Category Archives: Genome

Whole genome sequencing of modern and ancient horses unveils the genes that have been selected by humans in the process of domestication through the latest 5,500 years, but also reveals the cost of this domestication. A new study led by the Centre for GeoGenetics at the University of Copenhagen, in collaboration with scientists from 11 international universities, reports that a significant part of the genetic variation in modern domesticated horses could be attributed to interbreeding with the descendants of a now extinct population of wild horses. This population was distinct from the only surviving wild horse population, that of the Przewalski's horses. The study has been published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

The domestication of the horse some 5,500 years ago ultimately revolutionized human civilization and societies. Horses facilitated transportation as well as the circulation of ideas, languages and religions. Horses also revolutionized warfare with the advent of chariotry and mounted cavalry and beyond the battlefield horses greatly stimulated agriculture. However, the domestication of the horse and the subsequent encroachment of human civilization also resulted in the near extinction of wild horses.

The only surviving wild horse population, the Przewalski's horses from Mongolia, descends from mere 13 individuals, preserved only through a massive conservation effort. As a consequence of this massive loss of genetic diversity, the effects of horse domestication through times have been difficult to unravel on a molecular level. Says Dr. Ludovic Orlando, Associate Professor at the Centre for GeoGenetics, who led this work

"The classical way to evaluate the evolutionary impact of domestication consists of comparing the genetic information present amongst wild animals and their living domesticates. This approach is ill suited to horses as the only surviving population of wild horses has experienced a massive demographic decline in the 20th century. We therefore decided to sequence the genome of ancient horses that lived prior to domestication to directly assess how pre-domesticated horses looked like genetically."

Recent advances in ancient DNA research have opened the door for reconstructing the genomes of ancient individuals. In 2013, Ludovic Orlando and his team succeeded in decoding the genome of a ~700,000 year-old horse, which represents the oldest genome sequenced to date. This time, the researchers focused on much more recent horse specimens, dating from ~16,000 and ~43,000 years ago. These were carefully selected to unambiguously predate the beginning of domestication, some 5,500 years ago. The bone fossils were excavated in the Taymyr Peninsula, Russia, where arctic conditions favor the preservation of DNA.

The human reshaping of the horse

While the horse contributed to reshaping human civilization, humans in turn reshaped the horse to fit their diverse needs and the diverse environments they lived in. This transformation left specific signatures in the genomes of modern horses, which the ancient genomes helped reveal. The scientists were able to detect a set of 125 candidate genes involved in a wide range of physical and behavioral traits, by comparing the genomes of the two ancient horses with those of the Przewalski's horse and five breeds of domesticated horses. Says Dr. Dan Chang, post-doctoral researcher at the UCSC Paleogenomics Lab and co-leading author of the study:

"Our selection scans identified genes that were already known to evolve under strong selection in horses. This provided a nice validation of our approach."

Dr. Beth Shapiro, head of the UCSC Paleogenomics Lab continues: "We provide the most extensive list of gene candidates that have been favored by humans following the domestication of horses. This list is fascinating as it includes a number of genes involved in the development of muscle and bones. This probably reveals the genes that helped utilizing horses for transportation."

And Dr. Ludovic Orlando from the Centre for GeoGenetics at the University of Copenhagen concludes: "Perhaps even more exciting as it represents the hallmark of animal domestication, we identify genes controlling animal behavior and the response to fear. These genes could have been the key for turning wild animals into more docile domesticated forms."

Excerpt from:
Reshaping the horse through millennia

Scientists at Indiana University and colleagues at Stanford and the University of Texas have demonstrated a technique for "editing" the genome in sperm-producing adult stem cells, a result with powerful potential for basic research and for gene therapy.

The researchers completed a "proof of concept" experiment in which they created a break in the DNA strands of a mutant gene in mouse cells, then repaired the DNA through a process called homologous recombination, replacing flawed segments with correct ones.

The study involved spermatogonial stem cells, which are the foundation for the production of sperm and are the only adult stem cells that contribute genetic information to the next generation. Repairing flaws in the cells could thus prevent mutations from being passed to future generations.

"We showed a way to introduce genetic material into spermatogonial stem cells that was greatly improved from what had been previously demonstrated," said Christina Dann, associate scientist in the Department of Chemistry at IU Bloomington and a co-author of the study. "This technique corrects the mutation, theoretically leaving no other mark on the genome."

The paper, "Genome Editing in Mouse Spermatogonial Stem/Progenitor Cells Using Engineered Nucleases," was published in the online science journal PLOS-ONE.

The lead author, Danielle Fanslow, carried out the research as an IU research associate and is now a doctoral student at Northwestern University. Additional co-authors are from the Stanford School of Medicine and the University of Texas Southwestern Medical Center.

A challenge to the research was the fact that spermatogonial stem cells, like many types of adult stem cells, are notoriously difficult to isolate, culture and work with. It took years of intensive effort by multiple laboratories before conditions were created a decade ago to maintain and propagate the cells.

For the IU research, a primary hurdle was to find a way to make specific, targeted modifications to the mutant mouse gene without the risk of disease caused by random introduction of genetic material. The researchers used specially designed enzymes, called zinc finger nucleases and transcription activator-like effector nucleases, to create a double strand break in the DNA and bring about the repair of the gene.

Stem cells that had been modified in the lab were then transplanted into the testes of sterile mice. The transplanted cells grew or colonized within the mouse testes, indicating the stem cells were viable. However, attempts to breed the mice were not successful.

"Whether the failure to produce sperm was a result of abnormalities in the transplanted cells or the recipient testes was unclear," the researchers write.

Read more:
'Genome editing' could correct genetic mutations for future generations

December 15, 2014

Provided by Genome

Dr. Damon Little, Associate Curator of Bioinformatics in the Cullman Program for Molecular Systematics at The New York Botanical Garden, has just published a new study in the journal Genome investigating the use of DNA barcoding to test the authenticity of Ginkgo biloba (G. biloba), an herbal dietary supplement sold to consumers that is supposed to boost cognitive capacity. Unfortunately, herbal supplements on the market are subject to mislabeling, and therefore consumers may not be getting the products and benefits they believe they are getting.

Dr. Littles research is part of a larger effort to evaluate many of the popular herbal supplements on the retail market. He explains two potential dangers of mislabeled supplements: (1) some adulterants are toxic (alone or in combination with other supplements/drugs); and (2) consumers may not receive the health benefit they seek from mislabeled supplements, potentially worsening their health.

It seems herbal products can be mislabeled either because the supplier incorrectly identified the plant materials (some grow their own materials; some contract with growers; some buy raw materials in bulk; and some buy processed materials in bulk) or because another (usually less expensive) material was substituted.

Although it is difficult to determine how or why a supplement is mislabeled, the process developed with this new research can help to estimate the frequency of mislabeled supplements on the market. It also provides a validated method that can be used by supplement manufacturers for better quality control.

Dr. Little has designed a novel DNA mini-barcode assay that can validate authenticity of G. biloba in herbal dietary supplements.

I found that 83.8% of ginkgo supplements certainly contained ginkgo. In comparison, previous work has shown that 75% of black cohosh (Actaea racemosa) and 85% of saw palmetto (Serenoa repens) supplements contained the correct species, says Dr. Little. For the supplements in which I found no evidence of ginkgo, I cannot be sure if that is because the DNA was destroyed (for example by drying at very high temperatures) or if the samples simply do not contain any ginkgo.

In any case, it is hoped that this assay will be used by supplement manufacturers to ensure their supplements contain the expected ingredients.

Dr. Little intends to continue this line of research with a focus on other popular herbal supplements.

Continue reading here:
Is That Ginkgo Biloba Supplement Really What You Think It Is?

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Mass bird genome study reveals close links with dinosaurs
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Manuel Rivas - Python for Personal and Population Genome Interpretation
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Manuel Rivas - Python for Personal and Population Genome Interpretation - Video

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