from a single common ancestor, or in other words, eukarya are monophyletic.  Prokaryotes (bacteria and archaea which don't have a nucleus) have their DNA organised differently.  This all sounds very simple and clear, except that things are a bit more complicated (when in life are they not?).  When I said that the eukaryote nucleus contains the genome, this is only partly true.  There are some other organelles (structures within eukaryote cells) that also contain DNA.  The mitochondria, which generate energy for eukaryote cells contain DNA and, in the plants, the chloroplasts, which carry out that most planty of processes, photosynthesis, also contain DNA.

When organisms reproduce sexually, nuclear DNA from two parental cells comes together to make a 'daughter' genome, but the same thing doesn't happen for the organelle DNA - organelle DNA is generally inherited directly from the mother 'egg' cell.  This makes for some very different evolutionary trajectories for the different sets of DNA.  Recombination features strongly as an evolutionary force in nuclear DNA (due to the 'coming together'), but organelle DNA does not recombine in meiosis.  Recombination is still a force in organelle DNA evolution though, but through a different mechanism.  But we need to backtrack a little first, and look at where the organelles came from in the first place.

There's good evidence that the organelles did not start out as part of eukaryote cells.  It seems that they were originally free-living prokaryotes, that either invaded, or were subsumed by an ancient proto-eukaryote.  Somehow, rather than eating, or being eaten by one another, the prokaryote took up residence inside the proto-eukaryote, in either a symbiotic or parasitic arrangement.  We can tell this happened because of the similarities of the DNA in the organelles we find in eukaryotes today, and the DNA in the genomes of some prokaryotes.  The 'host' cell provides some kind of shelter or nutrients and the prokaryote provides energy or photosynthesis.  The question of when this event happened, and whether it happened once for a single cell, from which every eukaryote alive today has evolved, is open to question.

So now we know how the organelles got where they are, living inside the eukaryote cells, back to their DNA, and how recombination acts upon it.  Over the millennia since the endosymbionts took their places, there is very good evidence () that some of the genes from the original nuclear genome have migrated to the organelles, and some of the DNA from the original prokaryote have migrated from the organelle genomes to the nuclear genome of the host cells.    The reason why we can be so sure that this happened is that some of the nuclear genes in some eukaryotes look very much like some prokaryote genes, and some organelle genes look very much like some eukaryote nuclear genes.  There is evidence that this process is still happening in the flowering plants (Adams et al., 2002)

So we have said we know these things about the way genomes are structured, because we have found segments of DNA in different places that are too similar to have arisen by chance, so must have evolved from a common ancestral segment of DNA.  We call this homology - the fact that two biological features share similarity through descent.  But couldn't these things have arisen independently of each other? Isn't it possible that the same DNA evolved twice in separate organisms at random?  Isn't it possible that some gene sequences are so useful that they evolved twice independently by the force of natural selection?  Tricky questions indeed.  There are strong theoretical methods for determining whether we should accept or reject the hypothesis of homology in any given case.  Maybe I'll save the theory for another post on another day.

For now, I'll come back to what a plant is.  There's something about being a eukaryote that seems to help organisms grow bigger and more complex, rather than the apparently simple organisms that are the bacteria and archaea.  Some plants are single cells, but many have adopted multicellularity as a way of getting their heads above the crowd, into the light.

So plants are eukaryotes, with cells having a genome in their nuclei, and having tamed prokaryote chloroplasts harvesting all that lovely sunlight to help them grow and develop. We've also touched on what evolution is here.  I mentioned recombination (where pieces of DNA are exchanged between one DNA segment and another).  Generally DNA is a molecule that can reproduce itself, but if it always reproduced itself identically, there would be no such thing as evolution.  Recombination is one of the forces that act on DNA to cause it to evolve.  The DNA message may be different after the recombination occurs than it was before, and if the DNA is different then the organism might be different.  I'll come back to the other three evolutionary forces another time.

To finish for today, I'd like to share a very interesting paper about recombination that I came across.  I talked about recombination that occurs in meioses, and about recombination between nuclear and organelle DNA, but it does not stop there by any means.  Horizontal gene transfer is one of the other kinds of recombination, that is, the exchange of DNA between non-mating organisms.  Many bacteria regularly swap plastids with each other, and viruses recombine both with each other and with their hosts' DNA.  Single-celled eukaryotes are also known to engage in horizontal gene transfer, but we don't often come across instances of recombination between the genomes of completely unrelated complex eukaryotes.  Richardson and Palmer (2007) review horizontal gene transfer in plants, which has been found in a number of cases between mitochondrial genes in particular.  The extreme example is a very interesting plant, Amborella trichopoda, whose mitochondria may contain more 'foreign', or horizontally transferred genes, apparently 'captured' from a wide range of other mosses and plants, than 'native' genes.  A. trichopoda is endemic to the pacific island of New Caledonia, where it grows as a shrub in the understory of the forest, often covered with mosses, and other epiphytic  plants.  It seems possible that these plants have infiltrated the tissues of our shrub, in the past, and thereby transferred genes, but this isn't really clear, and although some of these 'foreign' genes are expressed in the living shrubs, it also isn't clear whether they are functional  It will be interesting to find out!

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Adams KL, Qui YL, Stoutemyer M, Palmer JD,  2002.  Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.  Proceedings of the National Academy of Sciences, USA 99: 9905-9912.

Richardson AO, Palmer JD.  2007.  Horizontal gene transfer in plants.  Journal of Experimental Botany 58(1): 1-9.

What is a plant? (part 1)

Plants are green aren't they? And they grow, and they don't walk about.  Well mostly...  As well as the green plants, Glaucophyta and Rhodophyta (red algae) are usually regarded as plants, but I'm going to leave them aside for the rest of this posting and focus on the green plants.

In the introduction to my PhD thesis I wrote that 'Green plants are characterised as containing chlorophyll a and b, storing photosynthetic products such as starch inside chloroplasts, and having cell walls made of cellulose (McCourt et al., 1996)'. In retrospect, this is a reasonable-ish definition, but is limited to describing shared morphological features, and doesn't necessarily speak to aspects of phylogeny and most recent common ancestry.  The word 'synapomorphy' might have been more specific, implying that the features were inherited from a common ancestor.  The Tree of Life web project (http://www.tolweb.org/green_plants) contains a similar morphological definition and also circumscribes the green plants as 'all organisms commonly known as green algae and land plants, including liverworts, mosses, ferns and other nonseed plants, and seed plants'. That page also has a great list of links and references. Now we know what we're talking about. Kind of.

Palaeos.org (http://www.palaeos.org/) takes quite a nice look at what a plant is, and makes an attempt at situating plants in time as well as space, explicitly delimiting the group of organisms (Chlorobionta) which we can call green plants, and which we think has a single common ancestor. They also observe that this involves the use of the taxonomic hypothesis of common ancestry, which, as a hypothesis, may well turn out to be incorrect, despite strongly supported phylogenies.

So now, as well as talking about what a plant is made of, and what kinds of different shapes and sizes they come in, we raise the question of time. When did the first common ancestor of all the things we call plants arise, and also, what (and when) was the first thing that we might recognise as a plant (the two might possibly be different). That can be another story for another day.

For now, I'd just like to share with you my favourite green algae, Aegagropila linnaei, or Marimo, as the Japanese know them, or Kuluskitur in Icelandic. They used to be called Cladophora aegagropila, when people thought they were closely related to the Cladophora seaweeds, but molecular evidence said otherwise (Hanyuda et al., 2002). Marimo are different from many plants, as they live under water (like lots of the green algae though). In fact, they live in only a few lakes in the far northern hemisphere, in cold, shallowish, brackish waters. Also, unlike lots of plants they are not anchored to a surface, they are free-living.

They grow in the form of green balls, up to several inches across, and either roll around on the bottom of the lake, or sometimes, photosynthesise and generate bubbles of oxygen which allow them to float up to the surface. Unlike their close relatives, the Cladophora seaweeds, they express chitin as part of their cell walls, so are quite 'crispy'. Also, unlike many plants, they seem able to shut down photosynthesis in the absence of light for long periods, then rapidly reform the chloroplasts when light is available again (Yoshida et al., 1998).

They are a protected species in both Japan and Iceland, but do pop up on ebay from time to time. I'm not sure of the original source of the ones for sale. In the 1990s there was a journal called 'Marimo Research', but it seems to have disappeared without a trace, and I haven't been able to get hold of a copy. If anyone knows where to find it, I'd be very pleased to know.

My pet marimo live in this jar, in ordinary mineral water from the supermarket. The water hasn't been changed for a year or so, and is still clear, and they are still growing happily, but I have seen recommendations that you change the water monthly, and massage the marimo to help them stay clean. They are somewhat sacred beings with many myths and legends surrounding them. A little bit fell off one, and I looked at it under my old russian microscope, you can see the chloroplasts quite clearly. This second pic was taken with a digital camera through the eyepiece.

To be continued...

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Hanyuda T, Wakana I, Arai S, Miyaji K, Watano Y,  Ueda K.  2002. Phylogenetic relationships within Cladophorales (Ulvophyceae, Chlorophyta) inferred from 18S rRNA gene sequences with special reference to Aegagropila linnaei. Journal of Phycology 38: 564-571.

McCourt RM, Chapman RL, Buchheim M, Mishler BD. 1996. Green plants. Version 01 January 1996 (under construction). http://tolweb.org/Green_plants/2382/1996.01.01 in The Tree of Life Web Project, http://tolweb.org/.

Yoshida T, Horiguchi T, Nagao M, Wakana I, Yokohama Y. 1998. Ultrastructural study of chloroplasts of inner layer cells of a spherical aggregation of “Marimo” (Chlorophyta) and structural changes seen in organelles after exposing to light. Marimo Research 7: 1-13.

In the beginning...

How to start a blog about plant evolution?

To introduce myself, I'm a researcher in plant evolution, with particular interests in crop domestication, and in polyploidy and transposable element dynamics.  I approach the subject from a deeply-held and long-standing interest in botany, and an almost equally deeply-held and long-standing interest in getting computers to do interesting things.

This blog will be a record of interesting things about plant evolution that I come across from time to time, interesting facts that come from live research projects, and whatever else seems to fit.

I don't take a position on whether plants were/are designed by a superior intelligence, supernatural or otherwise.  I think there are some problems with definitions of superior, intelligence and natural that would get in the way of a serious argument about whether our plants were designed by one.  Having said that, I think that the combined wisdom of a thousand generations of foragers, gardeners, farmers and plant breeders could legitimately be called a superior intelligence.

I do think that variations in DNA and morphology within and between individuals and populations can tell us some really interesting things about evolution, and I think that we are living in an exciting time in the search for knowledge of how recombination, mutation, selection, and genetic drift have shaped the plants our lives depend on.  But enough of that for now ...

I hope you enjoy reading this blog and return from time to time.  I hope you find somethings of interest, and feel moved to add your thoughts.