First goat genome sets a good example for facilitating de novo assembly of large genomes

Dec. 23, 2012 ? In a collaborative study published online today in Nature Biotechnology, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, BGI, and other institutes, have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and whole-genome mapping (WGM) technologies. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future.

Goats are recognized as an important member of the world livestock industry, and with many unique biological features. They are an important economic resource in many developing countries around the world, especially in China and India. However, despite their agricultural and biological importance, breeding and genetic studies of goats have been hampered by the lack of a high quality reference genome sequence. The goat genome sequence will be useful for facilitating the identification of SNP markers for marker-assisted breeding, and improving the utility of the goat as a biomedical model and bioreactor.

With the availability of next-generation sequencing (NGS), draft assemblies are easy to generate nowadays. However, to finish a sequence to the chromosome level remains a hard nut to crack. In this study, the results show that a single NGS platform, when combined with whole-genome mapping technology, could produce a finished assembly much faster and with high quality than other currently available mapping strategies such as BACs or FISH. Through this integrated approach, researchers obtained the ~2.66 Gb goat reference genome from a female Yunnan black goat.

Transposable elements (TEs) are major components of mammalian genomes and contribute to gene and/or genome evolution. The TEs in goat genome are similar to those of cattle, and contain large numbers of ruminant-specific repeats, such as SINE-tRNA and SINE-BovA. It is reported that SINE-BovA repeat expanded primarily in the cattle genome. However, in this study, researchers found the SINE-tRNA repeat expanded specifically in the goat genome.

Through constructing a phylogenetic tree among goats, cattle, horses, dogs, opossums and humans, researchers found the goat shared a common ancestor with cattle about 23 million years ago. Further comparison analysis revealed 44 rapidly evolving genes under positive selection, seven of which are immune-related genes and three are pituitary hormone or related genes. The immune-related genes identified also exist in cattle. The findings suggest that the rapid evolution of pituitary hormones may be related to the different features between goat and cattle in milk production, development rates of the fetus and/or hair variation.

The major histocompatibility complex (MHC) plays an important role in the immune system. In this study, the goat MHC was found to be located on chromosome 23 and contains two regions with length of 2.25 Mb and 360 kb, respectively. With the high quality genome assembly, further understanding of the goat MHC will be useful for immunological studies and vaccine development.

One of the distinguishing characteristics of mammals is the protective growth known as hair. It is produced by hair follicles within the skin, which could provide either protection (guard hairs) or insulation (underfur). The two major hair follicles include the primary hair follicle that produces only coat hair in all mammals, and the secondary hair follicle that can produce the cashmere or "fine hair" in certain mammals, including goats and antelopes. Despite a 2,500-year history and the extent of raw cashmere production, people are lack of understanding of the molecular mechanisms of cashmere formation and development.

Researchers conducted transcriptomic analysis on the primary and secondary follicles of a cashmere goat, revealing 51 genes that are differentially expressed between the two types of hair follicles. Keratin and keratin-associated proteins are the main structural proteins of hair fibers, determining the quality of fiber together. In the study, 29 keratin genes and 30 keratin-associated protein genes were detected in both types of follicles. Interestingly, they found two keratin genes and ten keratin-associated protein genes were consistently differentially expressed between primary and secondary hair follicles, suggesting that the keratin-associated protein genes may be more important in determining the structure of cashmere fibers. In addition to the keratin genes and keratin-associated protein genes, researchers also found several enzymes of amino acid biosynthesis, with implications in regulating primary hair growth and hair cycle.

Xun Xu, Deputy Director of BGI, said, "The goat reference genome is an important stepping stone in the molecular breeding of cashmere goats, and will help to advance the comparative studies on ruminants. The transcriptomic analysis on the primary and secondary follicles will open a new way for better improving the quality cashmere wool."

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The above story is reprinted from materials provided by BGI Shenzhen, via EurekAlert!, a service of AAAS.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Journal Reference:

1. Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Bertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao, Jun Wang, Wen Wang. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 2012; DOI: 10.1038/nbt.2478

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Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/~3/CNn97tXK9DU/121223152629.htm

Felix Baumgartner Little Nemo

Exploding star missing from formation of solar system

Dec. 16, 2012 ? A new study published by University of Chicago researchers challenges the notion that the force of an exploding star forced the formation of the solar system.

In this study, published online last month in Earth and Planetary Science Letters, authors Haolan Tang and Nicolas Dauphas found the radioactive isotope iron 60 -- the telltale sign of an exploding star -- low in abundance and well mixed in solar system material. As cosmochemists, they look for remnants of stellar explosions in meteorites to help determine the conditions under which the solar system formed.

Some remnants are radioactive isotopes: unstable, energetic atoms that decay over time. Scientists in the past decade have found high amounts of the radioactive isotope iron 60 in early solar system materials. "If you have iron 60 in high abundance in the solar system, that's a 'smoking gun' -- evidence for the presence of a supernova," said Dauphas, professor in geophysical sciences.

Iron 60 can only originate from a supernova, so scientists have tried to explain this apparent abundance by suggesting that a supernova occurred nearby, spreading the isotope through the explosion.

But Tang and Dauphas' results were different from previous work: They discovered that levels of iron 60 were uniform and low in early solar system material. They arrived at these conclusions by testing meteorite samples. To measure iron 60's abundance, they looked at the same materials that previous researchers had worked on, but used a different, more precise approach that yielded evidence of very low iron 60.

Previous methods kept the meteorite samples intact and did not remove impurities completely, which may have led to greater errors in measurement. Tang and Dauphas' approach, however, required that they "digest" their meteorite samples into solution before measurement, which allowed them to thoroughly remove the impurities.

This process ultimately produced results with much smaller errors. "Haolan has dedicated five years of very hard work to reach these conclusions, so we did not make those claims lightly. We've been extremely careful to reach a point where we're ready to go public on those measurements," Dauphas said.

To address whether iron 60 was widely distributed, Tang and Dauphas looked at another isotope of iron, iron 58. Supernovae produce both isotopes by the same processes, so they were able to trace the distribution of iron 60 by measuring the distribution of iron 58.

"The two isotopes act like inseparable twins: Once we knew where iron 58 was, we knew iron 60 couldn't be very far away," Dauphas explained.

They found little variation of iron 58 in their measurements of various meteorite samples, which confirmed their conclusion that iron 60 was uniformly distributed. To account for their unprecedented findings, Tang and Dauphas suggest that the low levels of iron 60 probably came from the long-term accumulation of iron 60 in the interstellar medium from the ashes of countless stars past, instead of a nearby cataclysmic event like a supernova.

If this is true, Dauphas said, there is then "no need to invoke any nearby star to make iron 60." However, it is more difficult to account for the high abundance of aluminum 26, which implies the presence of a nearby star.

Instead of explaining this abundance by supernova, Tang and Dauphas propose that a massive star (perhaps more than 20 times the mass of the sun) sheds its gaseous outer layers through winds, spreading aluminum 26 and contaminating the material that would eventually form the solar system, while iron 60 remained locked inside the massive star's interior. If the solar system formed from this material, this alternate scenario would account for the abundances of both isotopes.

"In the future, this study must be considered when people build their story about solar system origin and formation," Tang said.

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The above story is reprinted from materials provided by University of Chicago. The original article was written by Chelsea Leu.

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Journal Reference:

1. Haolan Tang, Nicolas Dauphas. Abundance, distribution, and origin of ⁶⁰Fe in the solar protoplanetary disk. Earth and Planetary Science Letters, 2012; 359-360: 248 DOI: 10.1016/j.epsl.2012.10.011

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Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/top_science/~3/plRwYZjQr60/121217091017.htm

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