The Tibetan antelope (Pantholops hodgsonii) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. Interestingly, it is the only member of the genus Pantholops. Tibetan antelope is a medium sized antelope with the unique adaptations to against the harsh high-altitude climate. For non-native mammals such as humans, they may experience life-threatening acute mountain sickness when visiting high-altitude regions.

In this study, researchers suggest that Tibetan antelopes must have evolved exceptional mechanisms to adapt to this extremely inhospitable habitat. Using next-gen sequencing technology, they have decoded the genome of Tibetan antelope and studied the underlying genetic mechanism of high-altitude adaptations. 

Through the comparison between Tibetan antelope and other plain-dwelling mammals, researchers found the Tibetan antelope had the signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission, indicating that gene categories involved in energy metabolism appear to have an important role for Tibetan antelope via efficiently providing energy in conditions of low partial pressure of oxygen (PO₂).

Further research revealed that both the Tibetan antelope and the highland American pika have signals of positive selection for genes involved in DNA repair and the production of ATPase. Considering the exposure to high levels of ultraviolet radiation, positive selective genes related to DNA repair may be vital to protect the Tibetan antelope from it.    

Qingle Cai, Project manager from BGI, said, “The completed genome sequence of the Tibetan antelope provides a more complete blueprint for researchers to study the genetic mechanisms of highland adaptation. This work may also open a new way to understand the adaptation of the low partial pressure of oxygen in human activities.”

About BGI

BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications. BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for the 1,000 genomes project. For more information about BGI please visit www.genomics.cn and www.bgiamericas.com.

Media Contacts:

Bicheng Yang, Ph.D.
Public Communication Officer
BGI
+86-755-82639701
yangbicheng@genomics.cn
www.genomics.cn

Joyce Peng, Ph.D.
Marketing Director
BGI Americas
(626) 222-5584
joyce.peng@bgiamericas.com
www.bgiamericas.com

Shenzhen, China – The Joint International Turtle Genomes Consortium, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, has completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas). These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan. The findings were published online in Nature Genetics.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years. As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes has been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle. They found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses. The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles. This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes may be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

To clarify the morphological specifications of turtle embryogenesis in late development, especially the formation of the carapacial ridge (CR), researchers investigated into CR-specific miRNA expression, found existence of tissue-specific miRNAs and involvement of Wnt signaling. Also they revealed the Wnt expression involved in the carapacial ridge (CR) formation of the turtle shell, researchers annotated all the Wnt genes in the two turtle genomes, identifying a total of 20 Wnt genes. Intriguingly, they discovered Wnt5a is the only Wnt gene expressed in the turtle CR region, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty.

Zhuo Wang, Project Manager from BGI, said, “The genome-wide phylogenetic analysis of two turtles in our project, along with two crocodile genomic data additionally, makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles. The genomic analyses and embryonic gene expression profiles have been combined to reveal the fundamental evo-devo questions on turtle evolution and development. These works have been highly appreciated by the editor and reviewers. Besides the interesting story, the genomic data we released here will provide a platform for more scientists to initialize their genome-wide studies on turtles. ”

Dr. Hongyan Zhang, Regional Director of BGI Tech Solutions Co., Ltd. for Japan, said, “The completed genome sequencing of soft-shell turtle and green sea turtle give an important hint to uncover the development and evolution mechanism of turtles. This scientific achievement is a joint effort supported by BGI’s advanced sequencing technologies and excellent bioinformatics capabilities, the profound basis research background of developmental biology from RIKEN, and other partners’ great contributions. We are looking forward to having more collaboration with other scientists for better exploring the secret of life together in the near future.”

About BGI

BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications. BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for the 1,000 genomes project.

For more information, please visit www.genomics.cn and www.bgiamericas.com.

Media Contacts:

Bicheng Yang, Ph.D.
Public Communication Officer
+86-755-82639701
yangbicheng@genomics.cn
www.genomics.cn

Joyce Peng, Ph.D.
Marketing Director
BGI Americas
(626) 222-5584
joyce.peng@bgiamericas.com
www.bgiamericas.com

Hong Kong – A partnership between the University of Birmingham, BGI and its open-access journal, GigaScience, has received funding from the UK’s Natural Environment Research Council (NERC) to develop a software platform for the analysis of large-scale environmental metabolomics data.

Metabolomics involves the detection and quantification of small molecules (metabolites) in living organisms and can provide an indication of their cellular condition and health. The toxicological responses of organisms to pollutants can be studied using environmental metabolomics, enabling researchers to discover diagnostic markers for monitoring and risk assessment of our environment. Research at Birmingham focuses extensively on the metabolic responses of the freshwater model organism, Daphnia, to both pollutants and engineered nanomaterials.                                                                                         

Sophisticated computational analyses must be performed on metabolomics data in order to measure the abundances of the metabolites. However, this typically requires expert knowledge in computer programming and biostatistics, restricting the usefulness of metabolomics to specialised laboratories. This project will develop a new software platform to make it much easier for non-specialist scientists to analyse their metabolomics datasets.

As the first metabolomics project in the recently announced Joint BGI-University of Birmingham Environment & Health Centre, the funding will enable a developer from the University’s School of Biosciences, to travel to Hong Kong and work with GigaScience in developing the popular Galaxy workflow system for use in metabolomics data analyses.

Dr. Peter Li, Data Organization Manager at GigaScience, commented, “This funding from NERC will enable a synergistic exchange of skills in the curation and automated analysis of large-scale data that we have in GigaScience with the University of Birmingham’s expertise in metabolomics”. He continued “This is an area of the life sciences that is of great interest to BGI as they move and broaden their expertise from being a major genomics organization into more integrative research in the life sciences”.

Professor Mark Viant from the University of Birmingham added, “This collaboration with BGI aligns perfectly with one of our major goals at Birmingham, to develop tools and resources to facilitate the wider use of metabolomics by environmental scientists, and subsequently to provide training in these tools”.

The project is funded by the UK NERC under the Mathematics & Informatics for Environmental Omic Data Synthesis programme.

About BGI

BGI was founded in Beijing, China, in 1999 with the mission to become a premier scientific partner for the global research community. The goal of BGI is to make leading-edge genomic science highly accessible, which it achieves through its investment in infrastructure, leveraging the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research: research that has generated over 200 publications in top-tier journals such as Nature and Science. BGI’s many accomplishments include: sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and the 2011 German deadly E. coli outbreak, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, more recently, the human Gut Metagenome, as well as a significant proportion of the genomes for the1000 Genomes Project.

For more information, please visit www.genomics.cn and www.bgiamericas.com.

Contact Information

Catherine Byerley
International Media Relations Manager
University of Birmingham
Tel: +44 (0)121 414 8254
Email: c.j.byerley@bham.ac.uk

Bicheng Yang
Public Communications Officer
BGI
Tel: +86-755-82639701
Email: yangbicheng@genomics.cn

NERC Press Office
Natural Environment Research Council
Polaris House, North Star Avenue
Swindon, SN2 1EU
Tel: 01793 411727 or 411561
Email pressoffice@nerc.ac.uk

The two-day program will present the latest developments in human, animal, plant and microbial genome sciences, comprising sessions on disease research, clinical diagnostics, microbes and evolution diversity, drug discovery and development, agricultural breeding, advanced bioinformatics technologies, etc.

Included among the featured speakers will be nobel laureates, famous scientists and university leaders, company directors, senior executives and CEOs from organizations such as National Academy of Sciences, University of California, Davis, University of Pennsylvania, Oregon State University, University of Copenhagen & UC Berkeley, AstraZeneca, Bill & Melinda Gates Foundation, New England Biolabs, Sanofi Oncology, United Nations Global Compact, Roche, H3 Biomedicine, Amgen, Inc., Bayer Crop Science, and many more.

Additional highlights of ICG Americas 2013 are pre-conference training programs from the UC Davis Genome Center and pre-conference microbial genomics meeting hosted by the FDA. In addition, a full-service dinner that brings Napa Valley to Sacramento with wine tasting, demonstration and live entertainment will be exclusively offered for conference speakers, luminaries and other conference attendees. Moreover, the conference venue offers close proximity to multiple international life sciences companies in the Bay Area and within great access to multiple national historical sites and museums in Sacramento and to world-class outdoor recreation in Lake Tahoe.

“The past ICG Americas has achieved great success. This year we are excited to present the 2nd ICG Americas in Sacramento”, said Professor Huanming Yang, Chairman of BGI, “I believe it will provide an excellent opportunity for researchers, academia and industries to exchange information, generate new ideas and accelerate applications of genomic data and to forge partnerships in Genomics and related fields.”

The list of speakers and program details are available at www.icg-americas.org

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