Open Access

Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.

  • Iain Anderson
  • , Huzuki Teshima,
  • , Matt Nolan
  • , Alla Lapidus,
  • , Hope Tice
  • , Tijana Glavina Del Rio
  • , Jan-Fang Cheng
  • , Cliff Han,
  • , Roxanne Tapia,
  • , Lynne A. Goodwin,
  • , Sam Pitluck
  • , Konstantinos Liolios
  • , Konstantinos Mavromatis
  • , Ioanna Pagani
  • , Natalia Ivanova
  • , Natalia Mikhailova
  • , Amrita Pati
  • , Amy Chen
  • , Krishna Palaniappan
  • , Miriam Land
  • , Manfred Rohde
  • , Elke Lang
  • , John C. Detter,
  • , Markus Göker
  • , Tanja Woyke
  • , James Bristow
  • , Jonathan A. Eisen,
  • , Victor Markowitz
  • , Philip Hugenholtz,
  • , Nikos C. Kyrpides
  • and Hans-Peter Klenk
Corresponding author

DOI: 10.4056/sigs.4338002

Received: 02 October 2013

Accepted: 02 October 2013

Published: 16 October 2013

Abstract

Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords:

strictly aerobicmotilerod-shapedacetogenicmesophilicAcetobacter aurantius’XanthomonadaceaeGEBA

Introduction

Strain Kondô 67T, also known as G-6T and as IFO 3245T (= DSM 6220 = ATCC 33424 = NBRC 3245) is the type strain of the species Frateuria aurantia [1], the type species in the bispecific genus Frateuria [1]. Kondô 67T was originally isolated from Lilium auratum Lindl and classified as a member of ‘Acetobacter aurantius’ from which it was reclassified 22 years later as the type strain of the type species of Frateuria [1]. The genus was named after the Belgian microbiologist Joseph Frateur (1903-1974) [1]; the species epithet is derived from the Neo-Latin adjective aurantia, referring to the gold-yellow color of the strain on MYP agar [1]. Strain Kondô 67T was characterized as ‘acetogenic’ [2] and as containing triterpenoids of the hopane family [3]. Here we present a summary classification and a set of features for F. aurantia Kondô 67T, together with the description of the genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA gene sequence of strain Kondô 67T was compared using NCBI BLAST [4,5] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [6] and the relative frequencies of taxa and keywords (reduced to their stem [7]) were determined, weighted by BLAST scores. The most frequently occurring genera were Dyella (34.3%), Rhodanobacter (24.0%), Frateuria (19.6%), Luteibacter (11.9%) and 'Luteibactor' (3.7%) (105 hits in total). Regarding the eleven hits to sequences from members of the species, the average identity within HSPs was 99.6%, whereas the average coverage by HSPs was 100.0%. Among all other species, the one yielding the highest score was Dyella ginsengisoli (EF191354), which corresponded to an identity of 98.2% and an HSP coverage of 99.0%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was HM556321 ('insect herbivore microbiome plant biomass-degrading capacity Atta colombica colony N11 fungus garden top clone TIBW663'), which showed an identity of 99.7% and an HSP coverage of 97.2%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'soil' (5.9%), 'sediment' (2.5%), 'microbi' (1.8%), 'enrich' (1.5%) and 'vent' (1.3%) (145 hits in total). The most frequently occurring keyword within the labels of those environmental samples which yielded hits of a higher score than the highest scoring species was 'atta, biomass-degrad, capac, colombica, coloni, fungu, garden, herbivor, insect, microbiom, plant, top' (8.3%) (6 hits in total), reflecting some of the known features of the strain’s origin.

Figure 1 shows the phylogenetic neighborhood of F. aurantia in a 16S rRNA based tree. The sequences of the four identical 16S rRNA gene copies in the genome differ by one nucleotide from the previously published 16S rRNA sequence (AB091194).

Figure 1

Phylogenetic tree highlighting the position of F. aurantia relative to the type strains of the other species within the family Xanthomonadaceae. The tree was inferred from 1,431 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 750 ML bootstrap replicates [12] (left) and from 1,000 maximum-parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.

Table 1

Classification and general features of F. aurantia Kondô 67T according to the MIGS recommendations [15] (published by the Genome Standards Consortium [16]) and NamesforLife [17].

MIGS ID

       Property

       Term

       Evidence code

       Current classification

       Domain Bacteria

       TAS [18]

       Phylum Proteobacteria

       TAs [19]

       Class Gammaproteobacteria

       TAS [20,21]

       Order Xanthomonadales

       TAS [20,22]

       Family Xanthomonadaceae

       TAS [20,22]

       Genus Frateuria

       TAS [1,23]

       Species Frateuria aurantia

       TAS [1]

       Type strain Kondô 67 = G-6 = IFO 3245

       TAS [1]

       Gram stain

       negative

       TAS [1]

       Cell shape

       rod-shaped, mostly strait

       TAS [1]

       Motility

       motile

       TAS [1]

       Sporulation

       not reported

       Temperature range

       mesophile

       TAS [1]

       Optimum temperature

       30°C

       TAS [1]

       Salinity

       0.2 - 2% NaCl (w/v)

       TAS [1]

MIGS-22

       Oxygen requirement

       aerobe

       TAS [1]

       Carbon source

       glucose, yeast extract, mannitol, peptone

       TAS [1]

       Energy metabolism

       organoheterotroph

       TAS [1]

MIGS-6

       Habitat

       Lilium auratum

       TAS [1]

MIGS-15

       Biotic relationship

       host-associated

       TAS [1]

MIGS-14

       Pathogenicity

       none

       NAS

       Biosafety level

       1

       TAS [24]

MIGS-23.1

       Isolation

       from Lilium auratum Lindl

       TAS [25]

MIGS-4

       Geographic location

       Kawasaki, Japan

       TAS [1]

MIGS-5

       Sample collection time

       1958 or before

       TAS [25]

MIGS-4.1

       Latitude

       35.50

       TAS [1]

MIGS-4.2

       Longitude

       139.77

       TAS [1]

MIGS-4.3

       Depth

       not reported

MIGS-4.4

       Altitude

       not reported

Evidence codes - 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). Evidence codes are from the Gene Ontology project [26].

F. aurantia Kondô 67T cells stain Gram-negative [1], were straight rod shaped, 0.5-0.7 μm in width and 0.7-3.5 μm in length (Figure 2) [1] and motile via polar flagella [1] (not visible in Figure 2). Cells occur singly or in pairs, rarely in filaments [1]. Cultures grow in dark, glistening, flat colonies with a soluble brown pigment [1]. They are oxidase positive and catalase negative [1]; physiological features and antibiotic susceptibilities were reported in great detail in [1]. Cells grow well at pH 3.6 and 34°C [1].

Figure 2

Scanning electron micrograph of F. aurantia Kondô 67T

Chemotaxonomy

Besides trace amounts of diploptene and rearranged compounds like fern-7-ene [3], the main lipids isolated from DSM 6220T are iso-branched fatty acids and triterpenoids of the hopane family, such as bacteriohopanetetrol and derived hopanoid. The organism also produces ubiquinone Q8 [27].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [28], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [29]. The genome project is deposited in the Genomes On Line Database [14] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI) using state of the art sequencing technology [30]. A summary of the project information is shown in Table 2.

Table 2

Genome sequencing project information

MIGS ID

      Property

     Term

MIGS-31

      Finishing quality

     Finished

MIGS-28

      Libraries used

     Two genomic libraries: one 454 PE library (7.5 kb insert size), one Illumina library

MIGS-29

      Sequencing platforms

     Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

      Sequencing coverage

     537.4 × Illumina; 8.6 × pyrosequence

MIGS-30

      Assemblers

     Newbler version 2.3-PreRelease-6/30/2009, Velvet 1.0.13, phrap version SPS - 4.24

MIGS-32

      Gene calling method

     Prodigal

      INSDC ID

     CP003350

      GenBank Date of Release

     June 14, 2012

      GOLD ID

     Gc02155

      NCBI project ID

     64505

      Database: IMG

     2509601034

MIGS-13

      Source material identifier

     DSM 6220

      Project relevance

     Tree of Life, GEBA

Growth conditions and DNA isolation

F. aurantia strain Kondô 67T, DSM 6220, was grown in DSMZ medium 360 (YPM medium) [31] at 30°C. DNA was isolated from 0.5-1 g of cell paste using standard procedures at the DSMZ DNA laboratory and quality control processes requested by the sequencing center (JGI). DNA is available through the DNA Bank Network [32].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [33]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 36 contigs in one scaffold was converted into a phrap [34] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (2,074.3 Mb) was assembled with Velvet [35] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 63.7Mb 454 draft data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [34] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [33], Dupfinisher [36], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 43 additional reactions and one shatter library were necessary to close gaps and to raise the quality of the final sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [37]. The error rate of the final genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 546.0 × coverage of the genome. The final assembly contained 163,130 pyrosequence and 25,455,174 Illumina reads.

Genome annotation

Genes were identified using Prodigal [38] as part of the DOE-JGI [39] genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [40]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [41].

Genome properties

The genome consists of a 3,603,458 bp long circular chromosome with a G+C content of 63.4% (Table 3 and Figure 3). Of the 3,288 genes predicted, 3,200 were protein-coding genes, and 88 RNAs; 99 pseudogenes were also identified. The majority of the protein-coding genes (79.6%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3

Genome Statistics

Attribute

     Value

       % of Total

Genome size (bp)

     3,603,458

       100.00%

DNA coding region (bp)

     3,189,580

       88.51%

DNA G+C content (bp)

     2,284,441

       63.40%

Number of replicons

     1

Extrachromosomal elements

     0

Total genes

     3,288

       100.00%

RNA genes

     88

       2.68%

rRNA operons

     4

tRNA genes

     73

       2.22%

Protein-coding genes

     3,200

       97.32%

Pseudo genes

     99

       3.01%

Genes with function prediction (proteins)

     2,616

       79.56%

Genes in paralog clusters

     1,350

       41.06%

Genes assigned to COGs

     2,610

       79.38%

Genes assigned Pfam domains

     2,724

       82.85%

Genes with signal peptides

     313

       9.52%

Genes with transmembrane helices

     722

       21.96%

CRISPR repeats

     1

Figure 3

Graphical map of the chromosome. From outside to center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content(black), GC skew (purple/olive).

Table 4

Number of genes associated with the general COG functional categories

Code

       value

       %age

        Description

J

       167

       5.7

        Translation, ribosomal structure and biogenesis

A

       1

       0.0

        RNA processing and modification

K

       192

       6.6

        Transcription

L

       145

       5.0

        Replication, recombination and repair

B

       1

       0.0

        Chromatin structure and dynamics

D

       30

       1.0

        Cell cycle control, cell division, chromosome partitioning

Y

       0

       0.0

        Nuclear structure

V

       56

       1.9

        Defense mechanisms

T

       129

       4.4

        Signal transduction mechanisms

M

       214

       7.3

        Cell wall/membrane biogenesis

N

       92

       3.1

        Cell motility

Z

       0

       0.0

        Cytoskeleton

W

       0

       0.0

        Extracellular structures

U

       112

       3.8

        Intracellular trafficking and secretion, and vesicular transport

O

       133

       4.5

        Posttranslational modification, protein turnover, chaperones

C

       186

       6.4

        Energy production and conversion

G

       170

       5.8

        Carbohydrate transport and metabolism

E

       209

       7.1

        Amino acid transport and metabolism

F

       68

       2.3

        Nucleotide transport and metabolism

H

       143

       4.9

        Coenzyme transport and metabolism

I

       101

       3.5

        Lipid transport and metabolism

P

       146

       5.0

        Inorganic ion transport and metabolism

Q

       63

       2.2

        Secondary metabolites biosynthesis, transport and catabolism

R

       323

       11.0

        General function prediction only

S

       246

       8.4

        Function unknown

-

       678

       20.6

        Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Markus Kopitz for growing F. aurantia cultures and Susanne Schneider for DNA extractions and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and in part by the Russian Ministry of Science Mega-grant no.11.G34.31.0068;  SJ O'Brien Principal Investigator.


This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

References

  1. Swings J, Gillis M, Kersters K, De Vos P, Gosselé F and de Ley J. Frateuria, a new genus for "Acetobacter aurantius". Int J Syst Bacteriol. 1980; 30:547-556 View Article
  2. Johnson DB, Rolfe S, Hallberg KB and Iversen E. Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ Microbiol. 2001; 3:630-637 View ArticlePubMed
  3. Joyeux C, Fouchard S, Llopiz P and Neunlist S. Influence of the temperature and the growth phase on the hopanoids and fatty acids content of Frateuria aurantia (DSMZ 6220). FEMS Microbiol Ecol. 2004; 47:371-379 View ArticlePubMed
  4. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-410PubMed
  5. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
  6. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  7. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
  8. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552 View ArticlePubMed
  10. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  11. Hess PN and De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond. 2007; 92:669-674 View Article
  12. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME and Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci. 2009; 5541:184-200 View Article
  13. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
  14. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM and Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012; 40:D571-D579 View ArticlePubMed
  15. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  16. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L and Karsch-Mzrachi I. PLoS Biol. •••; 9:e1001088 View ArticlePubMed
  17. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010; 37:9
  18. Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci USA. 1990; 87:4576-4579 View ArticlePubMed
  19. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
  20. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol. 2005; 55:2235-2238 View Article
  21. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
  22. Saddler GS, Bradbury JF. Order III. Xanthomonadales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 63.
  23. Zhang JY, Liu XY and Liu SJ. Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria. Int J Syst Evol Microbiol. 2011; 61:443-447 View ArticlePubMed
  24. BAuA. 2010, Classification of bacteria and archaea in risk groups. TRBA 466, p. 89.Web Site
  25. Kondô K and Ameyama M. Carbohydrate metabolism by Acetobacter species. I. Oxidative activity for various carbohydrates. Bull Agric Chem Soc Jpn. 1958; 22:369-372 View Article
  26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  27. Yamada Y, Okada Y and Kondô K. Isolation and characterization of “polarly flaggelated intermediate strains” in acetic bacteria. J Gen Appl Microbiol. 1976; 22:237-245 View Article
  28. Klenk HP and Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  29. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  30. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A and Klenk HP. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS ONE. 2012; 7:e48837 View ArticlePubMed
  31. List of growth media used at DSMZ: Web Site
  32. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG and Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank. 2011; 9:51-55 View Article
  33. . Web Site
  34. Phrap and Phred for Windows. MacOS, Linux, and Unix. Web Site
  35. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  36. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceedings of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
  37. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
  38. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  39. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM and Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009; 1:63-67 View ArticlePubMed
  40. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A and Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods. 2010; 7:455-457 View ArticlePubMed
  41. Markowitz VM, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed