JiaYan Wu

JingFa Xiao

Jun Yu

Science China Life Sciences

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Latest notable achievements in genomics

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SCIENCE CHINA 
Life Sciences 
© The Author(s) 2012. This article is published with open access at Springerlink.com life.scichina.com   www.springer.com/scp 
                  
†Contributed equally to this work 
*Corresponding author (email: junyu@big.ac.cn) 
• INSIGHT • July 2012  Vol.55  No.7: 645–648 
 doi: 10.1007/s11427-012-4331-x 
Latest notable achievements in genomics 
WU JiaYan†, XIAO JingFa† & YU Jun* 
Key Laboratory of Genomics Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China 
Received May 9, 2012; accepted May 22, 2012 
 
Citation:  Wu J Y, Xiao J F, Yu J. Latest notable achievements in genomics. Sci China Life Sci, 2012, 55: 645–648, doi: 10.1007/s11427-012-4331-x 
 
 
 
 
Within the past 10 years, the progress of genomics 
development in China exhibited a frogleap in terms of scale, 
quality, organization, and international collaboration. Human 
genome study has entered a new phase of interdisciplinarity in 
the history of life science in China. The rise of genomics 
relied on the development of technology and its integration 
with other academic disciplines, particularly in the 
following three areas. First, DNA sequencing technology 
has been improving its productivity and efficiency at an 
exponential growth rate. Second, bioinformatics supports 
the system of data collection, administration, annotation, 
distribution, and analysis for genome researchers. Third, the 
integration with the genomics data and other “omics” data 
provides hypotheses and building models for systems 
biology research. In 2009 and 2010, Science China Life 
Sciences published over 20 research papers and review 
articles about genomics. Authors of those publications are 
all leading life scientists, shared their understanding on 
different hot questions or focused on a single question of 
common interest from different views arisen from their 
respective expertise.  
Technological advancement in DNA sequencing has 
transformed the study of fundamental elements of life–– 
from individual, localized or clustered genes to the whole 
genomes, which in turn demands more competent and 
effecient sequencing technology. Zhou XiaoGuang et al. 
summarized all major emerging sequencing platforms [1–3] 
and provided a review of sequencing technology evolution, 
generational advancements with their merits and drawbacks, 
and prediction of possible direction of the field [4]. With the 
second generation platforms in hands and the third or single 
molecule platforms in the horizon, the goal of reaching “one 
thousand dollar per genome” will soon become tangible. 
Aside from sequencing technology, other important tools 
for large-scale and high-throughput genome research, such 
as various DNA microarrays and genotyping tools, are also 
brought out for revealing both structural and functional 
characteristics of genomes and transcriptomes [5]. We ex-
pect that Chinese scientists not only are among the best to 
utilize the emerging new technologies for genomics re-
search but also join the effort in developing alternatives to 
create friendly competitions that will ensure rapid and less 
expensive readout of sequence information providing ample 
possibilities in comparative genomics, disease diagnosis, 
and ultimately personalized (or individualized) medicine.  
In China, the incidence of common diseases has been 
increasing, such as cancer and cardivascular diseases. 
Newly emerging infectious agents are also a major threat 
to human health. In addition, there is a persistently high 
rate of hepatitis B virus (HBC) infection resulting in a 
large number of chronic hepatitis patients and some of 
them have a strong tendency to develop liver cirrhosis and 
eventually liver cancer. Collaborative research activities in this 
front have been quite fruitful [6]. Excellent investigations 
have been performed in etiology-associated genomic and 
genetic researches [7,8] as well as genomic instability and 
646 Wu J Y, et al.   Sci China Life Sci   July (2012) Vol.55 No.7 
expression pattern analysis of liver cancers [9–11]. Huang 
Jian has reviewed some recent epigenetics research progress 
referring to heritable changes for hepatocarcinomagenesis, 
including DNA methylation, genome imprinting, chromotin 
remodeling, histone modification, and microRNA regu-     
lations [12]. As to the research area of pathogenic bacteria, 
rapid accumulation of bacterial genomic data offered 
unprecedented opportunities to understand bacterial biology 
from a holistic point of view [13]. Recent progress in 
pathogenic bacterial genomics in China encompasses 
genomic diversity, molecular epidemiology, microbial 
forensics [14–16], diagnostics [17], vaccine design [18–20], 
novel antibacterial agent development [21], and meta- 
genomics for comprehensive understanding of human  
health [22]. 
Chinese genomicists have been working in the frontier of 
plant and animal genomics, such as rice [23] and giant 
panda [24]. The former not only produces the first plant 
genome sequence using the whole-genome shotgun strategy, 
but also is still generating large amounts of sequence 
information in genetics and gene expression. Li LiHua    
et al. [25] investigated the gene expression profile in rice 
roots at 6, 24 and 72 h under low phosphorus (P) stress and 
compared it with a control (normal P) profile, providing 
useful information in the molecular process associated with 
Pi deficiency and facilitating research on improving Pi uti-
lization in crop species. Kou YanJun et al. [26] analyzed the 
colocalization of a set of characterized rice defense-respon-     
sive genes and resistance QTLs against different pathogens 
and the expression patterns of these genes, which suggests 
that defense-responsive genes are important resources of 
resistance QTLs in rice. As to the giant panda (Ailuropoda 
melanoleuca), one of the most endangered species in the 
world known as the “Chinese treasure”, complete Sanger 
sequencing, assembly, annotation and comparative analysis 
were carried out on the selected BACs of a joined length of 
878 kb, which provided detailed sequence and structure 
information for new genes and repeats of the giant panda for 
further studies [27]. 
At the mean time, investigations on genomics of 
indigenous species and important genes are still hotspots in 
China. The study on Tibetan chicken’s embryonic adapta-
bility to chronic hypoxia showed that Tibetan chickens have 
much higher hatch-ability than low-land chicken breeds in 
high-altitude areas of Tibet [28]. Most Sox genes directly 
affect cell fate determination and differentiation. Lin 
YuShuang et al. [29] isolated two Sox genes from the closet 
living invertebrate relative of the vertebrates, Branchiosto-
ma belcheri, and aligned their protein sequences, discover-
ing that vertebrate homologs might arise from gene duplica-
tions during evolution. Miao YongWang et al. [30] figured 
out the allele EBR or the allele carrying the amino acid 
p104S in melanocortin-1 receptor (MC1R) is associated 
with the black coat color in buffalo, based on their genotype 
and phenotype analysis of the hybrid offspring of black river 
buffalo and gray swamp buffalo. Revealed by the full-      
length B′ cDNA and its encoding protein, Fu Hu et al. [31] 
suggested that B′ appears to play a very important role dur-
ing gold fish (Carassius auratus) development and also in 
adult tissue homeostasis. B′ protein is strongly expressed at 
the stage of two-cell, multiple-cell, blastula, gastrula, neu-
rula, and optic vesicle, and then decreased at the stages of 
brain differentiation and eye pigmentation. He Jing et al. 
[32] observed episodic evolution in the pre hormone gene 
sequences of the two members of a structure-function-       
related hormone family, Motilin and ghrelin, during primi-
tive placental mammal evolution, and predict that some of 
the lineage-specific physiological adaptations are due to 
episodic evolution of these two genes.  
The giant leap in sequencing technologies have sent the 
cost of sequencing tumbling, and the daily output of se-
quence has soared just in the past few years [33]. Although 
computational biology cannot handle all demands created 
by the exponentially increasing amounts of sequence data, 
bioinformatics and biostatistics have been recognized seri-
ously by increasingly more experimental life scientists. 
Chinese bioinformatic researchers have done great jobs in 
understanding structural dynamics of genomes. Transcrip-
tional regulation is one of the most critical pipelines in bio-
logical process, in which cis-elements work as gene expres-
sion regulators. By means of analyzing activities or behav-
iors of the shared cis-elements, Hao Pei et al. [34] discov-
ered those elements participating in controlling the expres-
sion pattern of “head-to-head” gene pairs and the whole 
transcription regulation system. Zheng LingLing and Qu 
LiangHu reviewed the main issues in “Computational 
RNAomics” of data storage and management, ncRNA gene 
identification and characterization, ncRNA target identifica-
tion and functional prediction, and summarized the main 
methods [35]. Explaining the “Tragedy of the Commons” of 
the evolution of cooperation remains one of the greatest 
problems for both biology and social science. Wang RuiWu 
and Shi Lei built a model and carried out simulations to 
show that the local but not the global stability of a coopera-
tive interaction can be maintained if the utilization of com-
mon resource remains unsaturated, achieved by density-     
dependent restraint or competition among the cooperative 
actors [36]. 
Human genetic variation study was ranked as one of 
the top ten breakthroughs in 2007 by Science [37]. For 
better understanding of human genetic diseases, better 
genotyping technology is of essence. Shi JinXiu et al. [38] 
reviewed the development and application of genotyping 
technologies, including a great number of accurate, rapid, 
and cost-effective technologies for SNP analysis, which 
promote the research of not only simple Medialian diseases 
 Wu J Y, et al.   Sci China Life Sci   July (2012) Vol.55 No.7 647 
but also complex genetic disorders. Another review 
summarized the commonly used technologies to discover 
both genomic structural variants and their potential impacts, 
highlighting array-based, PCR-based, and sequencing-based 
assays, as well as discussed limitations/challenges and gave 
advices on how to design more reliable genomics variation 
studies [39]. A specific case was investigated by Tan LiJun 
et al. [40]. They performed a genome-wide association 
study (GWAS) of wrist bone mineral density (BMD), 
combined with the functional relevance of SOX6 in cartilage 
formation, which all support that SOX6 gene works as a key 
gene for BMD variation. 
In the past two years, Chinese scientists working in 
domestic institutes have been very fruitful in genomics 
studies, coincident with the fast economic development in 
China and the public funding for sciences in general. As 
long as more young talents in life sciences, domestically 
educated or returning from abroad, are joining newly 
emerging research laboratories, scientific productivity will 
be boosted in China for the years to come. 
 
 
 
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