[Federal Register Volume 69, Number 74 (Friday, April 16, 2004)]
[Notices]
[Pages 20605-20608]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 04-8653]


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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

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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: 
[email protected] and [email protected].

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: 
[email protected]. 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://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:

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    (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

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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 [email protected] and 
[email protected]) 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/JGI_microbial/html/coming_soon.html;
    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