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High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

  • Sivan Laviad1,
  • Alla Lapidus2, 3,
  • James Han4,
  • Matthew Haynes4,
  • TBK Reddy4,
  • Marcel Huntemann4,
  • Amrita Pati4,
  • Natalia N Ivanova4,
  • Konstantinos Mavromatis4,
  • Elke Lang5,
  • Manfred Rohde6,
  • Victor Markowitz7,
  • Tanja Woyke4,
  • Hans-Peter Klenk5,
  • Nikos C Kyrpides4, 8 and
  • Malka Halpern1, 9Email author
Standards in Genomic Sciences201510:29

Received: 15 September 2014

Accepted: 16 April 2015

Published: 27 May 2015


Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.


Brachymonas chironomi Comamonadaceae Chironomid Chironomus Egg massToxicant


Strain AIMA4T (= LGM 24400T = DSM 19884T), is the type strain of Brachymonas chironomi, one out of two species in the genus Brachymonas. The genus Brachymonas was formed by Hiraishi et al. [1] while characterizing rhodoquinone-containing bacteria that had been isolated from soybean crude waste sludge in Japan. Strain AIMA4T, was isolated from an insect egg mass (Chironomus sp.) that was sampled from a waste stabilization pond in northern Israel [2]. Chironomids (Arthropoda; Insecta; Diptera; Chironomidae; Chironomus sp.) inhabit virtually every type and condition of aquatic habitats. They undergo a complete metamorphosis of four life stages (egg, larva, pupa and adult that emerges into the air) [3]. Eggs are laid in an egg mass at the water’s edge. Each egg mass contains hundreds of eggs. Chironomid egg masses were found to harbor Vibrio cholerae and Aeromonas spp. [3-10]. V. cholerae degrades chironomid egg masses by the secreted haemagglutinin protease (HAP) [11,12]. Strain AIMA4T was isolated in the course of a study that investigated endogenous bacterial communities that inhabit chironomid egg masses [2,13,14]. The species epithet chironomi was derived from the non-biting midge insect Chironomus (Diptera; Chironomidae), from where this species was isolated. Strain AIMA4T didn’t show the ability to degrade the egg masses like it was found for V. cholerae.

Here we describe a summary classification and a set of the features of Brachymonas chironomi strain AIMA4T (DSM 19884T), together with the genome sequence description and annotation.

Organism information

Classification and features

A taxonomic study using a polyphasic approach placed B. chironomi strain AIMA4T in the genus Brachymonas within the family Comamonadaceae (Figure 1). The family Comamonadaceae comprises a larger number of genera (as shown in Figure 1) and a larger variety of species and phenotypes [15,16].
Figure 1

Phylogenetic tree highlighting the position of Brachymonas chironomi relative to the type strains of the other species within the family Comamonadaceae. The sequence alignments were performed by using the CLUSTAL W program and the tree was generated using the maximum likelihood method in MEGA 5 software. Bootstrap values (from 1,000 replicates) greater than 50% are shown at the branch points. The bar indicates a 1% sequence divergence.

B. chironomi strain AIMA4T is a Gram-negative, non-motile coccobacillus or rod (Figure 2). After 48 h incubation on LB agar at 30°C, colonies are beige colored (opaque) that turn to light brown after few days of incubation. Strain AIMA4T is aerobic, chemoorganotrophic and does not produce acid from carbohydrates (including glucose) [2]. Growth is observed at 18–37°C (optimum 30°C), with 0–2.5% (w/v) NaCl (optimum 0.5% NaCl) and at pH 5.0–9.0 (optimum pH 6.0–8.0) (Table 1). The following enzymatic activities were observed in strain AIMA4T: catalase and oxidase, alkaline and acid phosphatases, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, trypsin and naphthol-AS-BI-phosphohydrolase. Strain AIMA4T produces acetoin and reduces nitrate to nitrite [2].
Figure 2

Scanning electron micrograph of B. chironomi AIMA4T.

Table 1

Classification and general features of Brachymonas chironomi strain AIMA4T according to the MIGS recommendations [ 40 ], published by the Genome Standards Consortium [ 41 ] and the Names for Life database [ 42 ]




Evidence code a



Domain Bacteria

TAS [43]


Phylum Proteobacteria

TAS [44]


Class Betaproteobacteria

TAS [45]


Order Burkholderiales

TAS [46]


Family Comamonadaceae

TAS [47]


Genus Brachymonas

TAS [1]


Species Brachymonas chironomi

TAS [2]


Type strain AIMA4T

TAS [2]


Gram stain


TAS [2]


Cell shape

Coccobacilli or rods

TAS [2]




TAS [2]






Temperature range


TAS [2]


Optimum temperature


TAS [2]


pH range; Optimum

5.0–9.0; 6.0–8.0

TAS [2]


Carbon sourceb

phenylacetic acid

TAS [2]



Aquatic/Insect host

TAS [2]



0-2.5% NaCl (w/v)

TAS [2]


Oxygen requirement


TAS [2]


Biotic relationship

Commensal (Insect, chironomid)

TAS [2]






Geographic location


TAS [2]


Sample collection

July, 2006

TAS [2]




TAS [2]




TAS [2]



40 m

TAS [2]

aEvidence 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). Evidence codes are from the Gene Ontology project [48].

bThe only carbon source that was positive for this strain, out of all carbon sources that were tested (strain AIMA4T does not use carbohydrates, not even glucose) [2].

Chemotaxonomic data

The dominant cellular fatty acids are C16:1 ω7c, C16:0 and C18:1 ω7c. The main isoprenoid quinone is Q-8. Phosphatidylglycerol, phosphatidylethanolamine and phosphatidylserine occur as polar lipids [2].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [17-19]. Sequencing of B. chironomi strain AIMA4T is part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project [20] which aims in increasing the sequencing coverage of key reference microbial genomes [21]. The genome project is deposited in the Genomes OnLine Database [22] and the permanent draft 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 [23]. A summary of the project information is shown in Table 2.
Table 2

Genome sequencing project information





Finishing quality

Level 2: High-Quality Draft


Libraries used

Illumina Std. shotgun library


Sequencing platforms

Illumina HiSeq 2000

MIGS 31.2

Fold coverage




Velvet v. 1.1.04, ALLPATHS v. R37654


Gene calling method

Prodigal 2.5


Locus Tag



GenBank ID



GenBank Date of Release

September 16, 2013








Source Material Identifier

DSM 19884T


Project relevance

Tree of Life, GEBA-KMG

Growth conditions and genomic DNA preparation

B. chironomi strain AIMA4T, DSM 19884T, was grown in DSMZ medium 1 (Nutrient Agar), at 28°C [24]. DNA was isolated from 0.5-1 g of cell paste using JetFlex Genomic DNA Purification Kit (GENOMED) following the standard protocol as recommended by the manufacturer, however with additional 50 μl protease K (20 mg/ml) during digest for 60 min. at 58°C. Protein precipitation was done with additional 200 μl Protein Precipitation Buffer, followed by over night incubation on ice. DNA is available through the DNA Bank Network [25].

Genome sequencing and assembly

The draft genome of B. chironomi strain AIMA4T was generated using the Illumina technology [23,26]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 14,014,260 reads totaling 2,102.1 Mb. All general aspects of library construction and sequencing performed at the JGI can be found at the institute website [27]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts [28]. Following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet [29], (2) 1–3 Kbp simulated paired end reads were created from Velvet Contigs using wgsim [30], (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG [31]. Parameters for assembly steps were: (1) Velvet (velveth: 63 –shortPaired and velvetg: −very clean yes –export-Filtered yes –min contig lgth 500 –scaffolding no –cov cutoff 10) (2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) (3) Allpaths–LG (PrepareAllpathsInputs: PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True). The final draft assembly contained 36 contigs in 36 scaffolds. The total size of the genome is 2.5 Mbp and the final assembly is based on 249.2 Mbp of Illumina data, which provides an average 99.6 × coverage of the genome.

Genome annotation

Genes were identified using Prodigal [32] as part of the DOE-JGI genome annotation pipeline [33,34], following by a round of manual curation using the JGI GenePRIMP pipeline [35]. The predicted CDSs were translated and searched against the Integrated Microbial Genomes (IMG) non-redundant database, UniProt, TIGERFam, 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 was performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) platform [36].

Genome properties

The assembly of the draft genome sequence consists of 36 scaffolds amounting to 2,509,395 bp, and the G + C content is 63.5% (Table 3). Of the 2,450 genes predicted, 2,382 were protein-coding genes, and 68 RNAs. The majority of the protein-coding genes (85.5%) 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



% of Total

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 4

Number of genes associated with the general COG functional categories



% age





Translation, ribosomal structure and biogenesis




RNA processing and modification








Replication, recombination and repair




Chromatin structure and dynamics




Cell cycle control, cell division, chromosome partitioning




Defense mechanisms




Signal transduction mechanisms




Cell wall/membrane/envelope biogenesis




Cell motility




Intracellular trafficking, secretion, and vesicular transport




Posttranslational modification, protein turnover, chaperones




Energy production and conversion




Carbohydrate transport and metabolism




Amino acid transport and metabolism




Nucleotide transport and metabolism




Coenzyme transport and metabolism




Lipid transport and metabolism




Inorganic ion transport and metabolism




Secondary metabolites biosynthesis, transport and catabolism




General function prediction only




Function unknown




Not in COGs

Insights from the genome sequence

Strain AIMA4T was isolated from chironomid egg masses. Using pyrosequencing method, we have recently shown that the prevalence of Brachymonas in the endogenous bacterial communities of chironomid egg masses and larva was 0.04% and 0.006%, respectively [37]. Chironomid tolerance towards pollution is well documented [38]. Senderovich and Halpern [37,39], demonstrated by using Koch’s postulates that endogenous bacteria in chironomids have a role in protecting the insect from toxicants. Although B. chironomi was isolated from chironomid egg masses, its features regarding its protective potential have never been examined. Nevertheless, its genome reveals the potential of this species to protect its host in polluted environments. Genes encoding arsenate detoxification are present in B. chironomi strain AIMA4T. These genes include an arsenical resistance gene cluster with candidates for transcriptional regulator, ArsR; arsenical resistance operon trans-acting repressor, ArsD; arsenite efflux ATP-binding protein, ArsA and a hypothetical arsenic resistance protein (ACR3 family). A gene for arsenate reductase (ArsC family) is present in a different operon. More genes which may indicate the potential of this bacterium to tolerate or detoxify metals are: copper resistance protein D, CopD; copper chaperone, copper-resistance protein, CopA; copper (or silver) translocating P-type ATPase; uncharacterized lipoprotein NlpE involved in copper resistance; magnesium Mg(2+) and cobalt Co(2+) transport protein, CorA. Moreover, two genes encoding ABC-type transport system involved in resistance to organic solvents, auxiliary and periplasmic components are also present.

The genome of B. chironomi strain AIMA4T reveals the potential of the species to produce a polysaccharide capsule. It includes two gene clusters with candidates for capsule polysaccharide export protein, periplasmic protein involved in polysaccharide export, ABC-type polysaccharide/polyol phosphate transport system, ATPase component, ABC-type polysaccharide/polyol phosphate export systems, permease component and predicted glycosyltransferase involved in capsule biosynthesis. Another feature that is found in the genome of B. chironomi AIMA4T is its potential to produce a pilus (or pili). The following predicted genes indicate this ability; type IV pilus assembly protein PilB; type IV pilus secretin PilQ; Tfp pilus assembly proteins PilP, PilO and PilV; type IV prepilin peptidase; prepilin-type N-terminal cleavage/methylation domain and pilus retraction ATPase PilT (indicating the ability of twitching motility).

Tolerance of 2.5% NaCl was described for strain AIMA4T by Halpern et al. [2]. The presence of ABC-type proline/glycine betaine transport system in the genome may explain the way this species can tolerate high salt concentrations. In respect to the ampicillin (beta-lactam) antibiotic resistance, the genome encodes one beta-lactamase class B and a negative regulator of beta-lactamase expression. Three genes encoding two component transcriptional regulators (LuxR family), can be found in the genome of strain AIMA4T and demonstrate quorum sensing skills.


In the current study, we characterized the genome of B. chironomi strain AIMA4T that was isolated from a chironomid egg mass [2]. B. chironomi belongs to the family Comamonadaceae (order Bukholderiales; class Betaproteobacteria) (Figure 1). Members of this family are known for their ability to cope with harsh environmental condition such as high concentration of toxic metals and other pollutants like aromatic compounds or polymers [e.g. poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [16]. Likewise, the genome of strain AIMA4T reveals the potential of this species to cope with toxic metals. These demonstrate that B. chironomi may have a role in protecting its aquatic host (chironomids) in polluted environments.



One thousand microbial genomes





We would like to gratefully acknowledge the help of Nicole Reimann for growing B. chironomi cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy's 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 Genome analysis was supported by the National Basic Research Program of China (No. 2010CB833801). A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI Dr Stephen J O’Brien). M. H. was supported in part by a grant from the US Civilian Research and Development Foundation (CRDF grant no. ILB1-7045-HA).

Authors’ Affiliations

Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
DOE Joint Genome Institute, Walnut Creek, USA
Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Helmholz Centre for Infection Research, Braunschweig, Germany
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, USA
Dept. of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
Dept. of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Kiryat Tivon, Israel


  1. Hiraishi A, Shin YK, Sugiyama J. Brachymonas denitrificans gen. nov., sp. nov., an aerobic chemoorganotrophic bacterium which contains rhodoquinones, and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes. J Gen Appl Microbiol. 1995;41:99–117.View ArticleGoogle Scholar
  2. Halpern M, Shaked T, Schumann P. Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas. Int J Syst Evol Microbiol. 2009;59:3025–9.View ArticlePubMedGoogle Scholar
  3. Halpern M, Landsberg O, Raats D, Rosenberg E. Culturable and VBNC Vibrio cholerae: interactions with chironomid egg masses and their bacterial population. Microb Ecol. 2007;53:285–93.View ArticlePubMedGoogle Scholar
  4. Broza M, Halpern M. Chironomid egg masses and Vibrio cholerae. Nature. 2001;412:40.View ArticlePubMedGoogle Scholar
  5. Halpern M, Broza YB, Mittler S, Arakawa E, Broza M. Chironomid egg masses as a natural reservoir of Vibrio cholerae non-O1 and non-O139 in freshwater habitats. Microb Ecol. 2004;47:341–9.View ArticlePubMedGoogle Scholar
  6. Halpern M, Raats D, Lavion R, Mittler S. Dependent population dynamics between chironomids (non-biting midges) and Vibrio cholerae. FEMS Microbiol Ecol. 2006;55:98–104.View ArticlePubMedGoogle Scholar
  7. Senderovich Y, Gershtein Y, Halewa E, Halpern M. Vibrio cholerae and Aeromonas; do they share a mutual host? ISME J. 2008;2:276–83.View ArticlePubMedGoogle Scholar
  8. Figueras MJ, Beaz-Hidalgo R, Senderovich Y, Laviad S, Halpern M. Re-identification of Aeromonas isolates from chironomid egg masses as the potential pathogenic bacteria Aeromonas aquariorum. Environ Microbiol Rep. 2011;3:239–44.View ArticlePubMedGoogle Scholar
  9. Beaz-Hidalgo R, Shakèd T, Laviad S, Halpern M, Figueras M. Chironomid egg masses harbour the clinical species Aeromonas taiwanensis and Aeromonas sanarellii. FEMS Microbiol Lett. 2012;337:48–54.View ArticlePubMedGoogle Scholar
  10. Halpern M. Chironomids and Vibrio cholerae. In: Rosenberg E, Gophna U, editors. Beneficial Microorganisms in Multicultural Life Forms. Berlin Heidelberg: Springer; 2011. p. 43–56.Google Scholar
  11. Halpern M, Gancz H, Broza M, Kashi Y. Vibrio cholerae hemagglutinin/protease degrades chironomid egg masses. Appl Environ Microbiol. 2003;69:4200–4.View ArticlePubMed CentralPubMedGoogle Scholar
  12. Halpern M. Novel insights into hemagglutinin protease (HAP) gene regulation in Vibrio cholerae. Mol Ecol. 2010;19:4108–12.View ArticlePubMedGoogle Scholar
  13. Raats D, Halpern M. Oceanobacillus chironomi sp. nov., a halotolerant and facultative alkaliphilic species isolated from a chironomid egg mass. Int J Syst Evol Microbiol. 2007;57:255–9.View ArticlePubMedGoogle Scholar
  14. Halpern M, Senderovich Y, Snir S. Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass. Int J Syst Evol Microbiol. 2007;57:1872–5.View ArticlePubMedGoogle Scholar
  15. Willems A, Pot B, Falsen E, Vandamme P, Gillis M, Kersters K, et al. Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquuspirillum aquaticurn, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol. 1991;41:427–244.View ArticleGoogle Scholar
  16. Weiss M, Kesberg A, LaButti K, Pitluck S, Bruce D, Hauser L, et al. Permanent draft genome sequence of Comamonas testosteroni KF-1. Stand Genomic Sci. 2013;8:2.View ArticleGoogle Scholar
  17. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, et al. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature. 2009;462:1056–60.View ArticlePubMed CentralPubMedGoogle Scholar
  18. Klenk HP, Göker M. En route to a genome - based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010;33:175–82.View ArticlePubMedGoogle Scholar
  19. Göker M, Klenk HP. Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. Stand Genomic Sci. 2013;8:360–74.View ArticlePubMed CentralPubMedGoogle Scholar
  20. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, et al. Genomic encyclopedia of type strains, phase I: the one thousand microbial genomes (KMG-I) project. Stand Genomic Sci. 2013;9:628–6234.View ArticleGoogle Scholar
  21. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, et al. Genomic Encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains. PLoS Biol. 2014;8:e1001920.View ArticleGoogle Scholar
  22. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, et al. The genomes OnLine database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012;40:D571–9.View ArticlePubMed CentralPubMedGoogle Scholar
  23. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One. 2012;7:e48837.View ArticlePubMed CentralPubMedGoogle Scholar
  24. List of growth media used at DSMZ []
  25. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, et al. The DNA bank network: the start from a German initiative. Biopreserv Biobank. 2011;9:51–5.View ArticlePubMedGoogle Scholar
  26. Bennett S. Solexa Ltd. Pharmacogenomics. 2004;5:433–8.View ArticlePubMedGoogle Scholar
  27. JGI web page []
  28. Mingkun L, Copeland A, Han J. DUK, unpublished, 2011Google Scholar
  29. Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.View ArticlePubMed CentralPubMedGoogle Scholar
  30. Scholar
  31. Gnerre S, MacCallum I. High–quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011;108:1513–8.View ArticlePubMed CentralPubMedGoogle Scholar
  32. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiati on site identification. BMC Bioinformatics. 2010;11:119.View ArticlePubMed CentralPubMedGoogle Scholar
  33. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009;1:63–7.View ArticlePubMed CentralPubMedGoogle Scholar
  34. Chen IM, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, et al. Improving microbial genome annotations in an integrated database context. PLoS One. 2013;8:e54859.View ArticlePubMed CentralPubMedGoogle Scholar
  35. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010;7:455–7.View ArticlePubMedGoogle Scholar
  36. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8.View ArticlePubMedGoogle Scholar
  37. Senderovich Y, Halpern M. The protective role of endogenous bacterial communities in chironomid egg masses and larvae. ISME J. 2013;7:2147–58.View ArticlePubMed CentralPubMedGoogle Scholar
  38. Armitage P, Cranston PS, Pinder LCV. The Chironomidae: The Biology and Ecology of Non-biting Midges. London: Chapman and Hall; 1995.View ArticleGoogle Scholar
  39. Senderovich Y, Halpern M. Bacterial community composition associated with chironomid egg masses. J Insect Sci. 2012;12:148.View ArticleGoogle Scholar
  40. Field D, Garrity GM, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.View ArticlePubMed CentralPubMedGoogle Scholar
  41. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, et al. The Genomic Standards Consortium. PLoS Biol. 2011;9:e1001088.View ArticlePubMed CentralPubMedGoogle Scholar
  42. Garrity GM. Namesforlife browser tool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010;37:9.Google Scholar
  43. Woese CR, Kandler O, Weelis ML. Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci U S A. 1990;87:4576–9.View ArticlePubMed CentralPubMedGoogle Scholar
  44. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl nov. In: Brenner DJ, Krieg NR, Stanley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology. volume 2 (The Proteobacteria part B The Gammaproteobacteria). 2nd ed. New York: Springer; 2005. p. 1.View ArticleGoogle Scholar
  45. Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria class. nov. In: Brenner DJ, Krieg NR, Stanley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology. Volume 2 (the Proteobacteria part C the alpha-, beta-, delta-, and Epsilonproteobacteria). 2nd ed. New York: Springer; 2005. p. 575.Google Scholar
  46. Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales ord. nov. In: Brenner DJ, Krieg NR, Stanley JT, Garrity GM, Brenner DJ, Krieg NR, Stanley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology. Volume 2 (The Proteobacteria part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria). 2nd ed. New York: Springer; 2005. p. 575.Google Scholar
  47. Willems A, De Ley J, Gillis M, Kersters K. Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Bacteriol. 1991;41:445–50.View ArticleGoogle Scholar
  48. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Gene Ontology Consortium. Nat Genet. 2000;25:25–9.View ArticlePubMed CentralPubMedGoogle Scholar


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