[Federal Register: April 16, 2004 (Volume 69, Number 74)]
[Notices]
[Page 20605-20608]
From the Federal Register Online via GPO Access [wais.access.gpo.gov]
[DOCID:fr16ap04-49]
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DEPARTMENT OF ENERGY
Recommendations for Sequencing Targets in Support of the Science
Missions of the Office of Biological and Environmental Research (BER)
AGENCY: Office of Science; Office of Biological and Environmental
Research; U.S. Department of Energy (DOE).
ACTION: Notice of recommendations for sequencing targets.
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SUMMARY: This Federal Register notice seeks the input and nominations
of interested parties for candidate microbes, microbial consortia, and
250Mb-or-less-sized organisms for draft genomic sequencing in support
of Office of Biological and Environmental Research (BER) programs,
among them, the Climate Change Research Program, the Natural and
Accelerated Bioremediation Research (NABIR) Program, the Environmental
Management Science Program (EMSP), the Microbial Genome Program (MGP),
the Ocean Science Program, and the Genomics: GTL Program. Nominated
candidates should be relevant to DOE mission needs, e.g., organisms
involved
[[Page 20606]]
in environmental processes, including waste remediation, carbon
management, and energy production. This announcement is not an offer of
direct financial support for research on these organisms. Those
nominations selected will result in the DNA sequence of selected
organisms being determined at a draft level (6-8 X coverage) at the DOE
Production Genomics Facility (PGF) at the Joint Genome Institute (JGI),
(http://www.jgi.doe.gov). A subset of the selected organisms may be
identified for sequence finishing. This announcement is designed to
assist DOE in determining and prioritizing a list of microbes,
microbial consortia, or modest-genome sized (not more than 250Mb)
organisms (including eukaryotes) that address DOE mission needs.
Following merit review, and subject to the availability of funding and
programmatic relevance, draft sequencing will be carried out at the
PGF.
DATES: To assure consideration, nominations in response to this notice
should be received by 4:30 p.m. (e.d.t.), July 1, 2004, to be accepted
for merit review. It is anticipated that review will be completed early
in the fall of 2004 with draft sequencing at the DOE PGF to commence in
early 2005, conditional upon the provision of high quality DNA.
ADDRESSES: Nominations responding to this notice should be sent to Dr.
Daniel W. Drell, Office of Biological and Environmental Research, SC-
72, Office of Science, U.S. Department of Energy, 1000 Independence
Ave., SW., Washington, DC 20585-1290; e-mail is acceptable and
encouraged for submitting nominations using the following addresses:
kim.laing@science.doe.gov and daniel.drell@science.doe.gov.
FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-72, Office of
Biological and Environmental Research, Office of Science, U.S.
Department of Energy, 1000 Independence Ave., SW., Washington, DC
20585-1290, phone: (301) 903-4742, e-mail:
daniel.drell@science.doe.gov. The full text of this notice is available
via the Internet using the following Web site address: http://www.sc.doe.gov/ober/microbial.html
.
SUPPLEMENTARY INFORMATION: The DOE Office of Biological and
Environmental Research supports fundamental research in a variety of
missions (http://www.sc.doe.gov/ober/ober_top.html). Relevant BER
programs may include the Climate Change Research Program, the Natural
and Accelerated Bioremediation Research (NABIR) Program, the
Environmental Management Science Program (EMSP), the Microbial Genome
Program (MGP), the Ocean Science Program, and the Genomics:GTL Program.
The Climate Change Research Program supports investigations of
microbially-mediated fixation of atmospheric CO2. The NABIR
Program supports research on microbial biotransformations and/or
immobilization of metal and radionuclide wastes. The EMSP supports
research into microbially-mediated biotransformations of DOE-relevant
organic wastes such as chlorinated solvents. The MGP supports key DOE
missions by providing and analyzing microbial DNA sequence information
to further the understanding and application of microbiology relating
to energy production, chemical and materials production, environmental
carbon management, and environmental cleanup. The Ocean Science Program
supports research in two areas, (1) the role of oceans in sequestration
of atmospheric CO2, and (2) the use of biotechnological
tools to determine linkages between carbon and nitrogen cycling in
coastal environments. The Genomics:GTL Program builds on the successes
of the DOE Human Genome Program (HGP) by seeking to understand
biological function in DOE mission relevant microbes with emphases on
identifying the multi-component protein complexes in cells,
characterizing gene regulatory networks, probing the functional
capabilities of the environmental microbial repertoire of genes, and
beginning to model these processes computationally. Both terrestrial
and ocean environments in which microbial flora sequester carbon,
particularly carbon dioxide, are of interest. Within the ocean
environment, microbial flora that sequester or process carbon dioxide
in both the eutrophic and ``twilight'' zones are of interest.
Over the last ten years, sequencing of a range of microorganisms
that live in a wide diversity of environments has provided a
considerable information base for scientific research related not only
to DOE missions, but also to other federal agency missions and U.S.
industry. (http://www.tigr.org/tdb/mdb/mdbcomplete.html http://www.ornl.gov/ microbialgenomes/organisms.html and http://
http://www.jgi.doe.gov/JGI_microbial/html/). Nonetheless, most of our current
knowledge of microbiology still is derived from individual species that
either cause disease or grow easily and readily as monocultures under
laboratory conditions and are thus easy to study. The preponderance of
species in the environment remains largely unknown to science. Many are
thought to grow as part of interdependent consortia in which one
species supplies a nutrient necessary for the growth of another. Little
is known of the organization, membership, or functioning of these
consortia, especially those involved in environmental processes of DOE
interest. Fungi and small multicellular eukaryotes play important roles
in the environment as well.
Genomic analyses of sequenced microbes have suggested that
processes such as lateral gene transfers at various times in the
evolutionary history of some microbial lineages may have blurred the
understanding of their phylogenetic relationships. For this notice,
groups of microbes that may have exchanged (or may be exchanging)
genetic information via lateral gene exchange or plasmid mediated
exchanges can be proposed if the processes of genetic exchange result
in functions relevant to DOE missions noted above.
Genomic analyses are badly needed of microbial consortia and
species refractory to laboratory culture that play important roles in
environments challenged with metals, radionuclides, chlorinated
solvents, or are involved in carbon sequestration. The candidate(s)
being proposed must mediate or catalyze metabolic events of energy or
environmental importance. Priority will be given to studies on those
microbes or microbial consortia that can bioremediate metals and
radionuclides, degrade significant biopolymers such as celluloses and
lignins, produce potentially useful energy-related materials
(H2, CH4, ethanol, etc.), or fix or sequester
CO2.
For this notice, candidate organisms (either individual organisms,
consortia of organisms, or eukaryotes with small genomes) comprised of
archaea, bacteria, fungi, algae, and other eukaryotes with genome sizes
not greater than 250 Mbp can be proposed for draft sequencing. For a
current list of microbes that have been and are being sequenced see
http://www.ornl.gov/microbialgenomes/organisms.html and http://www
.ornl.gov/microbialgenomes/seq2003.html.
Aims: This request for nominations of candidate sequencing targets
has two broad foci:
(1) Single organisms. These may be bacteria, archaea, fungi,
microalgae or multicellular organisms with genomes not larger than
250Mb. The criteria that will be used to evaluate proposed candidates
for draft sequencing will include:
[[Page 20607]]
(a) The candidate has significant relevance to the DOE missions
noted above;
(b) To assess suitability for whole genome shotgun sequencing,
preliminary data on genome size, repeat content, genome structure, GC
content, polymorphism, and other characteristics are provided,
especially for larger genomes;
(c) The source of genomic DNA (i.e., strain or isolate, and
researcher) is identified, and a clonal sample (or samples with low and
characterized polymorphism) are available;
(d) A brief description of post sequencing follow-up work (e.g., a
data use plan and how will data be annotated to enable rapid and open
use) is included;
(e) The availability of a DNA/gene transfer system supporting
genetic analyses is known;
(f) Biological novelty or uniqueness (i.e., unusual genetically
determined characteristics pertinent to DOE missions) is described;
(g) Place in the currently understood, 16s RNA based, ``Tree of
Life'' is identified, e.g., is the proposed candidate in a sparsely
populated or more heavily populated section of the tree?
(h) A brief description of the user community is given;
(i) The potential impact on the scientific community is large;
(j) Explicit commitment to a data-release schedule, consistent with
the guidelines given below is provided.
(2) Currently unculturable or hard-to-culture organisms and
environmental consortia. The review criteria that will be used to
evaluate proposed candidates for draft sequencing will include most of
the criteria listed above for single organisms (with less emphasis on
genome size/structure, presence/absence of a genetic system, or
position in the ``Tree of Life'' since it is recognized that few data
on these attributes will be available), but in addition, the following
considerations will be included:
(a) Some measure of the ``complexity'' of the target consortium
being proposed, e.g., approximate number of species, size(s) of
genomes, and proportions of different members (it is understood that in
most cases, only estimates of these parameters may be available) is
discussed. When the environmental consortia are complex, approaches
should be described to normalize the DNA libraries in order to reduce
the amount of sequencing required and assure adequate sampling of the
complexity of the consortia. Additionally, the proposer(s) should be
prepared to work together with JGI scientists to optimize the yield
from the sequencing effort required;
(b) Past attempts to cultivate consortium members are described,
e.g., have any members of this consortium been successfully cultured;
(c) Some spatial/temporal/hydrochemical/geochemical or other
characterization of the environment is given, e.g., the physicochemical
parameters of the site from which the selected community is derived; a
description of the site contaminants; the accessibility of the site for
future sampling; the adequacy of site documentation;
(d) If proposed, technical approaches and technology development
specific for defining and isolating members of a given consortium are
described;
(e) Some indication of the biological function of the
relationships, within consortium members where available, along with a
discussion of the scientific and programmatic importance of
understanding these relationships is given;
(f) Information where available is given about the phylogenetic
position(s) of the members of the consortium and what is known about
closely related organisms.
(g) Available informatics tools and annotation plan (e.g., for
annotating genes from a consortium analysis or grouping identified
genes into a putative ``consortium phenotype'' within the chosen
environment) are described;
(h) Explicit commitment to a data-release schedule, consistent with
the guidelines given below is provided.
Scientific community standards regarding access to sequencing data
are evolving. BER conforms to the general guidance contained within the
Draft Rapid Data Release Policy (http://www.genome.gov/page.cfm?pageID=10506537
) for ``community resource projects.'' The
usual and customary practice for the JGI is to put all sequencing data
up on its Web site (http://www.jgi.doe.gov/) at frequent and periodic
intervals. However, for the purposes of this notice, BER does not
regard individual genome sequencing efforts involving less than 250Mb,
or microbial community sequencing efforts, as requested herein, as
``community resource projects'' within the definition of the Draft
Rapid Data Release policy. BER's position, which is provisional and
subject to evolution, is that no more than 6 months from the completion
of a ``first assembly'' of the sequence for a single-genome project,
the data will be released on the JGI web site or to a publicly
accessible database with no use restrictions. For microbial community
projects, the JGI will conduct normal QA/QC assessments on the sequence
output (at approximately 2 x coverage), then discuss with the
proposer(s) and with BER staff the extent to which sequencing will be
continued to achieve a satisfactory genomic ``view'' of the selected
microbial community. From the time of initiation of this discussion,
not more than 6 months will be permitted to elapse before unconditional
release of these data. Proposers should clearly understand that the
priority in the sequencing queue that a selected project is given may
be linked to the willingness of the proposer(s) to shorten this
``embargo'' period. BER is fully aware that some ambiguity remains in
the precise initiation of this embargo period but stresses its
intention and commitment to the rapid release, without any use
restrictions, of this data into publicly accessible databases.
Upon selection of a nominated microbial sequencing target, BER
expects that Principal Investigators will collaborate with the JGI by
providing high quality, high MW genomic DNA for library construction as
well as assisting in annotating the draft sequence data until a
sufficiently complete annotation is achieved, understanding that this
will be sensitive to hypothetical gene predictions and the usual
uncertainties of annotation. (A separate communication with the
detailed requirements for DNA will be sent to proposers whose
nominations are accepted for sequencing.) Following data acquisition
and annotation, DOE expects that those whose nominations have been
sequenced will make good faith efforts to publish in the open
scientific literature the results of their subsequent work, including
both the genome sequences of the organisms sequenced under this notice
as well as the annotation. (BER also expects the Principal Investigator
of a selected effort to either deposit a culture of the microbe or
consortium into a publicly accessible collection or repository, or make
it available directly so others can have access.) These parties are
encouraged to create process- and cost-effective partnerships that will
maximize data production and analysis, data dissemination, and progress
towards understanding basic biological mechanisms that can further the
aims of this effort. Additionally, it must be explicitly understood
that DOE will provide an assembled and computationally annotated draft
(roughly 6 x; carried out in a paired-end sequencing approach) sequence
of the microbe(s) selected, but that research
[[Page 20608]]
using that sequence data should be funded from separate sources and/or
separate solicitations. Finally, there is no commitment to finish a
given drafted sequence, although this option may be considered at a
later time for a selected subset of proposed candidates.
Submission Information: Interested parties should submit a brief
white paper to either of the foci given above, consisting of not more
than 5 pages of narrative exclusive of attachments (which should be
kept to a minimum) responding to each of the specific criteria set
forth. Electronic submission (to
kim.laing@science.doe.gov and Daniel.drell@science.doe.gov) is strongly encouraged. It is expected
that the Principal Investigator will serve as the main point of contact
for additional information on the nominated microbe. Nominations must
contain a very short abstract or project summary and a cover page with
the name of the applicant, mailing address, phone, fax, and e-mail. The
nomination should include 2-page curriculum vitae of the key
investigators; letters of intent (or e-mails) from collaborators
(suggesting the size of the interested community) are permitted.
Nominations will be reviewed relative to the scope and research
needs of the BER programs cited above. A brief response to each
nomination will be provided electronically following merit and
programmatic reviews.
Other useful Web sites include:
DOE JGI Microbial Sequencing Priorities for FY2004: http://www.ornl.gov/microbialgenomes/seq2003.html; http://www.jgi.doe.gov/
v/
Microbial Genome Program Home Page--http://www.sc.doe.gov/ober/
microbial.html;
DOE Joint Genome Institute Microbial Web Page--http://www.jgi.doe.gov/JGI_microbial/html/
;
GenBank Home Page--http://www.ncbi.nlm.nih.gov/; Human Genome Home Page--http://www.ornl.gov/hgmis;
DOE Genomes to Life--http://DOEGenomestoLife.org;
DOE Natural and Accelerated Bioremediation Research (NABIR)
Program--http://www.lbl.gov/nabir; Ocean Science Program-- http://www.sc.doe.gov /ober/CCRD/
oceans.html.
Issued in Washington, DC, April 12, 2004.
Marvin E. Frazier,
Director, Life Sciences Division.
[FR Doc. 04-8653 Filed 4-15-04; 8:45 am]
BILLING CODE 6450-01-P