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genomics

Baby, you light up my world: Using genetics to understand how velvet belly lanternsharks produce light

Eat or be eaten is the way of the ocean, and many marine species have adapted ways to accomplish one while avoiding the other. The velvet belly lanternshark (Etmopterus spinax) is a small deep sea dogfish species found in the Northeast Atlantic Ocean. Lanternsharks get their name from their ability to light up like a lantern. These sharks, like many deep sea creatures, have special organs in their skin that emit light, called photophores. When photophores emit light, scientists call this bioluminescence. Bioluminescence allows the animal to blend with its surroundings or attract potenetial prey. Unique traits such as bioluminescence have scientists asking a lot of questions. Specifically, what genes are involved in  lanternshark bioluminescence?

A gene is a long strand of DNA made up of a unique sequence of four bases (A, T, C, and G). Similar to how 26 letters can make millions of words, four bases can make millions of unique sequences.  These unique sequences are translated into RNA, which then encodes for a protein (for more information on how this works, watch this video). This protein can have a multitude of different functions. Humans have approximately 20,000 coding genes, which create proteins involved in all of our bodily processes, from eyesight to brain function to fighting off diseases.  It’s safe to assume that if your body does something, there is a gene (or thousands of genes!) that encodes for that function. This isn’t just true for humans – all living things have genes that control their form and function. So which genes control bioluminescence in the velvet belly lanternshark? A new study released on New Year’s Eve takes the first step in answering this complex question.

 

Methods

To kick off this study, velvet belly lanternsharks were captured by longlines in Norway from 2014 to 2016. The sharks were humanely euthanized, and tissue was collected from their eyes and skin for genetic analysis.

Scientists used cutting-edge sequencing technology called Next Generation Sequencing to sequence RNA from both tissues. Sequencing allows scientists to read the long strings of bases and match them to known genes. Scientists were able to obtain hundreds of thousands of RNA sequences, which were then assembled to create a “transcriptome.” A transcriptome is a map of genes that have been transcribed from DNA to RNA.  Because only important coding strands of DNA are transcribed to RNA, transcriptomes contain only genes that code for proteins. This makes it easier for scientists to identify genes, as there is less to sift through.

Many genes are conserved between species, meaning that the sequence for a gene in one shark species is likely to be the same sequence for the gene in another shark species. By comparing the lanternshark’s transcriptome to the transcriptomes of other, more heavily studied sharks like the elephant shark, scientists were able to identify genes involved in light production in both the eyes and skin. While elephant sharks are not bioluminescent, all sharks (and all vertebrates) have many similar genes that are arranged in relatively the same way. By using the elephant shark’s genome as a map, it is easier to locate genes of interest, such as those involved in bioluminescence.

Results

Next generation sequencing produced 46,012,442 sequence reads for the eye transcriptome, and 51,160,110 for the skin transcriptome. Referring back to my earlier analogy, if DNA bases were letters, that would be the equivalent of 46,012,442 and 51,160,110 paragraphs. Genetics is no joke!

Reads were then combined into contiguous, or joined, sequences. Then, unique sequences, or unigenes, were identified. Scientists were able to identify 94,365 unigenes for the eye and 93,569 unigenes for the skin.

Many of these unigenes coded for known proteins involved in light perception, such as Es-rhodopsin and Es-peropsin, which indicate that velvet belly lanternsharks most likely have monochrome, or black and white, vision. In addition, the protein Es-enchaplopsin, while found in both the eye and the skin, had higher concentrations in the skin. Opsin genes such as Es-enchalopsin are typically found in the eyes, so high concentrations in the skin mean this gene is important for functions that take place in the skin.  The researchers believe that this protein may be involved in initiating pathways that cause bioluminescence.  In addition to the identification of genes, this study produced the first transcriptome for a lanternshark species.

 

So why does this matter?

The first step in protecting a species is to understand how it functions. Deep sea creatures are harder to study, because they are harder to reach. Because of this, very little is known about the creatures dwelling in the depths. Bioluminescence is the main source of light in the deep ocean, so understanding the genes involved in bioluminescence in lanternsharks will shed light (literally!) on how this elusive deep-water world operates.

This study also provides the first reported transcriptome for lantern shark species. Just as this study used transcriptomes from other sharks as references, the data presented in this study is now available for other researchers to use. Better genetic data about sharks comes supports further discoveries, and the more we know about sharks, the better we will be able to protect them.

 

Reference:

Delroisse J, Duchatelet L, Flammang P, Mallefet J (2018) De novo transcriptome analyses provide insights into opsin-based photoreception in the lanternshark Etmopterus spinax. PLOS ONE 13(12): e0209767. https://doi.org/10.1371/journal.pone.0209767

 

 

 

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