Calendar Name: seminars
Scheduled for: Thursday, March 25 2010, 10:00 - 12:00
Event text: Mini-Symposium on "BGI and Genomics in China - 'Life
Sciences for all' in the 21st Century"
Details: 10:00 - 10:40
"BGI and Genomics in China - Life Sciences in the 21st
Century"
Huanming Yang, Ph.D.
Professor & President
BGI (Beijing Genomics Institute)-Shenzhen, China
The recent progresses in biotechnology, such as iPS and
stem cell research, animal cloning and bio-plants,
synthetic biology and many others, have made it even
more obvious that life sciences would have significant
impact on every respect of our life and society in the
21st Century.
It is also widely accepted that reading and decoding
genome sequences of an organism is the basis and
beginning for any biological studies on it. Based on its
persistent belief that �life is of sequence� and �life
is digital�, BGI, a flagship in genomics in China for
the decade, has built its powerful capacity in
sequencing and bio-computing with its young and
innovative teams, and greatly contributed to the global
genomics and to the future development of biotechnology
as one of the biggest and most influential genomics
centers in the world.
As a later comer in the modern life sciences, the growth
of BGI is deeply rooted in the Chinese tradition and
Culture, for example:
1) Foresight: �Success could not be made without
foresight, failure from no prediction�.
2) Persistence: �Winners are only those with
persistence�.
3) Learning: �Among those three passing by, at
least one is qualified to be your teacher�.
4) Confidence: �The later comers always do a
better job because of the pioneers ahead�.
5) Collaboration: �Nobody could be a hero without
three partners�.
6) Appreciation: �When you drink sweet water, never
forget those helped dig the well�.
As an institute in the developing part of the world, BGI
has been raising the banner of both science and
humanity, and actively participating in the discussion
on HELSOC issues (Humanitarian, Ethical, Legal, SOcial,
and Cultural issues) that are essential to �life science
for all� in the 21st century.
10:40 - 11:20
"Harvest the fruits of genomics - to upgrade agriculture
with new breeding tools"
Sanwen Huang, Ph.D.
Key Laboratory of Genomics, Ministry of Agriculture
Chinese Academy of Agricultural Sciences (CAAS)
and Beijing Genomics Institute (BGI)
The global food security is in menace because of the
rapidly growing human population, the depletion of
agricultural resources as arable land, water, and
petroleum-based pesticide and fertilizer, and the
climatic changes. The genetic improvement of crops is
the most viable approach by which food production can
try to keep pace with the anticipated growth of the
human population. The efficiency of crop breeding relies
on our knowledge on the biology of the ~60 species that
uses about 95% of the arable land and a dozen of
livestocks. The most fundamental biological knowledge of
a crop is stored in its genome.
Next generation sequencing (NGS) technologies, such as
Illumina GA, SOLiD, and 454, made it feasible and
economical acceptable to sequence genomes of all crops.
However, as NGS often produces millions of shorter reads
in a single run, it also meet computational and
algorithmic challenges. BGI constructed a powerful
platform mainly based on sequencing-by-synthesis
technology, including >30 Illumina GA II, a 10,000-CPU
cluster, and a software package, Short Oligonucleotide
Analysis Program (SOAP). The genomes of cucumber (350
Mb), Brassica rapa (500Mb), potato (830Mb), duck (2 Gb),
and even giant panda (2.3 Gb)have been assembled and
analyzed, giving the first set of examples that NGS can
be used in de novo sequencing of large plant and animal
genomes. Large scale germplasm resequencing was
conducted on rice, silkworm, and cucumber, which
produced millions of SNPs and structural variations and
identified hundreds of genes that likely underwent
selection during domestications and breeding.
With the newly established Key Laboratory of Genomics
(MOA), BGI, CAAS, and other agricultural research
institutions will sequence 100 crops, 100 species of
livestocks and insects, core collection of every
important species, and also perform genome-scan of over
400,000 accessions of various crops are stored in the
National Seed Bank. Combined with genetic analysis and
robust phenotyping, this huge resource will lead to
high-throughput isolation of trait genes. The knowledge
of trait genes will give rise to new breeding tools that
can be used to deliberately design crops and animals
that suit to various environment, agricultural
practices, and applications.
11:20 - 12:00
"More than just sequencing - Bioinformatics tools
developed at BGI"
Ruibang LUO, B.S.
Bioinformatics project manager
BGI (Beijing Genomics Institute)-Shenzhen, China
�The day is not far off when more biology will be done
at the computer than at the bench!� Roos et al. said in
2002.
Nowadays, with the rapid development of information
technology, not only the computational resources but
also talents of this field could be acquired much more
easily. It has also demonstrated its powerful ability in
assistance of solving complex biological, especially
genomic problems. BGI, a flagship in genomics in China
for the decade, has created our own series of tools and
pipelines for the analysis including the genome, SNP,
structural variation, methylation, RNA, assembly and
etc.
Next-generation massively parallel DNA sequencing
technologies provide ultra-high throughput at a
substantially lower unit data cost; however, the data is
very short read length sequences, making de novo
assembly extremely challenging. We�ve just described a
novel method for de novo assembly of large genomes from
short-read sequences. We successfully assembled both the
Asian and African human genome sequences, achieving an
N50 contig size of 7.4 and 5.9 Kb and scaffold of 446.3
and 61.9 Kb, respectively. Comparison of these
assemblies to the NCBI reference genome demonstrated the
capability of accurate identification of structural
variations, especially small deletions and insertions
that are difficult to identify using a resequencing
method. The development of this de novo short-read
assembly method creates new opportunities for building
reference sequences and carrying out accurate analyses
of unexplored genomes in a cost effective way.
