Short genome report

Criteria

 Beginning on August 1, 2016 Short genome reports will be available only to authors describing taxonomic type strains, reference strains or other organisms that are available in viable form from one or more public repositories. Authors must include the appropriate accession numbers in the Short genome report at the time of submission.

Genome reports of wild-type isolates must be submitted in the Extended genome report format and authors must provide descriptions of the organism, the methods used to establish its identity and a comparison of its genome to that of its closest neighbors for which genomes are available at the time of writing.

  • Manuscripts must be submitted in doc, doc(x), rtf, or the OpenOffice equivalent using the Short genome report template. Any manuscript not using the template will be returned to authors.
  • Manuscripts that are missing key figures, tables and references (as per the guidelines below), or that include mandatory tables that deviate from the accepted layout will not be accepted for peer review and will be returned to authors for correction.
  • Please use the Genome Report Checklist before submitting your manuscript.

The rationale of the content model is to provide information that is consistently and uniformly presented for rapid and easy consumption by both human and machine readers. First-time authors are advised to familiarize themselves with the appropriate article type(s) and to carefully follow the SIGS style sheet to ensure an expedited review.

 A reduced rate of £890 applies to Short genome reports. Authors submitting such reports should enter the discount code SGREP on the payment page during the article submission process. The reduction, which applies to Short genome reports only, can only be granted through use of the code and cannot be granted retrospectively.

Preparing your manuscript

Authors

Authors should include each person who contributed to the generation, analysis and interpretation of the data that is being reported. Full author names should be as: (surname(s), middle initial(s), family name), using proper capitalization. For an example of properly formatted author and institutional information see http://standardsingenomics.biomedcentral.com/articles/10.1186/1944-3277-9-2

Institutional Affiliation

The institutional affiliation(s) of each author should be identified with a superscripted number in the order of first appearance in the author list. Author affiliations should be numbered, using Vancouver style.

Corresponding author

The author responsible for the submission and coordination of communication with the editorial office during peer review and with readers post publication should be identified along with their institutional email address. The editorial office will deal with only one corresponding author on a given manuscript.

Abstract (Heading 1)

Authors should provide a concise, non-redundant and meaningful abstract that describes the nature of the article. It should summarize the rationale, the objectives and the findings of the report and provide key details (e.g., relevant INSDC identifiers, culture collection identifiers, other project metadata that is accessible in standardized form).

Key words (Heading 1)

Authors should include five to seven descriptive keywords. These may include the name(s) of the organism(s) sequenced, the name of the next higher taxonomic rank, the sampling site and other significant details about the nature of the study.

Abbreviations (Heading 1)

Authors should include any non-standard abbreviations that are used throughout the article. Do not include well-known abbreviations (e.g., NCBI, EMBL, DNA, RNA) and do not use non-standard abbreviations for organism names. Species and subspecies names must be fully spelled out on first use as binomials (genus name and species epithet) or trinomials (genus name, species epithet subsp. subspecies epithet). Following first usage, the genus name may be abbreviated by using the first letter of the genus name, followed by a period and the epithets.

Introduction (Heading 1)

Authors are expected to provide readers with brief, high-level description of the source organism and the rationale for its selection for sequencing. It should be written in such a manner as to capture a reader’s attention. It should also indicate whether or not the organism is part of a larger genomic survey project.

Organism information (Heading 1)

Classification and features (Heading 2)

This should include succinct but detailed description of major phenotypic features (macro- and micromorphology, physiological characteristics), natural habitat, distribution, current classification and phylogenetic placement of the strain/specimen selected for sequencing. Authors should provide readers with additional background as to how the organism was isolated from nature (if a microbe), its association with other community members, any special properties that are noteworthy (e.g., pathogenic, symbiotic, industrial use, taxonomic type strain, model organism, etc.). In a separate subsection, of this section, authors should provide chemotaxonomic information (e.g. whole cell fatty acid composition, respiratory quinones, cell-wall composition, other unique or diagnostic cellular components).

This section should also include two figures: a phylogenetic tree indicating current placement and a photomicrograph or electron photomicrograph of the source organism. This section must also include a reference to Table 1, which provides a standardized summary of key features of the source organism. The layout of Table 1 is fixed and authors must not vary the appearance of information in the table. Rather, they must supply this information so that readers may view the descriptive information in a consistent fashion.

Chemotaxonomic data (optional, Heading 3)

See the above description (under Classification and features).

Symbiotaxonomy (optional, Heading 3)

See the above description (under Classification and features).

Genome sequencing information (Heading 1)

Genome project history (Heading 2)

This section of the manuscript should provide a detailed summary of the sequencing, assembly and annotation methodology. The section should include an introductory paragraph that provides the readers with specific information about the sequencing project, when the project began and was completed, whether the sequence is complete or remains as a draft genome, and the quality of the draft, which public databases contain the project data and other relevant information. These data should be summarized in Table 2.

Growth conditions and genomic DNA preparation (Heading 2)

In the case of cultivated organisms, please provide the source of the organism (e.g., culture collection and accession number) and the conditions that were used to grow the strains(s) for DNA extraction (media, temperature, aeration, volume of culture, length of incubation). Also provide the method used to harvest and lyse the cells, and to extract and purify the DNA and to assess its purity.

Genome sequencing and assembly (Heading 2)

Provide a succinct and detailed description of the methods used to sequence and assemble the genome(s). Identify the sequencing center where the work was performed, the sequencing technology(ies) used, library construction, number of reads and read length. Cite any relevant references regarding methods used. Also, provide a succinct and detailed description of the assembly, including the software used for preliminary assembly, finishing and error checking and correction of mis-assemblies. Provide a brief description of the size of the final assembly, the number of contigs, and coverage.

Genome annotation (Heading 2)

Provide a brief and succinct description of the methods used to identify and annotate genes, and any software used in the annotation pipeline.

Genome Properties (Heading 1)

Provide a summary description of the size of the genome(s) (in base pairs), the number of chromosomes and plasmids. Include the number of predicted genes (RNA genes, protein coding genes, pseudogenes) by number and percent of total. This section should be linked to a chromosome map, map(s) of any plasmids and two or three tables providing a more detailed summary of the genome properties.

Insights from the genome sequence (optional, Heading 1)

In many cases, authors may wish to provide a brief, yet more detailed description of major findings arising from the genome sequence. This can be a comparison of major differences found between the genome sequence that is the subject of the study and others (e.g., major differences is specific metabolic pathways, significant differences in gene content, etc.). This section is intended to permit the authors to make preliminary observations rather than to serve as detailed comparative study. In a short genome report, this section should be limited to two to three paragraphs. Authors wanting to provide greater detail and to incorporate additional genomes into their study, or to incorporate additional tables and figures are invited to submit their articles as extended genome reports.

Extended insights (optional, Heading 2)

Authors are encouraged to provide more detailed descriptions about insights gained from the genome sequence. This may include comparisons of the genome to that of closely relate species, detailed discussions about specific metabolic pathways that are noteworthy or unique, or other features that may be of interest to the readers. Authors may include additional tables and figures in this section (see below).

Conclusions (Heading 1)

Provide a brief summary of the findings arising from the genome sequence. This should place the current genome into context with genomes of closely or more distantly related.

Taxonomic and nomenclatural proposals (optional, Heading 1)

Authors are free to make taxonomic proposals and revisions of existing taxa, providing that the proposals are made in accordance with the rules of the relevant code of nomenclature. Taxonomic proposals must include the following sections appearing after the Conclusions section: A formal description for each taxon - Each taxonomic proposal must have its own subsection heading, and must appear in the proper order. Proposals for new genera must precede proposals for new species or subspecies. New species must precede new subspecies. A proposed name and etymology – For each new taxon proposed authors must propose a new name, in accordance to the appropriate rules of nomenclature. The proposed name should be followed by the etymology of the name, in grammatically correct Latin. Authors are responsible for ensuring that proposed names meet these requirements.

A protologue – for each new taxon and name that is proposed, authors must provide a description (also referred to as a diagnosis in botany) that provides readers with a summarized statement of differential features that can be used to distinguish the proposed taxon from other, closely related taxa. The protologue should include information about the morphology, physiology, habitat and genetics, along with any marker genes or features that can be used for identification purposes. The protologue must conclude with a statement that positively establishes the type strain (prokaryotes) or specimen (botany and zoology). If a new species or subspecies of bacteria or archaea is proposed, authors must provide the accession numbers from at least two internationally recognized culture collections (in different countries) from which viable samples of the type strain are available without restriction. Proposals that fail to provide this information cannot be considered for valid publication. If one or more new genera are proposed, the genus name(s) and description(s) must precede those of newly proposed member species. Genus descriptions must indicate the type species of the genus and differential/diagnostic features. In many cases, these may be the same as that for member species. Proposals for novel higher taxa (family and above) should appear after the species or subspecies proposals. Emendations of existing taxa should be made in separate sections, indicating the changes in membership and phenotypic and genotypic characteristics on which the taxa were originally formed. Assertions of synonymy should be presented in a separate section, with a full description of which taxa are being combined and an assertion of which name has priority. Taxonomic proposals of eukaryotic and virus taxa will follow the same general outline described above, but the identification and deposition of type material differs.

Competing interests (Heading 1)

All financial and non-financial competing interests must be declared in this section. See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.

Funding (Heading 1)

All sources of funding for the research reported should be declared. The role of the funding body in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript should be declared.

Authors' contributions (Heading 1)

The individual contributions of authors to the manuscript should be specified in this section. Guidance and criteria for authorship can be found in our editorial policies.

Acknowledgements (optional, Heading 1)

Please acknowledge anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.

See our editorial policies for a full explanation of acknowledgements and authorship criteria.

Group authorship: if you would like the names of the individual members of a collaboration group to be searchable through their individual PubMed records, please ensure that the title of the collaboration group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “Acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.

Please note that individual names may not be present in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.

Authors' information (optional, Heading 1)

You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.

Endnotes (optional) (Heading 1)

Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.

References (Heading 1)

All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. The reference numbers must be finalized and the reference list fully formatted before submission.

Examples of the BioMed Central reference style are shown below. Please ensure that the reference style is followed precisely.

See our editorial policies for author guidance on good citation practice.

Web links and URLs: All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link (e.g. for blogs) they should be included in the reference.

Example reference style:

Article within a journal
Smith JJ. The world of science. Am J Sci. 1999;36:234-5.

Article within a journal (no page numbers)
Rohrmann S, Overvad K, Bueno-de-Mesquita HB, Jakobsen MU, Egeberg R, Tjønneland A, et al. Meat consumption and mortality - results from the European Prospective Investigation into Cancer and Nutrition. BMC Med. 2013;11:63.

Article within a journal by DOI
Slifka MK, Whitton JL. Clinical implications of dysregulated cytokine production. Dig J Mol Med. 2000; doi:10.1007/s801090000086.

Article within a journal supplement
Frumin AM, Nussbaum J, Esposito M. Functional asplenia: demonstration of splenic activity by bone marrow scan. Blood 1979;59 Suppl 1:26-32.

Book chapter, or an article within a book
Wyllie AH, Kerr JFR, Currie AR. Cell death: the significance of apoptosis. In: Bourne GH, Danielli JF, Jeon KW, editors. International review of cytology. London: Academic; 1980. p. 251-306.

OnlineFirst chapter in a series (without a volume designation but with a DOI)
Saito Y, Hyuga H. Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Top Curr Chem. 2007. doi:10.1007/128_2006_108.

Complete book, authored
Blenkinsopp A, Paxton P. Symptoms in the pharmacy: a guide to the management of common illness. 3rd ed. Oxford: Blackwell Science; 1998.

Online document
Doe J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 1999. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.

Online database
Healthwise Knowledgebase. US Pharmacopeia, Rockville. 1998. http://www.healthwise.org. Accessed 21 Sept 1998.

Supplementary material/private homepage
Doe J. Title of supplementary material. 2000. http://www.privatehomepage.com. Accessed 22 Feb 2000.

University site
Doe, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (1999). Accessed 25 Dec 1999.

FTP site
Doe, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (1999). Accessed 12 Nov 1999.

Organization site
ISSN International Centre: The ISSN register. http://www.issn.org (2006). Accessed 20 Feb 2007.

Dataset with persistent identifier
Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, et al. Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. 2011. http://dx.doi.org/10.5524/100012.

Preparing figures and tables

Table 1 (required, fixed format)

The current taxonomic placement and names must be referenced to the appropriate literature at each rank in the hierarchy. This includes the references that establish the validity and availability of the names in use. In the case of bacteria and archaea, this information is available through the NamesforLife annotation services and the appropriate references should be cited and added to the bibliography. Summarized phenotypic features are based on either published reports from the literature, or if the source organism is not previously described, based on the authors’ observations.

Table 1. Classification and general features of Genus species strain designationT. [cite MIGS reference]

MIGS ID Property Term Evidence codea
ClassificationDomain Use only validly published orTAS [ ]
Phylum available names. Cite theTAS [ ]
Class appropriate taxonomic authorityTAS [ ]
Order and references establishing each of the namesTAS [ ]
Family -.TAS [ ]
GenusTAS [ ]
SpeciesTAS [ ]
(Type) strain: StrainT (Accession #s)TAS [ ]
Gram stainPositive/negative/variableTAS [ ]
Cell shapeRod/coccus/filaments/chains, etcTAS [ ]
MotilityMotile/non-motileTAS [ ]
SporulationSpore type/position or not reportedTAS [ ]
Temperature range°CTAS [ ]
Optimum temperature°CTAS [ ]
pH range; Optimume.g., 3.5–6.5; 5TAS [ ]
Carbon sourceSpecify known carbon sources sustaining growthTAS [ ]
GS-6HabitatTAS [ ]
MIGS-6.3Salinityas% NaCl (w/v) TAS [ ]
MIGS-22Oxygen requirementAerobic/anaerobic/microaerophilic/aerotolerant TAS [ ]
MIGS-15Biotic relationshipfree-living/symbiont/commensal TAS [ ]
MIGS-14PathogenicityPathogenic/non-pathogenTAS [ ]
MIGS-4Geographic locationCountry/region TAS [ ]
MIGS-5Sample collectionDateTAS [ ]
MIGS-4.1LatitudeDMSTAS [ ]
MIGS-4.2LongitudeDMSTAS [ ]
MIGS-4.4AltitudeMTAS [ ]

a Evidence codes – IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [cite this reference].

Table 2 (required, fixed format)

Project Information. Authors must provide the requested data, in conformance with the MIGS standard. Supply the information for column 3. Do not modify the order of columns or rows.

Table 2. Project information.

MIGS IDPropertyTerm
MIGS 31Finishing quality
MIGS-28Libraries used
MIGS 29Sequencing platforms
MIGS 31.2Fold coverage
MIGS 30Assemblers
MIGS 32Gene calling method
Locus Tag
Genbank ID
Genbank Date of Release
GOLD ID
BIOPROJECT
MIGS 13Source Material Identifier
Project relevance

Table 3 (optional, fixed format)

Summary of genome. This table should only be used if the report describes a chromosome and one or more plasmids.

Table 3. Summary of genome: one chromosome and X plasmids.

LabelSize (Mb)TopologyINSDC identifierRefSeq ID
Chromosome
Plasmid 1
Plasmid 2
Plasmid 3
Plasmid 4
Plasmid 5

Table 4, or 3 if optional table is not used (required, fixed format)

Genome statistics, listed in base pairs and percent of total. Provide values for columns 2 and 3. Do not modify ordering of rows.

Table 4. Genome statistics.

AttributeValue
Genome size (bp)
DNA coding (bp)
DNA G+C (bp)
DNA scaffolds
Total genes
Protein coding genes
RNA genes
Pseudo genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
CRISPR repeats

Table 5, or 4 if optional table is not used (required, fixed format)

Number of genes associated with general COG functional categories. Provide values for columns 2 and 3. Do not modify ordering of rows.

Table 5. Number of genes associated with general COG functional categories.

CodeValue%ageDescription
JTranslation, ribosomal structure and biogenesis
ARNA processing and modification
KTranscription
LReplication, recombination and repair
BChromatin structure and dynamics
DCell cycle control, Cell division, chromosome partitioning
VDefense mechanisms
TSignal transduction mechanisms
MCell wall/membrane biogenesis
NCell motility
UIntracellular trafficking and secretion
OPosttranslational modification, protein turnover, chaperones
CEnergy production and conversion
GCarbohydrate transport and metabolism
EAmino acid transport and metabolism
FNucleotide transport and metabolism
HCoenzyme transport and metabolism
ILipid transport and metabolism
PInorganic ion transport and metabolism
QSecondary metabolites biosynthesis, transport and catabolism
RGeneral function prediction only
SFunction unknown
-Not in COGs

The total is based on the total number of protein coding genes in the genome.

Instructions for additional tables

Any additional tables must be formatted in the same manner as tables 1-5. This format is detailed below in an example table:

Table Number. Table title.

Table header---
Row 1---
Row 2---
Row 3---

Table footer

Table title must not exceed one row and this row must begin with the table number. The top row of the table must have a top and bottom border and the bottom row of the table must have a bottom border. 12pt Times New Roman must be used for both table title and header. Table rows and footer must be 10 pt Times New Roman. Table footer is used to explain different elements. Authors should use superscript a, b, c, etc. to refer to the element which is being described (as in table one). All additional tables should be able to fit in a 10 × 9 space. Font should be no smaller than 10 pt. additional tables normally only appear in an extended genome report.

Figure legends

The legends should be included in the main manuscript text file at the end of the document, rather than being a part of the figure file. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals - i.e. Figure 1, 2, 3 etc.); short title of figure (maximum 15 words); detailed legend, up to 300 words.

Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.

Required Figure(s): a phylogenetic tree indicating current placement and a photomicrograph or electron photomicrograph of the source organism. Authors should include a brief explanation as to the source of the data, algorithms used to create the tree and any relevant references. Each terminal node should indicate the current name of the species from the 16 rRNA gene or other marker gene originated, and the Genbank identifier. Type strains should be identified as such using a superscripted “T”. Authors should also include information about which species/strains used in a tree have a sequenced genome. Trees should not exceed a single page (7 x 9 in, including figure legend). Text should be no smaller than 8 pt when drawn to scale and should not overlap.

Optional Figure: A genome map should be provided, for complete genome sequences, keyed to the COGS groups.

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