Making Eden

by David Beerling

  ‘a chicken has slightly less DNA than a Nobel laureate’, and that the ‘tiny plant Flowering plants (7538)

  Ferns (130)

  Other land plants (592)

  Vertebrates (5058)

  Other animals (2210)

  0

  50

  100

  150

  Genome size

  (billions of base pairs)

  Figure 4 The enormous range of genome sizes in different organisms shows that size does not correlate with complexity. The numbers in brackets after each is the number of species analysed. The units of genome size are billions of base pairs.

  44 a Genomes decoded

  Arabidopsis, a relative of the Brussels sprout, has more genes than either’. The comparison between the genetic content of a chicken and a Nobel laureate is broadly

  correct; chickens have about one-third the DNA of humans. However, the fact is

  that all humans, including winners of the 66-mm-diameter gold medals given out

  at Stockholm, have roughly the same number of genes as the weedy relative of the

  mustard family, Arabidopsis, and poultry (~25 000 genes).

  The first plant genome sequence, presented to the world in December 2000,

  belonged to Arabidopsis.5 The sequences for rice, then a tree, and then a moss, soon followed. Part of the fascination here is that each DNA sequence is really

  a molecular ‘living fossil’. It is an exquisitely detailed archive storing an enormous amount of information about the collections of genes needed to build an

  organism, and the instructions regulating when, where, and how those genes are

  expressed. Decode the genomes of individual species, and the past extends an arm

  to the present to provide unique insights on how they evolved, and bring a new

  perspective on how they became adapted to their environment. Fascinating and

  important though these genomic glimpses of the past lives of plants are, genome

  biology really comes into its own when we compare the sequences of everything

  from cyanobacteria to trees. Then we discover the ancestry, and changes in the

  diversity of genes, needed to reconstruct shifts in the genetic make-up of plants during major evolutionary transitions in their history. Called ‘comparative

  genomics’, this extraordinary branch of science decodes the archives of funda-

  mental molecular events written into the DNA code millions of years ago and

  connects them with transformative events throughout the deep evolutionary his-

  tory of plants.

  Obtaining genomic coverage of the plant kingdom to uncover the details of

  that evolutionary journey is very much a work in progress. We need to sample

  more of the diversity of species classified across diverse taxonomic groups to

  avoid the risk of misinterpreting the past.6 But the sequence data accumulated

  so far includes taxa on key nodes across the plant tree of life such as chlorophyte and charophyte algae, bryophytes (liverworts, mosses, and hornworts), a lycophyte, and gymnosperms, and is shedding light on the genetic processes shap-

  ing the evolution of biological novelty and complexity. Already, the genomic

  revolution is weighing in on profound questions about the origin, speciation,

  and extinction of plant life that captivated Wallace and Darwin; not to mention

  milestones in human civilization, such as the appearance of modern savannas, as

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  the ancestors of humans came down from the trees to live on the grassy plains,

  and domestication of crops that feed the world.

  Prerequisites to being a green plant are an ability to generate energy and an

  ability to photosynthesize. These functions are served by the mitochondria and

  chloroplasts of cells that descended from once free-living bacteria that were

  engulfed by a tiny host algal cell and escaped digestion. Some of the simplest and smallest unicellular marine algae contain a single mitochondrial powerhouse

  for energy production and a single chloroplast for conducting the business of

  photosynthesis. They belong to the genus Ostreococcus.7 Celebrated for their diminutive proportions, these tiny spherical algae are classified as chlorophyte

  algae and form part of the picoplankton living in the world’s oceans. Picoplankton form the base of food webs in marine and fresh waters. Roughly the size of a

  bacterium , these algae are the smallest known free-living eukaryotes (i.e., complex cells with a nucleus). Rightly dubbed by commentators ‘the reigning champion of

  cellular miniaturization’,8 Ostreococcus has a correspondingly tiny genome of 12–13

  million base pairs (denoted 12–13 Mb) and around 8000 genes.9 For comparison,

  the small(ish) genome of Arabidopsis is about ten times larger and codes for approximately 27 000 genes.

  Those 8000 genes are all Ostreococcus needs for running its cell biology and metabolic pathways, including processes like making cell walls, photosynthesis,

  and respiration. Around 30% of its genes are also present in land plants, with

  which it last shared a common ancestor over a billion years ago. Of those 30%,

  land plants use some to control the branching patterns of shoots and the develop-

  ment of leaves. How strange. Obviously, tiny single-celled photosynthesizing algae are not using them for doing such jobs,10 and these bits of algal DNA are being

  redeployed for new purposes later down the evolutionary line. There is also the

  strong possibility that Ostreococcus has a special mode of photosynthesis that is able to concentrate carbon dioxide around the photosynthetic enzyme systems to

  improve efficiency.11 It represents a simplified version of a mode found in grasses of tropical savannas, the so-called C photosynthetic pathway that evolved hun-4

  dreds of millions of years later. Yet there it is. Complex computational analyses of the Ostreococcus genome show that it contains a near-complete set of biochemical reactions for photosynthesizing in this mode (with only a handful of reactions to be added to fill in the gaps).12 But what conceivable use is this to an alga living in the sea? Probably, the answer is that the pathway enables Ostreococcus to cope

  46 a Genomes decoded

  when algal blooms rapidly deplete dissolved carbon dioxide from the surface

  waters, causing temporary carbon dioxide starvation.

  Plant genomes do not come any more stripped down than that of Ostreococcus.

  Its freshwater cousin, the famous unicellular green alga Chlamydomonas, found in stagnant waterbodies, soils, and snow, has a ten-fold bigger genome.13 It contains nearly three times as many genes as its distant picoplankton cousin, including

  those required for the usual things organisms do, like swimming, finding food,

  mating, and building chloroplasts. In evolutionary terms, Chlamydomonas diverged from flowering plants about a billion years ago. Compare its genome with that of

  other organisms and you find it shares about 35% of its genes with flowering

  plants and humans. It also has an additional 10% it shares with humans, but not

  flowering plants.

  Many of the genes Chlamydomonas shares with humans are for building flagella, whip-like structures rotated by molecular motors that function to move it around.

  Flagella genes have been lost in most seed plants, which evolved novel fertiliza-

  tion mechanisms involving pollen grains that finally freed land plants from their inherited aquatic ancestry and aquatic fertilization.14 The earlier-evolving groups, such as algae, bryophytes, ferns, and some gymnosperms, produce motile sperm

  cells propelled along by single or multiple flagella. Animals, including humans,

  retained and modified these useful structures in a shortened form to make fine,<
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  waving threads called cilia. Cilia play crucially important roles in the normal

  functioning of our brains, our kidneys, where they bend as fluid passes over them allowing cells to sense flow, and our lungs, where they beat in co-ordinated waves to sweep up dirt and mucus.15 Signs of our single-celled ancestry spring from

  every cell in our bodies. If we develop faults in ciliary proteins, our health can suffer. Defects in cilia are linked to many illnesses, with one of the best-documented examples being a rare human genetic disease called Bardet–Biedl syndrome,

  which affects anatomical development, leading to extra fingers, blindness, and

  obesity. The identification of one of the human genes linked to the disease ( BBS5), that disrupts the making of cilia, came from analysis of the genome of the humble alga Chlamydomonas.16

  Being green and single-celled is a promising start, but what the history of life on Earth makes clear, for plants at least, is that eventually a multicellular lifestyle beckons. Once life gets going, the emergence of complex multicellular life forms

  from single-celled ancestors is seemingly inevitable.17 This momentous event

  Genomes decoded a 47

  probably happened around 700 million years ago when single cells clubbed

  together, perhaps using flagella and other similar structures, to co-operate, communicate, and form the first multicellular green algae. What did it take to make

  the crucial evolutionary transition from single-celled to multicelled algae? The

  question is a profound one, as the arrival of multicellular green algae in the late Precambrian ocean proved a watershed moment in Earth’s history, presaging the

  invasion of the land by millions of years.

  The answer is that multicellular plants required genetic toolkits for solving a

  new set of challenges, such as how to get cells to adhere and communicate with

  each other, and how to get oxygen into tissues as the organism becomes larger.

  Co-operation between individual cells is the key, because in a multicellular organism, the fates of the many cells that make up the new entity become bound col-

  lectively to the fate of a single individual. Decoding the genome of the beautiful multicellular green algae Volvox provided the best insights for how this might have happened. Around half a millimetre in diameter, Volvox is just visible to the naked eye. Antonie van Leeuwenhoek (1632–1723), the Dutch father of microscopy, first

  viewed these little round green ‘animalcules’ with utter fascination over three

  centuries ago.18 Using microscopes of his own design that could magnify by

  270 times, he observed Volvox in drops of pond water with a motion that ‘twas wonderful to see’. Later named Volvox by Linnaeus in 1758 (from the Latin volvere, to roll), these delightful green ‘fierce rollers’ move through the water by division of labour into two cell types—small and large. Each green sphere consists of

  some 2000 of the small cells (the number varies with species), embedded into a

  gelatinous matrix on the outer surface, which use pairs of flagella beating in waves to roll the colony forwards. Some cells form anterior eyespots, enabling the

  colony to swim towards light. Inside are 16 or so much larger sex cells involved

  in reproduction.19

  Surprisingly, for all its multicellular glory, the genomic distinction between

  Volvox, with its complex life cycle, and Chlamydomonas is almost trivial and did not apparently involve large changes in its genetic repertoire.20 Both organisms

  have around 15 000 genes, with few of those in Volvox being different from Chlamydomonas, though of course, we find extra genes involved in building that gelatinous matrix—the glue that holds the many cells together.21 The evolutionary transition from being single-celled to multicellular is not large increases in genes but changing the way those genes are used. Back in the Triassic, 200 million

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  years ago, it took Volvox’s predecessors some 35 million years of tinkering with the ancestral algal genetic blueprint to navigate towards the transition from single

  cells to multicellular colonies.22

  The key point to remember here is that algae such as Chlamydomonas and Volvox belong to the great chlorophyte division of algae that is distantly related to land plants. The truth is that land plants evolved from freshwater charophyte algae,

  from which they inherited an array of biochemical, physiological, and cell biol-

  ogy attributes. We can expect, then, that the genomes of charophytes hold deeper

  genetic insights into the origin of those traits that allowed algae to give rise to terrestrial plant life. At least that is the standard line of thinking. Yet, various complex lines of evidence are leading to the growing suspicion that charophyte algal lineages may have evolved to occupy terrestrial environments before giving rise

  to land plants.23 The idea that freshwater algae were the first ‘invaders of the land’

  gives you pause for thought. If this scenario is correct, we can anticipate ‘terrestrialization’ signatures for conquering soil and sediments to be written in their

  genomes. And, to some extent, this view was confirmed when a team sequenced

  and analysed the genome of a filamentous terrestrial alga, Klebsormidium flaccidum. 24 Klebsormidium has the genetic machinery for protecting its photosynthetic apparatus against damage from high intensity light, typically encountered on

  land, and for synthesizing hormones and metabolic signalling pathways to sur-

  vive environmental stress.

  Not only that, but it was further reinforced when the genome biologist Stefan

  Rensing undertook the most comprehensive genome sequencing project yet of a

  charophyte alga, focusing on a species that lives fully in freshwater called Chara braunii. C. braunii has a wonderfully elaborate body plan and is more closely related to land plants than Klebsormidium. Its genome codes for ca. 23 500 genes,25 substantially more than Chlamydomonas (ca. 19 000) or Klebsormidum (ca. 16 000), but similar to some land plants (e.g. moss ~ 35 000 and Arabidopsis 27 000). Much of the expansion of gene numbers in the genome of this species underpins its

  remarkably complex morphology, including its rhizoids and elaborate structures

  for sexual reproduction. The genome also has both striking similarities to land

  plants, and important differences. Rensing’s results are redefining the list of whole families of genes that were thought previously to be specific to land plants and, we now realize, are important for living in shallow freshwater environments that

  occasionally subject the plants to dry air.

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  Sequencing the genomes of additional charophyte species is an urgent priority,

  but in the meantime others have adopted the next best thing, that of determining

  a compact ‘snapshot’ of a species known as the transcriptome. Obtaining such a

  snapshot is a neat trick of cell biology pioneered by scientists from the human

  genome project. It involves isolating and extracting the messenger RNA from the

  tissues of the selected organism. Messenger RNA is present inside all living cells and is synthesized during the first step in gene expression to mirror the DNA

  code. These stringy molecules are exported out of the nucleus carrying the amino

  acid code for making proteins. Complex molecular machines (ribosomes), which

  read the message and link the specified amino acid building blocks together, carry out the conversion of messenger RNA into proteins. But the step that interests us here is the conversion of the original DNA code into the complementary language of messenger RNA molecules. In the lab, an enzyme called ‘reverse tran-

  scriptase’ is used to translate these snippets of RNA back into the original DNA

  message. The sequencing of the DNA message, essentially a copy of a
gene, is then undertaken to determine the identity and order of the bases. What you end up

  with is a condensed version of an organism’s genome containing all genes that are being expressed (i.e., those that are active) in the tissues sampled at a given time—

  the transcriptome.

  Obtained in this way, the transcriptomes of charophytes confirm that these

  diverse algae have sophisticated collections of genes responsible for the synthesis, perception, and signalling of major plant hormones.26 As anticipated, they also

  have a genetic repertoire predisposing them to make the bold transition from

  water to the land—a repertoire absent from the chlorophyte algae. The transcrip-

  tomes of the filamentous Spirogyra (Zygnematales) and the flying-saucer-shaped Coleochaete (Coleochaetales)27 have been analysed in detail, and found to harbour the genetic machinery for two important cellular features, plasmodesmata and

  phragmoplasts. Plasmodesmata are the pores in plant cell walls that allow neigh-

  bouring cells to communicate with each other and distribute water and nutrients

  to nourish the developing embryo. Phragmoplasts are microfibres involved in cell

  division that these algae share with all land plants. The early ancestors of land plants underwent cell division without the help of phragmoplasts but the course

  of evolution gradually modified the cell division apparatus to provide a higher

  degree of developmental flexibility.28 By flexibility, I mean it allowed asymmetrical cell division in shoot tips and/or rotation of the plane of cell division to permit

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  branching. In other words, it helps provide the fundamental basis for 3D plant

  development.

  The earliest proper land plants that descended from these algae were tiny, rudi-

  mentary photosynthetic organisms. They left behind mysterious fossilized spores

  in the rock record as tell-tale signs of their existence, and little else. The decoded genomes of the bryophytes (liverworts, hornworts, and mosses), the oldest

  surviving lineages of those pioneering plants, speak to us of the genetic innovations that define a terrestrial plant. Bryophytes entered the genomic era back in 2008, when the DNA sequence of a moss ( Physcomitrella patens) was published in the journal Science, by a team also led by Rensing as it happens.29 The sequence of a liverwort ( Marchantia polymorpha) followed a decade later,30 and the first genome sequencing of a hornwort ( Anthoceros agrestis) is in the pipeline.31 These genomes are giving us clues as to what it took to make a multicellular terrestrial plant from a charophyte algae ancestor.