Category Archives: Transhuman News

DNASTAR - Illumina Reference Guided Genome Assembly
See how to align Illumina data for a bacterial genome against a reference sequence using Lasergene Genomics Suite

By: DNASTARInc

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DNASTAR - Illumina Reference Guided Genome Assembly - Video

When the workday ends at BGIs factory in Shenzhen, the headquarters of the largest genome mapping company in the world, its like a bell has gone off at math camp. The companys scientists and technicians spill out of the doorways of the building, baby-faced and wearing jeans and sneakers. Some still have braces. Several young women link arms and skip toward a bus line. Others head next door to the dorm or over to the canteen where young couples are holding hands across plastic trays. This work we do is tiring and requires focus, says Liu Xin, a 26-year-old team leader in the bioinformatics division, as he sinks into a couch in one of BGIs conference rooms. So its good that they allow us to date.

Liu is one of a small army of recent college graduates at BGIs largest facility, a former shoe factory. Two gray buildings, the factory and the dorm, are wedged between one of Shenzhens industrial zonesa grid of high-rises, apartment buildings, and several hospitals and medical equipment companiesand a lush, jungly hill thats in the process of being bulldozed. Liu is stocky and serious, glad that he already has a steady girlfriend so he can focus on his career. He arrived at BGI three years ago, a biology major from Peking University with little experience in the study of the genome, the term for the entirety of an organisms genetic information. Now hes one of the senior people in his department. He works 12-hour days and oversees the sequencing of multiple genomes at a time. He specializes in plantshis team is currently sequencing a species of orchid. The bioinformatics teams around him are picking through the genomes of animals, microbial organisms, humans, and anything else that comes with a genetic code. Everyone is just out of college, he says. I am now more sophisticated than most of the newcomers.

Ten years after the mapping of the human genome, BGI has established itself as the worlds largest commercial genetic sequencer. The ranks of Chinas college graduates are expanding faster than the country can employ them, and BGI is leveraging this cheap, educated labor pool. At the factory in Shenzhen, more than 3,000 employees (average age, 26) spend their days preparing DNA samples, monitoring sequencing machines, and piecing together endless strings of As, Cs, Ts, and Gs, the building blocks of genetic material.

This is big data analysis, says Wang Jun, BGIs 36-year-old executive director. Wang, who regularly wears tennis shoes and untucked polo shirts, has published more than 35 articles in Science and Nature magazines and also teaches at the University of Copenhagen. Genomics, he says, is a new field and experts are being created from scratch. We dont need Ph.D.s to do this work, Wang says. Instead, he believes genomics is best learned the old-fashioned way. You just throw them in, he says of BGIs technicians. The best way is hands-on experience. When the first draft of the human genome was released in 2000 as part of the international Human Genome Project, it seemed inevitable that scientists would soon crack the codes of disease, health, and human development. But the genome has proved more complicated. What scientists produced in 2000 was a long list of nucleotides, the combinations of markers in DNA that specify the makeup of an organism. It was just a list, and only a fraction of it is understood. Scientists were quick to identify fragments of the genome that translate into proteins, which control things like eye color, but these make up only 1.5percent of the entire thing. As geneticists like to put it, they produced a map without a legend. This is where BGI comes in.

Photograph by Luke Casey for Bloomberg BusinessweekExecutive director Wang Jun (left)

The company was founded in 1999 with state funding to lead Chinas participation in the Human Genome Project. We didnt think about any business model; we basically didnt plan further than the human genome, says Wang, who was brought on in the early days of BGI to provide expertise in computers. China, he points out, was the only developing country working on the international project, and although the BGI team contributed only 1percent of the finished project, it did it quickly and with little previous experience. Even Bill Clinton thanked us for our participation, he says. Wang joined the project when he was just 22 and worked under BGIs two founders, the scientists Wang Jian, then 45, and Yang Huanming, then 47.

For its next challenge, BGI decided to tackle rice, whose genome is significantly shorter than that of humans but still large enough to impress. We recruited a bunch of undergraduates, and lots of them had no working experience on any project, Wang Jun says. The schedule was tight; Wang and his team barely slept. We can do these kind of crazy things in BGI, he says. We can get 100 people together, very fresh, no experience at all, and get it done.

In 2002, BGI published a paper on the rice project in Science and again attracted attention and money from the Chinese government, though its a private company. The company was rewarded with entry into the state-run Chinese Academy of Sciences, a distinction that secured additional funding. As part of CAS, however, BGI was limited to only 90 scientists. Its leaders had their eyes on expansion. Our boss wanted to buy more sequencing machines, says Deng Wenxi, a 24-year-old communications officer at the BGI factory. But the Beijing government would not support us. In 2007 the company found a solution by way of Shenzhens city government, which offered the factory 10million yuan (about $1.6 million in todays exchange rates) to cover startup fees and 20million yuan in annual grants. The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory. Beijing is more strict, says Deng. Shenzhen wanted to welcome us. The factory, she says, actually belongs to the Shenzhen government. When asked about the move, Wang Jun answers the question a little more vaguely, Well, he says, the weather is definitely nicer here.

Today, BGI organizes its operations into three categorieshealth care, agriculture, and the environment. When scientists look at the genome, theyre looking for variations from one individual to another, from species to species, or population to population. Theyre looking to understand which variations link to specific traits or diseases.

As Wang Jun says, decoding any genome is a big data endeavor, and theres no other research institution or for-profit sequencing company in the world that has the capacity of BGI. In health care, it offers straightforward sequencing services for universities and corporations globally, which ask BGI to sequence a genome and send it back for analysis. More often than not, BGI works in partnerships to map, analyze, and publish the findings.

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BGI's Young Chinese Scientists Will Map Any Genome

Public release date: 5-Feb-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

February 5, 2013, Shenzhen and Kunming, China - In a collaborative study published online today in Nature Communications, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, and BGI have completed the genome sequencing of Chinese tree shrew, a small animal widely distributed in South Asia, Southeast Asia, and South and Southwest China. This work provides new insights for researchers to use tree shrew as a model in studying hepatitis C virus (HCV) and hepatitis B virus (HBV) infections, myopia, as well as social stress and depression.

Tree shrews are similar to squirrels in their external appearance and habits. They have a higher brain to body mass ratio than any other mammals, and even than humans. Currently, tree shrews have been considered as a useful experimental model for researchers to design and develop new animal models for human diseases. However, the lack of a high-quality genome has greatly hampered the deeper understanding of this animal's biological features, evolutionary mechanisms, among others.

In this study, researchers conducted whole genome sequencing on a male Chinese tree shrew from Yunnan Province of China, and yielded a high-quality reference genome about 2.86Gb. Compared to the previous version reportedly in 2007, a significantly improved annotation was also generated, which contains 22,063 genes that is similar with the number of human genes. To identify the phylogenetic position of tree shrew in Euarchontoglires, they compared the tree shrew genome with other genomes, including human's, and revealed a closer relationship between tree shrew and primates.

When identifying the genetic features shared between tree shrew and primates, researchers found 28 genes previously considered as primate specific genes also present in tree shrew genome such as psoriasin protein and NKG2D ligands, indicating the tree shrew's immune system may employ the same indicators as in humans to eliminate infected and damaged cells. They also found some unique genetic features of tree shrew, such as immunoglobulin lambda variable gene family strikingly expanded to 67 copies in tree shrews but only 36 copies in the human genome.

Tree shrew has a well-developed brain structure that is similar with primate's. Researchers in this study detected 23 known neurotransmitter transporters in the tree shrew genome that are associated with the corresponding features of depression. These transporters are highly conserved in amino acid sequence with the human counterparts. All the findings provide a genetic basis for researchers making tree shrews an attractive model for experimental studies of psychosocial stress and evaluation of pharmacological effect of antidepressant drugs.

To understand the genetic basis underlying the visual system of tree shrew, researchers investigated the relevant genes involved in visual system, and found the tree shrew genome encompassed the orthologues of almost all the 209 known vision-related human genes. However, the lack of two cone photoreceptors, the middle wave-length sensitive proteins, may lead to the trichromacy in higher primates. The absence of these proteins is consistent with the fact that tree shrew is short of green pigment and possess dichromats, which is similar to some lower primates. Due to tree shrew's adaptation to the diurnal life, researchers found a looser evolutionary constraint of dim-light vision. Rod photoreceptor rhodopsin had a faster evolutionary rate in the tree shrew lineage, which is responsible for the night vision. A variant p.F45C that causes incurable night blindness disease in humans was detected in tree shrew species, suggesting a potentially functional degeneration of this gene in tree shrews.

The previous reports showed human HBV and HCV could infect tree shrew. Through investigating tree shrew immune genes associated with viral hepatitis, researchers found most of the genes respond in HBV and HCV infection showed a relatively high sequence identity between tree shrew and human genomes. They found the tree shrew lost DDX58, a key gene to produce interferon to against virus, and TRIM5 has achieved five Trim5 copies. One of TRIM5 copy has a CypA retrotranposition that present in only several primate species, implying the potential importance of this fused transcript.

Professor Yong-Gang Yao from Kunming Institute of Zoology, the leading author of this paper, said, "Since 1970s, researchers of our institute carried out many studies on the biology of Chinese tree shrews, and we published the first monograph of tree shrew in 1991. Currently, we are focused on establishing animal models of human diseases using this animal. The available genome data will greatly facilitate our efforts and speed up the process to design and develop new tree shrew models for human diseases, drug screening and safety testing"

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The genome of Chinese tree shrew provides new insights into facilitating biomedical researches