Category Archives: Genome

When humans tamed rabbits, we changed around 100 regions of their genome. The shifts were subtle, but they may have made domestic rabbits less fearful than wild ones.

Pet rabbits will happily sit in their owner's lap, but wild rabbits are famously timid, fleeing at the slightest hint of a human, let alone a fox or hawk. This tolerance for human company was only bred into bunnies recently: about 1400 years ago in southern France. But it was not clear how this worked at the genetic level. Did domestication make drastic changes to a few important genes, or many subtle alterations?

To find out, Leif Andersson at Uppsala University in Sweden and his colleagues compared the genomes of pet rabbits with those of their wild counterparts (Oryctolagus cuniculus) from Spain and southern France.

No genes had been turned off outright, a process that in theory might have helped reduce fear of humans. "Gene loss has not played a prominent role during rabbit domestication," says Andersson.

Instead, the team found that lots of small, pre-existing genetic variations became more common in rabbits as they were domesticated. Most of these variations involved just one letter of DNA code. All in all, about 100 regions were selected to be different in the domesticated rabbits.

Rather than affecting the genes themselves, most of the DNA tweaks were in regulatory regions of the genome, which control whether genes are switched on or off. "Wild and domestic rabbits do not differ so much in actual protein sequences, but in how gene and protein expression is regulated," says Andersson.

The genetic shifts were often associated with regions of the genome involved in the development of neurons and the brain. That makes sense, says Andersson, considering the differences in behaviour between domestic and wild rabbits.

"Selection during domestication might have focused on tameness and lack of fear," says Pat Heslop-Harrison of the University of Leicester in the UK. "As a farmer, you neither want the animal to hurt you, nor for the animal to die from stress." Keeping lookout and fleeing from potential predators uses up lots of an animal's energy, which humans would rather see turned into meat.

Because rabbits were only domesticated relatively recently, the new sequences are not all present in all domestic rabbits. As a result, Andersson says escaped domestic rabbits could revert to wild-like forms over just a few generations - assuming they survived in the wild.

Journal reference: Science, DOI: 10.1126/science.1253714

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Taming of the bunny rewrote rabbit genome

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Inferring Intra-Tumor Heterogeneity from Whole-Genome/Exome Sequencing Data - Layla Oesper
May 13, 2014 - The Cancer Genome Atlas 3rd Annual Scientific Symposium More: http://www.genome.gov/27557040.

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The ctenophore genome and the evolutionary origins of neural systems - Supplementary Video 1
Leonid L. Moroz, Kevin M. Kocot, Mathew R. Citarella, Sohn Dosung, Tigran P. Norekian, Inna S. Povolotskaya, Anastasia P. Grigorenko, Christopher Dailey, Eug...

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The ctenophore genome and the evolutionary origins of neural systems - Supplementary Video 1 - Video

Genome research has been a boon for unravelling the mysteries surrounding autism, allowing scientists to identify around 100 altered genes associated with the neurodevelopmental disorder.

But genome research has also compounded the puzzle of autism. Those who display the symptoms of autism spectrum disorder (ASD) may carry the same number of genetic mutations as their unaffected siblings. One person with ASD will carry mutations totally different from the next, and half of those diagnosed will have none of the known mutations at all.

There are no common patterns, says Stephen Scherer, director of the Hospital for Sick Childrens Centre for Applied Genomics.

By examining a different part of the genome than previously studied, a team of scientists led by Scherer has created a formula for determining which mutations are likely to lead to ASD and which are not. In the process, they also flagged more than 1,600 genes not previously linked to autism that may hold new clues for discovering what causes the disorder that now affects 1 in 68 children.

The new research, published in the journal Nature Genetics, suggests that autism begins to develop in the womb. It will help clinicians diagnose ASD earlier hugely important, since autism is easier to treat the earlier it is caught.

Kathryn Roeder, a statistical geneticist at Carnegie Mellon University in Pittsburgh who was not involved in the study, called it a tremendous stride forward, saying she planned to distribute it as soon as she could.

The new formula, Roeder said, will be able to erase a lot of noise.

The formula came about after researchers in Scherers lab decided to examine exons, small segments of DNA that are protein-coding. An average gene has 10 exons, but may have fewer or many more.

The team discovered that when they compared mutations in the exons of those who have ASD and those who do not, rather than comparing the whole genome, they came up with a statistically significant way of predicting ASD symptom risk.

You have to look at the small segment level, the exon level. Thats really the key here, says Scherer.

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Autism researchers make huge step in discovering genetic mutations that may lead to the disorder

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The Pan-Cancer Proteomic Landscape of The Cancer Genome Atlas Projects - Rehan Akbani
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The publication of the draft genetic sequence of a comb jelly reveals a nervous system like no other

Pleurobrachia bachei lacks many common genes. Credit:Leonid L. Moroz/Mathew Citarella

Comb jellies, or ctenophores, look like tiny disco balls and propel themselves around oceans using specialized hairs, lapping up small prey with their sticky tentacles. They are aliens whove come to Earth, says Leonid Moroz, a neuroscientist at the University of Florida in St Augustine.

The genome of the Pacific sea gooseberry (Pleurobrachia bachei), which Moroz and his team report online today inNature, adds to the mystery of ctenophores (L. L. Morozetal. Nature http://dx.doi.org/10.1038/nature13400; 2014). The sequence omits whole classes of genes found in all other animals, including genes normally involved in immunity, development and neural function. For that reason, the researchers contend that ctenophores evolved a nervous system independently.

Ctenophores have long vexed taxonomists. Their resemblance to jellyfish earned them a spot on the tree of life as a sister group to cnidarians (the phylum that includes jellyfish). On the basis of their nervous systems which can detect light, sense prey and move musculature many researchers had them branching off from the common ancestor of other animals after the sponges and flattened multicellular blobs known as placozoans, neither of which have a nervous system. Now armed with data showing that ctenophores lack many common genes, some scientists contend that these are the closest living relatives to the first animals.

Morozs team argues that theP.bacheigenome, along with gene-expression data from other ctenophores, supports this theory. For example, microRNAs, which regulate gene expression in other animals, are completely missing from the sea gooseberry genome.

The biggest surprise, Moroz says, was the absence of many standard components of a nervous system. Nearly all known nervous systems use the same ten primary neurotransmitters; the Pacific sea gooseberry seems to employ just one or two. Moroz speculates that the organism might complete its nervous system using molecules that researchers have not yet found in this species, such as specialized protein hormones.

The uniqueness of this ctenophores nervous system leads Moroz and his team to argue that it must have evolved independently, after the ctenophore lineage branched off from other animals some 500million years ago. Everyone thinks this kind of complexity cannot be done twice, Moroz says. But this organism suggests that it happens.

Gert Wrheide, an evolutionary geobiologist at Ludwig Maximilian University in Munich, Germany, is intrigued by the theory that the nervous system evolved twice in different animal branches, but disputes that ctenophores are the closest relatives of the first animals.

The common ancestor of all animals may have looked nothing like comb jellies, and theP.bachei nervous system may be a more recent adaptation, he says. I think the last word is not spoken yet on where the ctenophores go.

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Comb Jelly Genome Grows More Mysterious