Open Access

High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T)

  • Erko Stackebrandt1,
  • Olga Chertkov2, 3,
  • Alla Lapidus2,
  • Matt Nolan2,
  • Susan Lucas2,
  • Cliff Han2, 3,
  • Jan-Fang Cheng2,
  • Roxanne Tapia2, 3,
  • Lynne A. Goodwin2, 3,
  • David Bruce2, 3,
  • Sam Pitluck2,
  • Konstantinos Liolios2,
  • Konstantinos Mavromatis2,
  • Ioanna Pagani2,
  • Natalia Ivanova2,
  • Natalia Mikhailova2,
  • Marcel Huntemann2,
  • Amrita Pati2,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Manfred Rohde5,
  • Brian J. Tindall1,
  • Markus Göker1,
  • Tanja Woyke2,
  • John C. Detter3,
  • James Bristow2,
  • Jonathan A. Eisen2, 6,
  • Victor Markowitz4,
  • Philip Hugenholtz2, 7,
  • Hans-Peter Klenk1 and
  • Nikos C. Kyrpides2
Standards in Genomic Sciences20138:8010037

https://doi.org/10.4056/sigs.3537045

Published: 15 April 2013

Abstract

At present, Joostella marina Quan et al. 2008 is the sole species with a validly published name in the genus Joostella, family Flavobacteriacae, phylum Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which little has been reported other than the chemotaxonomic features required for initial taxonomic description. The genome of J. marina strain En5T complements a list of 16 Flavobacteriaceae strains for which complete genomes and draft genomes are currently available. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. This is the first member of the genus Joostella for which a complete genome sequence becomes available. The 4,508,243 bp long single replicon genome with its 3,944 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

Gram-negative non-motile aerobic mesophile Flavobacteriaceae Bacteroidetes GEBA

Introduction

Strain En5T (= DSM 19592 = KCTC 12518 = CGMCC 1.6973) is the type strain of Joostella marina [1], which is the type species of the monospecific genus Joostella that was named after P.J. Jooste, who first proposed the family Flavobacteriaceae [1]. A second species name, ‘Joostella atrarenae’ [2] has been effectively published but not yet appeared on a validation list. J. marina was isolated by dilution-plating on marine agar 2216 (Difco) from coastal seawater in the East Sea of Korea. The phylogenetically neighboring genera are Zhouia [3] and Galbibacter [4]. Here we present a summary classification and a set of features for J. marina En5T together with the description of the complete genomic sequencing and annotation. The genome of strain En5T complements a list of 16 Flavobacteriaceae [5,6] strains for which complete genomes and draft genomes are already available.

Classification and features

16S rRNA gene sequence analysis

A representative genomic 16S rRNA gene sequence of J. marina En5T was compared using NCBI BLAST [7,8] 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 [9] and the relative frequencies of taxa and keywords (reduced to their stem [10]) were determined, weighted by BLAST scores. The most frequently occurring genera were Cellulophaga (15.8%), Aquimarina (14.2%), Flavobacterium (10.7%), Formosa (6.9%) and Psychroserpens (6.1%) (123 hits in total). Regarding the single hit to sequences from members of J. marina, the average identity within HSPs was 100.0%, whereas the average coverage by HSPs was 99.0%. Among all other species, the one yielding the highest score was ‘Venteria marina’ (DQ097522), which corresponded to an identity of 100.0% 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 record for DQ097522 was, however, subsequently removed from Genbank at the submitter’s request, because the source organism could not be confirmed. The highest-scoring environmental sequence was DQ490025 (Greengenes short name ‘Microbial life ridge flank crustal fluids clone ODP-33B-02’), which showed an identity of 99.7% and an HSP coverage of 100.0%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘marin’ (5.2%), ‘water’ (3.7%), ‘microbi’ (3.1%), ‘sea’ (2.9%) and ‘north’ (2.0%) (127 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.

Figure 1 shows the phylogenetic neighborhood of J. marina in a 16S rRNA based tree. The sequences of the three identical 16S rRNA gene copies in the genome do not differ from the previously published 16S rDNA sequence (EF660761).
Figure 1.

Phylogenetic tree highlighting the position of J. marina relative to the type strains of the type species of the other genera within the family Flavobacteriaceae. The tree was inferred from 1,370 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 600 ML bootstrap replicates [15] (left) and from 1,000 maximum-parsimony bootstrap replicates [16] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, those also listed as ‘Complete and Published’ with two asterisks (see CP003283 for Ornithobacterium rhinotracheale and [1823]).

Morphology and physiology

The rod-shaped cells of strain En5T (0.2-0.3 µm wide and 1.0–2.0 µm long) stain Gram-negative [1] (Figure 2). Flexirubin-type pigments are not formed and gliding motility is absent. The optimal NaCl concentration for growth is 1–3% but cells can grow in up to 15% NaCl. Optimal growth temperature is 30°C and no growth is observed at 4°C or at 42°C. Growth occurs at pH 5.3–10.5 with an optimum between pH 5.3 and 7.6. The organism is oxidase- and catalase-positive and strictly aerobic. Nitrate and nitrite are not reduced. Starch, aesculin and Tween 80 are hydrolyzed, but agar, casein and gelatin are not hydrolyzed. Glucose, sucrose, arabinose, mannose and maltose are utilized as sole carbon source while mannitol, N-acetylglucosamine, gluconate, caprate, adipate, malate, citrate and phenylacetate are not utilized. Acid is produced from cellobiose, but not from glucose. Cells are positive for α-glucosidase, β-glucosidase, β-galactosidase, α-mannosidase, alkaline phosphatase, acid phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, naphthol-AS-BI-phosphohydrolase and N-acetyl-β-glucosaminidase and negative for the other enzyme activities tested by the API ZYM (bioMérieux) panel [1].
Figure 2.

Scanning electron micrograph of J. marina En5T

Chemotaxonomy

Major fatty acids (>10% of total) are branched-chain acids iso-C15:0, iso-C17:0 3-OH and iso-C17:1 ω 9 c and an unidentified fatty acid (ECL 13.566); minor amounts (>5%-<10%) are iso-C15:1 and summed feature 3 comprising C16:1 ω 7 c and/or iso-C15:0 2-OH. It should be noted that the original paper indicates that the fatty acid composition was determined using the MIDI system and in the peak naming tables iso-C15:1 is usually not listed without the addition of further information (e.g. iso-C15:1 F, iso-C15:1 G, iso-C15:1 H, with the capital letters indicating different isomers where the location of the double bond is not determined). Herzog et al. [36], have indicated that the fatty acid listed as iso-C17:1 ω 9 c may be incorrectly annotated in the MIDI system. Furthermore the resolution of summed feature 3 into C16:1 ω 7 c and/or iso-C15:0 2-OH is also significant in understanding the membrane structure/function as well as the evolution of the underlying biochemical pathways, since the synthesis of 2-OH fatty acids requires a specific enzyme, whereas the synthesis of unsaturated fatty acids (with different positions of unsaturation) also requires a specific set of enzymes. MK-6 is the major respiratory quinone. The DNA G+C content was initially reported with 30.1 mol% [1], much lower than the 33.6% inferred from the genome sequence (see in third table). No information is available for the peptidoglycan composition as this feature is not listed as a minimal standard for the descriptions of novel Flavobacteriaceae species [33]. No data is available on the polar lipid composition.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [37], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [38]. The genome project is deposited in the Genomes OnLine Database [17] 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 [39]. A summary of the project information is shown in Table 2.
Table 1.

Classification and general features of J. marina En5T according to the MIGS recommendations [24].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [25]

 

Phylum Bacteroidetes

TAS [26,27]

 

Class Flavobacteriia

TAS [2830]

 

Order Flavobacteriales

TAS [27,31]

 

Family Flavobacteriaceae

TAS [5,6,32,33]

 

Genus Joostella

TAS [1]

MIGS-7

 

Species Joostella marina

TAS [1]

MIGS-12

Subspecific genetic lineage (strain)

En5T

TAS [1]

 

Reference for biomaterial

Quan et al. 2008

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

non-motile

TAS [1]

 

Sporulation

non-sporulating

TAS [1]

 

Temperature range

10–37°C

TAS [1]

 

Optimum temperature

30°C

TAS [1]

MIGS-22

Salinity

0–15% NaCl, optimally 1–3% NaCl

TAS [1]

 

Relationship to oxygen

obligate aerobe

TAS [1]

 

Carbon source

monosaccarides

TAS [1]

MIGS-6

Energy metabolism

not reported

 

MIGS-6.2

Habitat

mud

TAS [1]

MIGS-15

pH

optimum 5.3 – 7.6

TAS [1]

MIGS-14

Biotic relationship

free living

TAS [1]

MIGS-16

Known pathogenicity

not reported

 

MIGS-18

Specific host

none

NAS

 

Health status of host

not reported

 

MIGS-19

Biosafety level

1

TAS [34]

MIGS-23.1

Trophic level

not reported

 

MIGS-4

Isolation

coastal seawater

TAS [1]

MIGS-5

Geographic location

East Sea of Korea

TAS [1]

MIGS-4.1

Time of sample collection

May 2007

NAS

MIGS-4.2

Latitude

not reported

 

MIGS-4.3

Longitude

not reported

 

MIGS-4.4

Depth

100 m

TAS [1]

 

Altitude

−100 m

TAS [1]

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 [35].

Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved high quality draft

MIGS-28

Libraries used

Two genomic libraries: one 454 PE library (8 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

1,149.8 × Illumina; 8.6 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3-PreRelease-6/30/2009, Velvet 1.0.13, phrap version 1.080812

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

AJUG00000000

 

GenBank Date of Release

May 4, 2012

 

GOLD ID

Gi05349

 

NCBI project ID

65069

 

Database: IMG

2509276026

MIGS-13

Source material identifier

DSM 19592

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

J. marina strain En5T, DSM 19592, was grown in DSMZ medium 514 (Bacto Marine Broth, DIFCO 2216) [40] at 28°C. DNA was isolated from 1–1.5 g of cell paste using Jetflex Genomic DNA Purification Kit (GENOMED 600100) following the standard protocol as recommended by the manufacturer with modification but with additional 10 µl proteinase K digestion for cell lysis (40 min incubation at 58°C). DNA is available through the DNA Bank Network [41].

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 [42]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly, consisting of 240 contigs in 6 scaffolds, was converted into a phrap [43] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (5,373.5 Mb) was assembled with Velvet [44] 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 76.9 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 21. The Phred/Phrap/Consed software package [43] 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 [42], Dupfinisher [45], or by 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 193 additional reactions and one shatter library were necessary to close some gaps and to raise the quality of the final contigs. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [46]. 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 1,158.4 × coverage of the genome. The final assembly contained 219,876 pyrosequence and 68,081,556 Illumina reads.

Genome annotation

Genes were identified using Prodigal [47] as part of the DOE-JGI genome annotation pipeline [48], followed by a round of manual curation using the GenePRIMP pipeline [49]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [50].

Genome properties

The genome statistics are provided in Table 3 and Figure 3. The improved-high-quality-draft genome consists of two scaffolds with a length of 3,959,031 bp and 558,212 bp, respectively, and a G+C content of 33.6%. Of the 4,004 genes predicted, 3,944 were protein-coding genes, and 60 RNAs; 86 pseudogenes were also identified. The majority of the protein-coding genes (69.4%) 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.
Figure 3.

Graphical maps of the largest, 3.96 Mbp long, scaffold. From bottom to top: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew (purple/olive).

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

4,508,243

100.00

DNA coding region (bp)

3,886,653

86.21

DNA G+C content (bp)

1,514,507

33.59

Number of scaffolds

2

 

Extrachromosomal elements

unknown

 

Total genes

4,004

100.00

RNA genes

60

1.50

rDNA operons

3

 

tRNA genes

45

1.12

Protein-coding genes

3,944

98.50

Pseudo genes

86

2.15

Genes with function prediction

2,777

69.36

Genes in paralog clusters

2,029

50.67

Genes assigned to COGs

2,678

66.88

Genes assigned Pfam domains

3,099

77.40

Genes with signal peptides

1,055

26.35

Genes with transmembrane helices

940

23.48

CRISPR repeats

1

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

153

5.29

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

203

7.01

Transcription

L

225

7.77

Replication, recombination and repair

B

0

0.00

Chromatin structure and dynamics

D

23

0.79

Cell cycle control, cell division, chromosome partitioning

Y

0

0.00

Nuclear structure

V

50

1.73

Defense mechanisms

T

123

4.25

Signal transduction mechanisms

M

222

7.67

Cell wall/membrane/envelope biogenesis

N

6

0.21

Cell motility

Z

0

0.00

Cytoskeleton

W

0

0.00

Extracellular structures

U

62

2.14

Intracellular trafficking, secretion, and vesicular transport

O

119

4.11

Posttranslational modification, protein turnover, chaperones

C

133

4.60

Energy production and conversion

G

189

6.53

Carbohydrate transport and metabolism

E

211

7.29

Amino acid transport and metabolism

F

64

2.21

Nucleotide transport and metabolism

H

144

4.98

Coenzyme transport and metabolism

I

97

3.35

Lipid transport and metabolism

P

206

7.12

Inorganic ion transport and metabolism

Q

50

1.73

Secondary metabolites biosynthesis, transport and catabolism

R

346

11.96

General function prediction only

S

268

9.26

Function unknown

-

1326

33.12

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Helga Pomrenke for growing J. marina 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 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.

Authors’ Affiliations

(1)
Leibniz-Institute, DSMZ - German Collection of Microorganisms and Cell Cultures
(2)
DOE Joint Genome Institute
(3)
Bioscience Division, Los Alamos National Laboratory
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
HZI - Helmholtz Centre for Infection Research
(6)
University of California Davis Genome Center
(7)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

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