Nucleic Acids Research 2006 34(Database Issue):D390-D393; doi:10.1093/nar/gkj070
Nucleic Acids Research, 2006, Vol. 34, Database issue D390-D393
© The Author 2006. Published by Oxford University Press. All rights reserved
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Megx.net—database resources for marine ecological genomics
Thierry Lombardot1,
Renzo Kottmann1,
Hauke Pfeffer1,
Michael Richter1,
Hanno Teeling1,
Christian Quast1 and
Frank Oliver Glöckner1,2,*
1Microbial Genomics Group, Max Planck Institute for Marine Microbiology D-28359 Bremen, Germany
2International University Bremen D-28759 Bremen, Germany
*To whom correspondence should be addressed. Tel: +49 0421 2028938; Fax: +49 0421 2028580; Email: fog{at}mpi-bremen.de
Received August 8, 2005. Revised October 8, 2005. Accepted October 8, 2005.
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ABSTRACT
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Marine microbial genomics and metagenomics is an emerging field
in environmental research. Since the completion of the first
marine bacterial genome in 2003, the number of fully sequenced
marine bacteria has grown rapidly. Concurrently, marine metagenomics
studies are performed on a regular basis, and the resulting
number of sequences is growing exponentially. To address environmentally
relevant questions like organismal adaptations to oceanic provinces
and regional differences in the microbial cycling of nutrients,
it is necessary to couple sequence data with geographical information
and supplement them with contextual information like physical,
chemical and biological data. Therefore, new specialized databases
are needed to organize and standardize data storage as well
as centralize data access and interpretation. We introduce Megx.net,
a set of databases and tools that handle genomic and metagenomic
sequences in their environmental contexts. Megx.net includes
(i) a geographic information system to systematically store
and analyse marine genomic and metagenomic data in conjunction
with contextual information; (ii) an environmental genome browser
with fast search functionalities; (iii) a database with precomputed
analyses for selected complete genomes; and (iv) a database
and tool to classify metagenomic fragments based on oligonucleotide
signatures. These integrative databases and webserver will help
researchers to generate a better understanding of the functioning
of marine ecosystems. All resources are freely accessible at
http://www.megx.net.
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INTRODUCTION
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Over the last decade microbiology has undergone several changes.
Robert Koch's invention of pure culture techniques at the end
of the 19th century focussed microbiology on the isolation of
bacteria for laboratory studies. In 1987 Carl Woese introduced
the ribosomal RNA as a stable molecular marker for the classification
and identification of microorganisms (
1). The ‘winds of
change’ blew in the field of microbiology (
2) when the
first cultivation-independent investigations reported an immense
array of completely unexpected microbial diversity in the environment
(
3). The landmark publication of the first complete genome sequence
of
Haemophilus influenzae in 1995 (
4) has transformed biology
into a massively parallel and high throughput endeavour. This
‘genomic revolution’ finally reached the field of
marine ecological genomics in the year 2000, defined as: ‘The
application of genomic sciences to understanding the structure
and function of marine ecosystems’ (
5). Since 1995, >260
microbial genomes have been fully sequenced, and 600 more are
well on their way (
5). While most projects focus on microorganisms
of medical or biotechnological interest, 22 complete marine
genomes of environmental organisms are already available, and
130 marine isolates are currently sequenced (Moore foundation
http://www.moore.org). Recently, this cultivation-based approach
has been complemented by a number of groundbreaking cultivation-independent—metagenomic—studies,
the most prominent being the Venter Sargasso Sea expedition
in 2004 (
6), delivering >1.2 million new genes. This wealth
of information caused a quantum leap in marine sciences and
demands for different kinds of databases to transfer information
into knowledge (
7). The sequences, genomes, genes and predicted
metabolic functions can not longer be regarded in an organism
centric view but have to be handled in the context of the environment
surrounding them. Therefore, it is necessary to link any environmental
sequence information with its geographical location. This allows
to correlate the genomic features found at a distinct sampling
site with physical, chemical and biotic information to identify
organism-specific adaptations and their role and impact on the
environment. This new kind of integrative data resource opens
the path to address questions like: Are there differences in
the genetic repertoire when travelling from coastal marine sites
to the open ocean? or Do habitat specific gene patterns with
yet unknown functions exist? If the latter is true the correlation
with site specific environmental parameters might allow predicting
a potential function for them. Can these genetic properties
in turn explain the distribution of the organisms?
Megx.net is designed to tackle these tasks linking marine genome and metagenome sequences not only with geography but providing additional information about annotation highlights, presence of environmentally relevant protein families and group-specific genes as well as a Geographic-BLAST server to trace genes across the marine environment.
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SOURCES OF GENOMIC AND METAGENOMIC DATA
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The genome sequences of all currently available marine microorganisms
have been retrieved from the EMBL and GenBank databases (
8,
9).
Twenty-two bacteria and archaea originating from the water column
of the ocean and from marine sediments have been completely
sequenced (October 2005). The sequences and associated gene
annotation have been imported into a local relational database
allowing fast data retrieval. The corresponding annotations
originate from independent submissions to the EMBL or the GenBank
databases, and are of variable quality owing to the following
reasons: (i) the original annotations were performed at different
times; (ii) no controlled vocabulary is used for gene product
names; and (iii) the effort expended in assigning functions
to genes is variable between genome projects. Ecologically relevant
annotation highlights were selected from original genome publications
for each organism.
Metagenomic fragments originating from marine systems have been selected according to semi-automatic literature screening. Seventy-eight original publications were found to deal with metagenomic fragment sequencing, corresponding to a total of 21 distinct marine geographic sampling sites (August 2005). The sequences and associated gene annotation were imported into a newly designed geographic database. New genomes or metagenomes will be integrated in the database and mapserver as soon as they become available. Precomputed searches will be updated every 2 months.
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GENOME BROWSING
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The genome browser allows easy and fast access to the sequences,
their geographical location and the annotation highlights of
each marine microorganism in the database. For example, the
unexpected archaea-like C1 metabolism genes found in the genome
of
Rhodopirellula baltica can be accessed in their genomic context
by a simple mouse click (
Figure 1). Fast text search in the
original annotations and BLAST searches are also available.
View larger version (42K):
[in this window]
[in a new window]
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Figure 1 Fast access to the annotation highlights of marine microorganisms. Here, the archaea-like C1 metabolism key gene is R.baltica.
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PRECOMPUTED INFORMATION
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Environmentally relevant protein families
Some gene families are of particular interest for ecological
genomics, as they play key roles in the environment or give
insights into the adaptation of microorganisms to their respective
niche. Glycosylhydrolases, sulphatases, peptidases and transcriptional
regulators are some examples of gene groups that have been automatically
extracted based on selected profile hidden Markov models originating
from the Pfam database (
10). The results can be browsed graphically
on our web page. This search strategy allows consistent quantitative
comparisons, as the publicly available original annotation can
not easily be compared. For example, the outstanding number
of genes encoding sulphatases in the genome of
R.baltica (
11)
or the reduced dataset of transcriptional regulators in
Prochlorococcus marinus strains (
12,
13) can be compared with the corresponding
gene content of other marine microorganisms.
Group-specific genes
Group-specific genes are defined as those found exclusively in a defined subset of genomes. The definition of groups is variable and can be based on a phylogenetic affiliation, a common metabolism or related habitats. An example for group specific genes for phylogenetically closely related organisms are the three available P.marinus strains. The results show that some light-inducible proteins are exclusively found in those organisms (13). Moreover, we present a set of proteins of yet unknown function which are P.marinus specific. The corresponding genes represent interesting targets for functional genomics and further wet-lab experiments.
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TETRA SERVER
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TETRA is a software tool for genomic and metagenomic analysis.
It can assess the relatedness of genomic fragments by computing
correlations between their tetranucleotide usage patterns (i.e.
statistical over- and under-representation of tetranucleotides)
(
14,
15). The new version includes chaos game plot representations
for DNA sequences, which can be used to get additional information
on the relatedness of genomic fragments. Moreover, TETRA can
plot fluctuations of tetranucleotide usage patterns within DNA
sequences. This is particularly useful to identify irregular
regions in entire genomes or larger genomic fragments like laterally
transferred genes or transposase and phage insertions.
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GENOMES MAPSERVER
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Geographic information systems (GIS) are commonly used in the
field of geology for data integration. A GIS is a combination
of elements designed to store, retrieve, analyse and display
geographic data. We introduce here the Genomes Mapserver, a
GIS that allows access to genomic and metagenomic sequence data
in their geographic and ecological contexts. The sampling sites
of marine (meta)-genomic studies are displayed within a browsable
world map (
Figure 2). Each sampling site can be selected to
display the corresponding sequences and additional contextual
information. The underlying database is designed to enable future
data mining tasks to reveal possible gene patterns associated
with a particular environmental context. For targeted searches,
a geographic-BLAST tool has been developed, allowing to perform
‘spatial’ queries for sequences based on the popular
BLAST algorithm (
16). The Geographic-BLAST/Genomes Mapserver
combination allows to systematically study the biogeography
of particular genes in the environment (
Figure 2).
View larger version (71K):
[in this window]
[in a new window]
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Figure 2 The Genomes Mapserver. (A) Marine genomes and metagenomic fragments can be browsed and searched on a world map on our web-based system. (B) An example showing a Geographic-BLAST search for genes encoding proteorhodopsins in the currently available dataset.
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ADDITIONAL FEATURES
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A software tool for microarray data evaluation and a database
of aligned ribosomal proteins for phylogenetic analysis (Ribalign)
will soon be available on the webpage.
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DATABASES ACCESS
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The precomputed genome searches and group-specific genes, the
TETRA server and the Metagenomes Mapserver are freely available
through
http://www.megx.net.
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ACKNOWLEDGEMENTS
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We thank the Max Planck Society for initial funding and the
EU Sixth Framework Programme (FP6-NEST) for providing financial
support for further development of the Genomes Mapserver (contract
no. 511784). Funding to pay the Open Access publication charges
for this article was provided by the Max Planck Society.
Conflict of interest statement. None declared.
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