Animal with the most genes? A tiny crustacean: First crustacean genome sequenced

Feb 03, 2011
The freshwater zooplankton Daphnia pulex (water flea), a near-microscopic crustacean that lives in ponds and lakes, has a translucent body and a compound eye. Credit: Jan Michels, Christian-Albrechts-Universitaet zu Kiel

Complexity ever in the eye of its beholders, the animal with the most genes -- about 31,000 -- is the near-microscopic freshwater crustacean Daphnia pulex, or water flea. By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The findings are part of a comprehensive report in this week's Science by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics and Bioinformatics (CGB) at Indiana University Bloomington and the U.S. Department of Energy's Joint Institute. A bullet-point list of the Science paper's most important findings appears at the end of this release.

"Daphnia's high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species," said project leader and CGB genomics director John Colbourne. "We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

Daphnia Genomics Consortium projects can be found here, as well as a link to the nearly 40 companion papers based on the data reported in the Science paper.

Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress. Predators signal some of the animals to produce exaggerated spines, neck-teeth or helmets in self-defense. And like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males -- by clonal reproduction, until harsh environmental conditions favor the benefits of sex.

Daphnia's genome is no ordinary genome.

"More than one-third of Daphnia's genes are undocumented in any other organism -- in other words, they are completely new to science," says Don Gilbert, coauthor and Department of Biology scientist at IU Bloomington.

Sequenced genomes often contain some fraction of genes with unknown functions, even among the most well-studied genetic model species for biomedical research, such as the fruit fly Drosophila. By using microarrays (containing millions of DNA strands affixed to microscope slides) that are made to measure the conditions under which these new genes are transcribed into precursors for proteins, experiments that subjected Daphnia to environmental stressors point to these unknown genes having ecologically significant functions.

"If such large fractions of genomes evolved to cope with environmental challenges, information from traditional model species used only in laboratory studies may be insufficient to discover the roles for a considerable number of animal genes," Colbourne said.

Daphnia is emerging as a model organism for a new field of science -- Environmental Genomics -- that aims to better understand how the environment and genes interact. This includes a practical need to apply scientific developments from this field toward managing our water resources and protecting human health from chemical pollutants in the environment.

James E. Klaunig, professor and chair of the School of Health, Physical Education, and Recreation's Department of Environmental Health at IU Bloomington, predicts the present work will yield a more realistic and scientifically-based risk evaluation.

"Genome research on the responses of animals to stress has important implications for assessing environmental risks to humans," Klaunig said. "The Daphnia system is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary. With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

The scientists learned that of all sequenced invertebrate genomes so far, Daphnia shares the most genes with humans.

The idea behind environmental genomics for risk assessment is fairly simple. Daphnia's gene expression patterns change depending on its environment, and the patterns indicate what state its cells are in. A bobbing in water containing a chemical pollutant will express by tuning-up or tuning-down a suite of genes differently than its clonal sisters accustomed to water without the pollutant. Importantly, the health effects of most industrially produced compounds at relevant concentrations and mixtures in the environment are unknown, because current testing procedures are too slow, too costly, and unable to indicate the causes for their effects on animals, including human. The new findings suggest that Daphnia's research tools (like microarrays) and genome information can provide a higher-throughput and information-rich method of measuring the condition of our water supply.

The freshwater zooplankton Daphnia pulex (water flea) with a brood of genetically identical future offspring. Credit: Paul D.N. Hebert, University of Guelph

"Until now, Daphnia has primarily been used as sentinel species for monitoring the integrity of aquatic ecosystems," said Joseph Shaw, coauthor and IU School of Public and Environmental Affairs biologist. "But with many shared genes between Daphnia and humans, we will now also apply Daphnia as a surrogate model to address issues directly related to human health. This puts us in a position to begin integrating studies of environmental quality with research of human diseases."

A requisite for reaching model system status is a large research community that contributes to its growing body of knowledge and resources. Over the course of the project, the Daphnia Genomics Consortium has grown from a handful of founding members to more than 450 investigators distributed around the globe. Nearly 200 scientists have contributed published work resulting from the genome study, many in open-source journals published as a thematic series by BioMedCentral. A list of these publications can be found here.

"Assembling so many experts around a shared research goal is no small feat," said Peter Cherbas, director of the CGB. "We're obviously proud of the CGB's catalytic role. The genome project signals the coming-of-age of Daphnia as a research tool for investigating the molecular underpinnings of key ecological and environmental problems."

Colbourne agreed, adding, "New model systems rarely arrive on the scene with such clear and important roles to play for advancing a new field of science."

The scientists present findings on the pace at which copied genes gain new functions, including a novel theory that accounts for the apparent rapid evolution of some of Daphnia's gene families (suites of related genes that result from repeated duplication events).

"Gene functions can become distinct very quickly," said Michael Pfrender, coauthor and associate professor of biology at the University of Notre Dame. "We had all assumed that newly copied genes that code for the same proteins would initially have the same functions, and that new functions evolve slowly with age, by acquiring rare beneficial mutations. Instead, we found that half of the newly copied genes had changed their expression very soon, possibly at the time of their origin."

Like in a mystery novel, the DNA evidence presented by examining the patterns of gene duplication in the study's first chapters was combined with clues of the genes' functions in later chapters to propose a new model for how genes accumulate in genomes.

"The smoking gun in this investigation was clear," said Kelley Thomas, coauthor and Hubbard Professor in Genomics at the University of New Hampshire. "A high rate of gene duplication, which produces a steady pool of new genes that have different expressions can facilitate the preservation of some gene-copies by natural selection."

Like most theories for how new genes evolve, their common fate is to wither by disabling mutations. For a new gene to persist, its function must give an advantage to the organism -- and the earlier the better for the gene to avoid bad mutations. In Daphnia's case, there seems to be a sufficiently large pool of young gene copies that some will be expressed in novel circumstances, and by chance be compatible with expression patterns of interacting genes required to perform its new function.

"At first glance, amplified gene families in Daphnia are more likely to be functionally related than not," said Michael Lynch, coauthor and distinguished professor of biology at IU Bloomington. "This suggests that gene functions via duplication often evolve in cooperation with other genes in the genome. We are not yet prepared to generalize our findings until we broaden our investigation to include more Daphnia lineages having different population histories. However, it's quite clear that this genome project opens up enormous opportunities that are not readily accomplished using other models with poorly understood -- and not terribly accessible -- ecologies."

So what other reasons might Daphnia have so many genes compared to other animals? The coauthors of the Science paper begin addressing that issue as well as others related to the genomic architecture and evolution of the species.

"We don't yet have final answers," Pfrender said. "The sequenced isolate did originate from a naturally inbred population, which may contribute to some features of this genome -- and Daphnia's partial asexuality may have a hand to play."

Another possibility, Colbourne said, is that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

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InsaniD
3.6 / 5 (7) Feb 03, 2011
This could be totally incorrect, but seems, from what I've been reading, that the more "complex" an organism is, the fewer genes that organism has. Almost like the more complex, the more streamlined the code becomes...
Sort of like comparing it to computer code. Code from 40 years ago was vast for doing simple tasks. Now we can do amazing things with very sleek code.

What do you think?
Aranea_hirsuta
5 / 5 (7) Feb 03, 2011
I am not in a biology field, but I would also think the expression of the existing genes would be of importance.

I am not sure if we can measure "complexity" based simply off of the number of genes.

Quite a complex topic.
gwargh
4.6 / 5 (11) Feb 03, 2011
What do you think?


Not quite. The genomes of more complex organisms are much larger, they just contain relatively fewer protein coding genes. Furthermore, while humans have only 23000 coding genes, we express nearly a million different proteins, since each gene can be expressed in multiple ways. It seems to be the case that more complex organisms rely on more intricate control of genetic expression(produce precisely what you need, and nothing else), while very simple organisms (bacteria, for example), have far simpler genetic expression (a "produce everything and hope it works" approach).

The complexity of organisms, in short, can be measured based off the ratio of coding/non-coding DNA. Part of the reason why the Daphnia sequence is exciting is because it has more coding than non-coding DNA, making it much easier to recognize the different response pathways.
gmurphy
5 / 5 (4) Feb 03, 2011
@gwargh, nicely put. That said, the influence of "non-coding" DNA on the behavior of genetic regulatory networks has yet to be quantified and there is some suspicion that it may play a subtle but important role.
pauljpease
5 / 5 (5) Feb 03, 2011
@gwargh, nicely put. That said, the influence of "non-coding" DNA on the behavior of genetic regulatory networks has yet to be quantified and there is some suspicion that it may play a subtle but important role.


Yes. In fact, it's way more than just suspicion at this point. There are tons of regulatory elements we know about that are part of our genome that are not part of genes. Measuring complexity by counting genes is like rating the complexity of an argument based on the number of words. Obviously, what the words are and how they are strung together into phrases is more important than the number of words.
gvgoebel
5 / 5 (4) Feb 03, 2011
Hmm, my own notes say the water flea sequence was announced in mid-2009. Anyway, from my notes:

BEGIN QUOTE:

Said one genomic researcher: "It's a big surprise that critters you think wouldn't have a high gene count do ... " -- but adds that we are "probably naive in defining what is biological complexity."

The water flea actually has a highly adaptable biology, generally cloning itself but resorting to sexual reproduction under some circumstances. Eggs can hatch immediately, or remain dormant for more than a century. Water fleas can alter form in different ways in environments with different types of predators, for example growing spines or helmets. They can live in fresh water or salt, and in fact are borderline "extremophiles", able to live in very salty or acidic waters. As another researcher put it: "It's almost as if they have more than one genome" to allow them to deal with a wide range of environments.

END
Birthmark
5 / 5 (1) Feb 03, 2011
It BLOWS my mind that something so complex as primates have less genes than a tiny crustacean! Science is beautiful.
gvgoebel
5 / 5 (1) Feb 03, 2011
The whole notion of genomic complexity is very tricky. It's like trying to figure out how much information there is in a book ... yeah, one can rate the number of pages, but that doesn't reveal what the book really has to say.
la7dfa
not rated yet Feb 03, 2011
Interesting how new stuff pops up, when we think the riddle is solved :-) Reminds me of splitting an atom, and finding new exiting particles. I am pleased to live in this age of discoveries!
mrlewish
3.7 / 5 (3) Feb 03, 2011
the length of a book does not tell you how good it is.
InsaniD
not rated yet Feb 03, 2011
BEGIN QUOTE:

Said one genomic researcher: "It's a big surprise that critters you think wouldn't have a high gene count do ... " -- but adds that we are "probably naive in defining what is biological complexity."
END


Glad to know that my thoughts are in line with at least one genomic researcher. And I agree - it is a simplistic view, but if the people in the know share it too, then hey - makes me feel better.
:P
SmartK8
not rated yet Feb 04, 2011
I don't want to break your flow of anthropocentric rationalization, guys. But what if - just an opinion - are those organisms really more complex than us.
soulman
1 / 5 (1) Feb 04, 2011
I don't want to break your flow of anthropocentric rationalization, guys. But what if - just an opinion - are those organisms really more complex than us.

Self evidently, they are not. Unless you have a different than normal definition of complexity. And even if it were true, so what? What are you implying with your 'what if' question?
gvgoebel
5 / 5 (2) Feb 04, 2011
I don't want to break your flow of anthropocentric rationalization, guys. But what if - just an opinion - are those organisms really more complex than us.


Which is a fun question, since we don't have any useful measure of biological complexity -- we can cook up various ad-hoc measures but they can't be reduced to a numeric value that buys anything.

Parasites -- that is, eukaryotic internal parasites -- can have big genomes. The protozoan parasite that causes malaria goes through multiple life-cycles in which its form changes from generation to generation. Anyone who wants to argue the relative complexity of the malaria protozoan versus, say, a human, could argue all day and not get much of anywhere.

And, unfortunately, the whole notion of "biological complexity" has been thoroughly hijacked by creobots. "Last refuge of a scoundrel" and all that good stuff.
NameIsNotNick
5 / 5 (2) Feb 04, 2011
Sort of like comparing it to computer code. Code from 40 years ago was vast for doing simple tasks. Now we can do amazing things with very sleek code.

What do you think?


I'm no expert on biology, but the analogy to computer code is incorrect.
Skeptic_Heretic
5 / 5 (2) Feb 04, 2011
It BLOWS my mind that something so complex as primates have less genes than a tiny crustacean! Science is beautiful.

Well there's a few problems with this statement.
Your initial assumption that because your brain operates in a more complex manner that you are biologically more complex than a filterfeeder on the bottom of the ocean. Most plants have more complex genomes than primates. Biologically, they are vastly more complex than you or I, and their genome typically shows it in length, not necessarily in expression.

In short, our definition of biologically complex appears to be more a creation of our wholly complex thought processes. Not our relatively moderate genome complexity.
SmartK8
5 / 5 (2) Feb 04, 2011
soulman: Just that humans tend to think that they're the pinnacle of evolution, while there is none. So they project their expectations onto genome size, or complexity. When confronted with data showing differently, they're making funny excuses on how to integrate the latest fact to their world view. Nothing less.

gvgoebel: Good point. I would say that in this case the complexity is usually such measurement, which supports one's world view.
gvgoebel
not rated yet Feb 04, 2011
Good point. I would say that in this case the complexity is usually such measurement, which supports one's world view.


Thanks. "The impression on a sofa of the last bottom that sat on it."

People CAN make arguments about biological complexity. The difficulty is that they don't accomplish much, and worse, such arguments are only too often for dishonest reasons and have cast disrepute on the notion.
soulman
1 / 5 (1) Feb 04, 2011
soulman: Just that humans tend to think that they're the pinnacle of evolution

Well, only those that don't understand science and evolution in particular.
while there is none.

Agreed, glad you think so too.
So they project their expectations onto genome size, or complexity. When confronted with data showing differently, they're making funny excuses on how to integrate the latest fact to their world view.

Yes, that effect is well known and in evidence on this board from some individuals.
DKA
1 / 5 (2) Feb 05, 2011
Useless to say that primates, human, we are not superior in our biology than many other species. Is using brain, as we do, very complex biologically? Maybe not. We should not expect to be more complex in any biological way to many other species. That would be typical of our arogance to believe that we are more complex in a way or another. Maybe nature will prove that we have nothing to brag about. Men is maybe more like a rat or crow that multiplies in favorable conditions only.
Birthmark
not rated yet Feb 05, 2011
Well there's a few problems with this statement.
Your initial assumption that because your brain operates in a more complex manner that you are biologically more complex than a filterfeeder on the bottom of the ocean [...]
In short, our definition of biologically complex appears to be more a creation of our wholly complex thought processes. Not our relatively moderate genome complexity.


I was not referring to the brain, but more it's structure. I was referring to the 220 types of cells, the way we conceive (meiosis), the structure of our brain, the processes that involve every cell in our body, our veins and blood cells and everything. It seems these small animals are missing so much of our complexity (not mentally), and this is why it amazes me, but I can understand, partly, why they do have more genes or more "complexity"
Ethelred
5 / 5 (1) Feb 06, 2011
Most plants have more complex genomes than primates. Biologically, they are vastly more complex than you or I, and their genome typically shows it in length, not necessarily in expression.
I think there is a better way to say that.

BioCHEMICALLY they are more complex than us.

They have to respond biochemically to things we and many other organisms use brains for.

Ethelred