*alternative titles include “Looking a gift seahorse (genome) in the mouth”, “My kingdom for a seahorse genome”, “Hold your seahorses“, and “The galloping evolution of seahorses“.

Let’s face it, seahorses, pipefishes, and seadragons are messed up. That’s not a subjective opinion but an evolutionary fact.  It’s like all the approximately 300 species in Syngnathidae (the family of fish that contains all these critters) held a meeting and decided unanimously “Nah, screw it, we’ll do things however we damn well please.”  The Syngnathids are revolutionaries of the fish world.  ¡Viva la Evolución Revolución!

Seriously, almost everything in these species is different.  There is the elongated snouts and small mouths and jaws.  The pelvic and caudal fins are often gone.  The scales are replaced with an armor of bony plates.  Let’s not forget about the whole “male pregnancy” thing where the males nourish the developing embryos in a pouch.  Seahorses take it all to a whole other level with the prehensile tail and the vertical body axis.

So ultimately, one is left wondering what’s up with those genes?  Well, thanks to an intrepid group of geneticist, the complete genome of the tiger tail seahorse, Hippocampus comes, is complete.  With the full genome comes great power, the ability to compare this genome to the other sequenced fish.

Part of the story regarding the bizarreness of seahorses is gene loss.   Secretory calcium-binding phosphoprotein (SCPP) genes code for matrix proteins that are important in the formation of bone and teeth.  These genes are completely missing in Hippocampus comes and may explain why seahorses do not have teeth.  Did I forget to mention that?  Yeah seahorses and seadragons are toothless. The tbx4 gene, conserved in jawed vertebrates, acts as a regulator of hindlimb formation.  The gene is completely absent in the seahorse genome and explains the absence of those pesky pelvic fins.

What about that whole “male pregnancy” thing?   The H. comes genome contains six pastn genes, part of a family of genes that regulate the hatching of embryos.  The researchers conducted extra work, like the genome was not enough, suggesting a role for these pastn genes in brood pouch development and/or hatching of embryos within the brood pouch prior to birth.

Seahorses have also apparently lost many conserved noncoding genes (CNEs) that function as enhancers, repressors, and insulators of other genes.  1,612 CNEs have been lost in seahorses.  Compare this to the 281 in the Nile perch.  It is unclear how the loss of the CNEs may be related to some of the oddities of the seahorse, but loss of CNEs is tied to moderate short stature and shortened limbs in humans.

How I imagine the scientists of the study acted once they finished the genome

The awesomeness of this kind of work cannot even be articulated.  The researchers have done an amazing job of unpacking the genome of a seahorse and showing how genome evolution directly leads to all the uniqueness of seahorses.  Admittedly, I am little disappointed in not seeing a discussion of the prehensile tails genes and armored plating discussed. I guess I’ll need to wait a bit to build my army of aquatic minions to take over the world.

The post In the evolution of fishes, this is a one seahorse race* first appeared on Deep Sea News.

The above photo is of Apolemia lanosa a type of siphonophore belonging to phylum Cnidaria that also includes corals and jellies.  It’s basically the ocean’s way of celebrating Christmas all year long.  Like many other Cnidarians, siphonophores bud new individuals—exact clones themselves.  In a manner similar to Christmas elves although this is not proven by science. In the case of some Cnidarians, the clones never leave home so family never has to travel for the holidays.  In some Cnidarians, clones in the colony will specialize but among siphonophores the specialization is unrivaled. Clones will specialize for feeding, defense, locomotion or reproduction. The feeding clones catch food by tentacles equipped with cells that shoot out poisonous harpoons stinging and stunning their prey.  In the most popular of all siphonophores, the Portuguese man o’ war, with a large gas filled buoyant bladder adapted for catching the wind and sailing.  Interestingly, all the clones are attached via a single digestive and circulatory system.  Research is still needed on which clones are adapted for drinking eggnog, singing carols, and wrapping gifts.

Apolemia belongs to a special set physonect siphonophores. Recently Dr. Stefan Siebert at Brown University with Phil Pugh (NOC), Steven Haddock (MBARI), and Casey Dunn (Brown University) described two new species in the family Apolemiidae, for which only three species had been described previously.  The species of Apolemiidae may be record holders for the longest animals on earth.

Fragments of specimens of this family with a length of over 30 meters have been reported from the French Mediterranean coast in the bay of Villefranche-sur-Mer.

In most physonect siphonophores clones are arranged along a central stem, it itself the founding clone developed from a single egg.  At the front end, is a group of clones that are propulsion clones. Basically, Santa’s reindeer if Dasher, Dancer, Prancer, Vixen were all budded from and identical to Santa.  In the larger and remaining region of a physonect siphonophore, one can find the clones for engaging in the spirit of Christmas, eating and…  New clones are formed in special growth regions of the siphonophore.  As new clones are formed the old clones get pushed down the line. But Apolemia species are special.  In addition to other clones Apolemia can also add new feeding clones along the entire length of the stem.

This fact might be the reason why members of this particular family of siphonophores can grow to such tremendous length.

Research by Siebert in collaboration with others uses these as the perfect organism to understand how an organism develops (check out some of their work which features DSN’s Rebecca Helm). Basically Apolemia is the biological Christmas gift that keeps on giving.

From a developmental point of view siphonophores are a very interesting and promising system since collection of a single colony gives the researcher access to complete developmental series of particular bodies – from the youngest bud to a mature body in older parts of the colony. Our work aims at increasing our understanding on how these different bodies can evolve using the same genome.

Siebert’s work looks for when genes turn on and off to trigger the growth and specialization of all the clones.  But the road is not easy going

 The interesting questions to be answered are, how to we get from one body type to another? How are genes sets differentially utilized to make body A or body type B and what has happened on the molecular level when evolutionary novelties, i.e. a new body type, can be observed in a particular [group] of siphonophores.

 A special thanks to Stefan Siebert who provided the quotes and a lesson on siphonorphore biology to me.

The post The Ocean’s Gelantinous Christmas Tinsel first appeared on Deep Sea News.

Even in the face of massive environmental change, bivalves are able to mount up and regulate.

The Pacific Oyster, Crassostrea gigas, may not look like the most badass of all living animals but it survives in the toughest of toughs, the intertidal.  Not that pretty rocky picturesque Maine intertidal either, but that nasty, stanky, murky water of the estuary.  When they are not surviving being out of the water half the day, they face rapid changes in temperature and salinity, exposure to toxics metals, and predation.  And that’s just Friday.

A team of too many authors to count in an open access paper has sequenced this oyster’s genome to uncover what makes this bivalve so bad ass.  It is the genes (not the apple bottom variety).  The group found over 28,027 genes and 8,654 of these were oyster-specific genes, key to bivalve bad assery.  In the words of the authors “[we found an] over-representation of some host-defence genes against biotic and abiotic stress.” More specifically over abundance of genes were found to combat air exposure (3,155 unique genes), heavy metals (840), salinity (347), and temperature.”   These numbers don’t even include the over 1,000 genes that can simultaneously deal with air exposure, heavy metals, salinity, and temperature.

The oyster genome contains 88 heat shock protein 70 (HSP70) genes, which have crucial roles in protecting cells against heat and other stresses, compared with ,17 in humans and 39 in sea urchins…. The oyster genome has 48 genes coding for inhibitor of apoptosis proteins (IAPs), compared with 8 in humans and 7 in sea urchins

Damaged cells, injured by mechanical damage or exposure to toxins, often go through a programed suicide, called apoptosis.  The oyster genome reveals a set of genes that inhibits this process.  We ain’t going out like that!

Many of the immune-related genes are expressed in the digestive gland, suggesting the gut is first line defense again pathogens.  Dodgy taco truck at 2 am? Filtering mucky turbid estuary water for food? No problem.

Of course the ultimate defense for bivalves is the shell.  The team found that the genome codes for 259 different shell proteins and potentially solved a key question of shell formation.  Is new shell material constructed inside or outside of cells?  Answer: within.  And in order to two do this it a super expanded set of genes.  For example human have but one measly gene to code for tryosinase, a enzyme that regulates melanin production oysters have 26.  Melanin is the pigment that determines your skin color and serves as excellent UV protector.  So you the next time you gaze upon dark beautiful oyster shell, recognize that you just got smacked up side the face with 26 genes worth of melanin.  Black is back!

Can bivalves kick it? Yes they can! Probably for another 400 million years with genes likes these.

Zhang et al. (2012) The oyster genome reveals stress adaptation and complexity of shell formation doi:10.1038/nature11413

The post Can Bivalves Kick It? Yes they can! first appeared on Deep Sea News.

As the title suggests, we’re looking at real data from the genome project of the Little Skate (Leucoraja erinacea). Why is this cool? Well firstly because all marine animals are totally awesome (Even vertebrates…I guess). Secondly, the Little Skate is often used as a model organism for understanding the human biology. L. erinacea is a Chondrichthyan fish, a primitive jawed vertebrate that branched off early from all living vertebrate species. The Little Skate functions like any typical vertebrate, possessing an adaptive immune system and a pressurized circulatory system (plus it grows fairly easily in tank); this species has significantly enhanced our knowledge of human physiology, immunology, stem cell and cancer biology, pharmacology, toxicology, and neurobiology. Having a complete genome sequence for the Little Skate will have huge benefits for developmental biology and biomedical research, and will also help to decipher evolution in sharks, rays, and higher vertebrates . With 49 chromosomes and an estimated genome size of 3.42 billion base pairs (slightly larger than the human genome), this species has considerably less genetic matter than other cartilaginous fishes (the genome of the dogfish shark, another closely related model organism, is double the size).

The most awesome thing about the Little Skate is its phenomenal power of regeneration. As in, it can grow back organs and amputated limbs. One of the big reasons for sequencing the genome is to characterize the genetic pathways and patterns of gene expression that enable this wound-healing response. If the Little Skate is an ancient vertebrate, then you could reason that limb regeneration is an ancestral trait that was subsequently lost in higher-level vertebrates. If we understand which genes turn on, could we eventually learn how to switch on limb regeneration in humans?

A smaller genome  is also cheaper to sequence (making scientists happy) and equals a better chance of a successful assembly. Although we hear about new genomes being sequenced on a weekly basis, this stuff is hard work. Take the human genome—our Homo Sapiens genome assembly is pretty damn good (nevermind ten years old already), yet there are STILL bits and pieces of sequence that don’t seem to fit in anywhere. Imagine you’re thisclose to completing a 2,000 piece puzzle, but you’ve got a bunch of holes and your extra pieces are all the wrong shape and size (e.g. you probably wrongly jammed in a piece somewhere in there…now you have to find it and swap it out). In a genome, we’ve got genes flanked by repetitive ‘junk’ DNA. A lot of times we don’t have long enough sequence bridges to span the gap of these repetitive regions; with the newest technologies each sequenced strand of DNA (what us biologists refer to as ‘reads’) is 100-150 base pairs long, but repetitive regions can be thousands of bases in length. The Skate Genome project currently has sequenced over 3 BILLION reads and given us 59x coverage of the genome (meaning every position in the genome has theoretically been sequenced 59 times) but there STILL isn’t enough data for a good assembly. The current assembly has the genome spit into 3 million contigs (longer stretches of DNA stuck together), with the longest contigs around 21,000 bases in length. Curse you, repetitive elements!  Nevertheless, we’re making slow and steady progress; the data that we do have is helping to train undergrads, postdocs, and new genomicists in genome assembly and protein identification.  Our undergrad from UNH was dreaming about gene annotation by the end of the week…

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The post Assembling the Little Skate Genome first appeared on Deep Sea News.

But for Daphnia, a.k.a. the ‘water flea’,  we have a REALLY good idea of what this species actually DOES in the wild.  These animals are small (0.2-0.5 mm), free-swimming crustaceans that are fairly ubiquitous in freshwater.  They can tolerate a huge range of aquatic conditions, and their sensitivity to toxins makes them an ideal indicator species for assessing the health of an environment.  They also don’t live long (big plus for growing them in the lab), with their life cycle (reproducing by cloning vs. sexually) and anatomical features (cool anti-predator defenses) affected by the environment in which they live:

Armed with this information, a bunch of scientists said “Hey, lets grow this weird animal in a whole bunch of different toxins and water conditions, sequence the genome, and then see how gene expression changes across the different treatments”.  Which is exactly what the Science paper is about.  It turns out that Daphnia pulex has a tiny genome containing only 200 million base pairs (compared to 3 billion in humans), yet has a whopping 31,907 genes within it (that’s more than humans, who have 20-25,000 genes!).  More than a third of Daphnia genes are unique to this species. The high number of genes is a result of duplication, where the genome contains multiple copies of similar genes–this explains how Daphnia can adapt to a wide range of environmental conditions and stress.  The rationale for maintaining duplicate genes is kind of like my black shoe collection.  Black shoes go with everything, but not all pairs are interchangeable: sky-high black stilettos are appropriate for a martini bar (but not for work!) while my black granny pumps are reserved for job interviews (and I wouldn’t be caught dead wearing them on a date).

So as genes have duplicated in Daphnia, the two new copies a given gene (called paralogs) have acquired slightly different characteristics.  The animal’s environment may then determine which gene gets expressed–i.e. which gene allows it to adapt better to its surrounding ecosystem.  Gene duplication isn’t this cut and dry–sometimes duplicated genes are lost and become non-functional, or the expression of duplicated genes diverges wildly as mutations accumulate over time–but its pretty cool nonetheless.  Now that the Daphnia genome is published, we have a better understanding of how an animal’s environment impacts cellular machinery.

Reference:
John K. Colbourne, et al. (2011)  The Ecoresponsive Genome of Daphnia pulex. Science 331: 555-561. DOI: 10.1126/science.1197761

The post Release of the Daphnia Genome first appeared on Deep Sea News.