A skull recovered from a cemetery in London provided DNA of the bacterium responsible for the Black Death. Credit: Museum of London

For the first time, scientists have reconstructed the genome of an ancient pathogen: the bacterium that caused the Black Death, or bubonic plague. This plague killed approximately 50 million people between 1347 and 1351, about half the European population. Similar strains still circulate today, but with much less devastation, killing about 2,000 people per year.

Researchers pulled DNA fragments of the Yersinia pestis bacterium, which causes the plague, from remains buried in the East Smithfield "plague pits" in London. They had previously developed a way to distinguish ancient DNA from modern DNA; one of the challenges in analyzing ancient DNA is getting rid of contamination from modern organisms. They then sequenced that DNA, reading about 99 percent of the genome, and compared it to modern strains.

Surprisingly, "we do not see single position in this ancient genome that cannot be found in modern strains," said Johannes Krause, a researcher at the University of Tübingen, Germany, in a press conference.

Researchers say it's not yet clear why this ancient version was so deadly or why the modern versions, which are genetically highly similar, are less virulent. "There is no particular smoking gun," said Hendrik Poinar, a geneticist at McMaster University, at the press conference. The research was published online today in the journal Nature.

The devastation of the Black Death may have been due to the climate at the time—a rapid onset of cold, wet weather—and the onset of a new bacterium in an immune-challenged population. Scientists are also exploring the possibility that the original plague put evolutionary pressure on humans, leaving behind those with better innate immunity.

But it may be that the particular combination of genetic factors in the ancient strain was more deadly. While each individual genetic change can be found in modern strains, the specific constellation of genetic factors in the genetic strain has not.

Researchers have developed the most sophisticated map yet of the human genome, highlighting the regions where maternal and paternal chromosomes recombine, or swap parts. Recombination is one of the driving forces of genetic variability, which underlies evolution.

The genetic "hotspots" where recombination is most likely to take place are also linked to inherited diseases, since these regions are vulnerable to errors in the genetic code. "When recombination goes wrong, it can lead to mutations causing congenital diseases, for example diseases like Charcot-Marie-Tooth disease, or certain anemias," said Simon Myers, a lecturer in the Department of Statistics at the University of Oxford who led the research, in a release from Harvard Medical School.

"Charting recombination hotspots can thus identify places in the genome that have an especially high chance of causing disease," said David Reich, professor of genetics at Harvard Medical School, who co-led the study, in a release from Stanford.

The map is the first constructed from recombination data collected from African Americans. Previous maps have used genome information primarily from people of European decent. Researchers found that African Americans and Europeans have different recombination sites.

According to the release;

These findings are expected to help researchers understand the roots of congenital conditions that occur more often in African Americans (due to mutations at hotspots that are more common in African Americans), and also to help discover new disease genes in all populations, because of the ability to map these genes more precisely.

The new map is so accurate because African American individuals often have a mixture of African and European ancestry from over the last two hundred years. David Reich and Simon Myers are experts in analyzing genetic data to reconstruct the mosaic of regions of African and European genetic ancestry in DNA of African Americans. By applying a computer program they previously wrote, Anjali Hinch identified the places in the genomes where the African and European ancestry switches in almost 30,000 people, detecting about 70 switches per person. These areas corresponded to recombination events in the last few hundred years. Thus, the researchers identified more than two million recombination events that they used to build the map.

It's been ten years since Science and Nature, the two most prestigious science journals in the world, published the first detailed look at the sequence of the human genome. Both journals are commemorating the event with special sections looking back at the progress the field has made over the last decade and the hurdles that still remain.(Check out our January issue for TR's take on the genome ten years later, our understanding of inheritance, and the implications for cancer .)

A series of short essays in Science, authored by Francis Collins, who oversaw the Human Genome Project and now runs the National Institutes of Health, Desmond Tutu, archbishop emeritus of South Africa, and many others, explore the facets of the genome.

Collins describes one of the field's successes: the case of a 6-year-old Wisconsin boy who had suffered for years with a severe form of inflammatory bowel disease.

Despite numerous tests and more than 100 surgeries, doctors remained at loss for a diagnosis and the little boy grew sicker. Then, researchers at the Medical College of Wisconsin carried out whole-exome sequencing, examining the protein-coding regions of every gene in Nic's genome. They identified a mutation in his XIAP gene. XIAP mutations were not previously associated with bowel symptoms, but had been linked to a severe blood disorder that is curable through bone marrow transplantation. The medical team raised the possibility of a transplant, which would not have been considered without a firm diagnosis. It was performed in July 2010, using stem cells from the cord blood of a matched, healthy donor. Seven months later, Nic appears to be on the road to recovery. While he is still on immunosuppressants, doctors report the new stem cells are stably engrafted, blood counts are good, and there's been no return of bowel disease (http://journals.lww.com/geneticsinmedicine/Documents/GIM200819_Revised.pdf). More important to Nic, he can finally eat solid foods!

Craig Venter, a genomics pioneer who ran the private arm of the genome race, outlines a major missing chunk of information that is necessary to interpret the meaning of the genome.

Among the many improvements that are needed in human genome research, the most important is the collection of human phenotypes (according to agreed-upon parameters and standards), in conjunction with tens of thousands of accurate human genome sequences. Such data sets will be the foundation for accurately predicting clinical outcomes from DNA sequence information. This is true not only for diagnosis but also in foreseeing and avoiding drug side effects, as well as monitoring stem cell genome mutations and/or variations before cell therapies.

Desmond Tutu, who had his genome sequenced as part of a study of human genetic diversity, writes about how important it is to understand the genomes of all the world's peoples.

As a nation, however, we need to continue to fight against racial inequalities and socioeconomic disparities on a daily basis. My participation in the Southern African Genome Project was a step in this direction, generating the first Southern African Genome to be sequenced—exactly 9 years after the publication of the human genomes.

My reasoning was simple. Southern Africans are victims of many devastating diseases whose eradication requires immediate attention and international resources. My hope is that my genetic code may provide a voice for the region and serve as the starting point for a map of DNA variation significant for Southern African peoples, to be used for medical research efforts and effective design of medicines. I implore the scientific community to continue what I hope was just a first step to further medical research within the region.

Kari Stefansson, chief executive officer of DeCode Genetics, a leader in the study of genomics and disease, points out that what we call a complete genome is not truly complete.

However, still today, we do not have "the complete sequence" of the reference human genome as parts (such as the centromeres or regions of copy number variation) are still incomplete. The suboptimal quality of the reference sequence is one of the limiting factors in the work of those who are using whole-genome sequencing to understand human biology. Hence, this is an anniversary of a moment in the history of our quest for an instrument (the reference sequence) to use in better understanding ourselves.

Eric Schadt, chief scientific officer of Pacific Biosciences of California, one of several companies racing to develop cheaper and faster sequencing technology, describes how complex the genome has revealed itself to be.

We have learned that the human genome is much more dynamic than previously thought. Elucidating its complexity will require a more systems-level approach, including comprehensive integration with other data dimensions, such as RNA, metabolite, protein, and clinical data. For me, although this past decade has exposed many amazing aspects of the genome, it has revealed the existence of a world about which we know very little. We will have to become masters of information if we ever hope to go from the big data sets coming to dominate biology to knowledge and to understanding.

On Thursday, Nature will feature a piece by Eric Green, current director of the National Human Genome Research Institute, outlining the institute's vision for the next ten to 20 years. Check back Thursday for a Q&A with Green.