Nucleic Acids Research 2005 33(Database issue):D25-D28;
doi:10.1093/nar/gki020
Nucleic Acids
Research, 2005, Vol. 33, Database issue D25-D28
© 2005, the authors
Nucleic
Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all
rights reserved
DDBJ in collaboration with mass-sequencing teams on annotation
Y. Tateno*, N.
Saitou1, K. Okubo, H. Sugawara and
T. Gojobori
Center for Information Biology and DNA Data Bank of Japan and 1
Laboratory of Evolutionary Genetics, National Institute of Genetics, Research
Organization of Information and Systems, Yata, Mishima, 411-8540, Japan
* To whom correspondence should be addressed. Tel:
+81 55 981 6857; Fax: +81 55 981 6858; Email: ytateno{at}genes.nig.ac.jp
Received September 15, 2004; Revised and Accepted September 17,
2004
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ABSTRACT |
In the
past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp/)
collected and released 1 066 084 entries or 718 072 425 bases
including the whole chromosome 22 of chimpanzee, the whole-genome
shotgun sequences of silkworm and various others. On the other
hand, we hosted workshops for human full-length cDNA annotation
and participated in jamborees of mouse full-length cDNA annotation.
The annotated data are made public at DDBJ. We are also in
collaboration with a RIKEN team to accept and release the CAGE (Cap
Analysis Gene Expression) data under a new category, MGA (Mass
Sequences for Genome Annotation). The data will be useful for
studying gene expression control in many aspects.
 |
INTRODUCTION |
As one of
the International Nucleotide Sequence Databases (INSD), DDBJ's
primary mission is undoubtedly to collect, annotate and release the
original and authentic DNA sequence data. In fact, the amount of data
collected and released by DDBJ has continued to grow. However,
annotation has not caught up with these activities. The reason for
that may be attributed to our limited labor power and knowledge that
cannot meet biological examination and verification of all submitted
data, though this may not be our task. At any rate, this problem will
unfortunately remain to be resolved.
Fortunately, however, there have been other approaches to conducting
annotation at DDBJ. One of them is to hold or participate in a
workshop at which a number of experts systematically annotate some
specified data. We actively participated in the annotation jamborees,
FANTOM I and II, to annotate and release mouse full-length cDNAs (1). We also hosted the
workshops, H-Invitational I and II, to annotate 21 037 human
full-length cDNAs (2).
The data annotated at the workshops have been made public on http://hinv.ddbj.nig.ac.jp/index.html
at DDBJ and on another site at the Japan Biological Information
Research Center (JBIRC). Accordingly, we have updated our home
page as shown in Figure 1. The numbers of
accesses to the H-Invitational data and our paper (2) indicate that both have
apparently made a great impact on research communities of biology,
medicine and others. A similar activity is in the process for rice
genome annotation. As another approach, we are in collaboration
with a research team of RIKEN to process and release their data
that will be useful for annotation of genome data from different
angles.
In
this paper, we report our primary activity of data collection and
release in the past year and our approach to the collaboration in
genome annotation.
|
RECENT
TRENDS IN DATA SUBMISSION |
In the
past year, we at DDBJ collected and released 1 066 084 entries or 718
072 425 bases. This includes the complete chromosome 22 sequence data
of chimpanzee, Pan troglodyte. The chimpanzee chromosome was
sequenced and submitted by two Japanese, three German, one Chinese,
one Korean and one Taiwanese groups (3). This is the
first case of data submission for the entire chromosome of non-human
primates. Contrary to our expectation for the genetic similarity
between man and chimpanzee (4), the new data
revealed that 83% of the coding sequences on the corresponding
chromosomes differed at the amino acid level between the two species.
This would make the relationship between the two species more
complicated and interesting than previously considered. Also included
is the whole-genome shotgun (WGS) data of silkworm, Bombyx
mori, submitted by the Silkworm Genome Research Program of the
National Institute of Agrobiological Sciences, Japan (5). It covers about
80% of the whole genome of the species.
In addition to the data collection and release, we edit all the
data made public by INSD (DDBJ/EMBL/GenBank) and publish as a DDBJ
release four times a year. The main reason for editing and publishing
the release is to regularly take statistics of the submitted data to
INSD in several aspects. For example, the most recent one published
as release 58 in June 2004 contains 34 917 581 entries or 39 812 635
108 bases. Release 58 also shows that the total number of bases
increased by 73 billion bases in the past year or 1.23 times as large
as the number of the last year.
To indicate the recent trends in data submissions, we extracted
and obtained the statistics focusing on the top nine species in
the past four years, from 2001 to 2004. The result is given in Figure 2. It is clear
from the figure that Homo sapiens have been ranked top in the
past 4 years. Human genes and genomic regions have been extensively
sequenced and submitted even after the completion of human genome
sequencing in 2001 (6).
The H-Invitational I and II workshops mentioned above apparently
contributed to maintaining the human data highest. With the
accumulation of chimpanzee genome data, human genes and genomic
regions will further be sequenced and studied to clarify what makes
man a man at the genome level.
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Figure 2. Recent trends in data
submission. Successions of data submissions in the past four years
are shown for the top nine species. H. s., Homo sapiens; M.
m., Mus musculus; R. n., Rattus norvegicus; D. r.,
Danio rerio; Z. m., Zea mays; D. m., Drosophila
melanogaster; O. s., Oryza sativa; G. g., Gallus
gallus; A. t., Arabidopsis thaliana.
| |
The
mouse, Mus musculus, and rat, Rattus norvegicus, data steeply
increased in the past years. The two rodent species have been
recognized and used as the model experimental animals closest
to man. This tendency has particularly been strengthened with
some recent genome-scale works for the species (7,8). Below the
three major species, several species are clustered in Figure 2.
Among them zebrafish, Danio rerio, is slightly ahead,
indicating that the fish has recently been recognized as the most
suitable model system for genetic study of vertebrate development (9). In the
cluster, there are three plant species in which maize, Zea
mays, has been more extensively sequenced than the other two
species, Oryza sativa and Arabidopsis thaliana.
The trends in the data submissions in Figure 2 clearly
demonstrate that as research for a particular species progresses,
sequence data of the species are produced and accumulate
accordingly, which further stimulates the research to advance, and so
forth. Data sharing certainly promotes the progress of research.
This should be truly understood by those who are not willing to
share their data with others.
|
COLLECTION OF DATA FOR GENOME ANNOTATION |
With the
accumulation of genome sequence data at INSD, genome research has
turned also on non-coding regions such as 5' UTRs and microRNA
regions. Those regions are known to be responsible for regulation of
gene expression. However, their roles have not exactly been
understood. For example, no one knows completely about how gene
expression is regulated at the promoter region. The regulation of
gene expression is unquestionably important for understanding many
aspects in biology, including development, metabolism, aging and
speciation for closely related species. With this in mind, a RIKEN
team sequenced a huge number of expressed sequences in 5' UTR, CAGE
(Cap Analysis Gene Expression) sequences, for mouse (10) and plans to submit
the data to DDBJ. A CAGE sequence more specifically is the initial 20
bases from a 5' end mRNA. CAGE is expected to produce 10 000 to 500
000 sequences in a tissue of a species, which makes it possible to
conduct high-throughput analysis of gene expression, profiling of
transcriptional start points and others.
At the collaborative meeting of INSD in 2004, we thus proposed a
new division to accept and release the CAGE data and those similar to
them, because we understood and expected that the data would be
crucially important for studying comprehensive aspects of promoter
usage. The new division was finally accepted and named MGA (Mass
sequences for Genome Annotation). The definition of MGA is the
sequences that are produced in large quantity in view of genome
annotation. MGA thus includes sets of short sequences that are
meaningful in the genome context, such as sequences from libraries of
CpG islands (11–12) and DNase
hypersensitive sites (13–14).
|
CONCLUDING REMARKS |
As gene
expression research rapidly advances, microarray data have
accumulated at many individual laboratories. Some of the data were
submitted to the public databases such as ArrayExpress, GEO and
CIBEX. The open letter (15) sent by the MGED
(Microarray Gene Expression Data) Society to the editors of relevant
journals will certainly accelerate data submission to the public
databases. Then the user of the public gene expression databases will
demand the link between the gene expression databases and INSD,
because they naturally need information not only on gene
expression but also on the relevant DNA sequences. Perhaps,
discussion about gene expression will not be settled until
information on the pertinent DNA sequences is provided. Currently,
the only vehicle connecting these two types of the databases is the
accession number issued by INSD.
|
Notes
|
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.
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