MARGEN-00294; No of Pages 2 Marine Genomics xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
1
Genomics/technical resources
4Q3
Qiang Zheng ⁎, Yanting Liu, Jia Sun, Nianzhi Jiao ⁎
5
State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
6
a r t i c l e
7 8 9 10 11
Article history: Received 28 January 2015 Received in revised form 7 February 2015 Accepted 8 February 2015 Available online xxxx
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Keywords: Erythrobacter Bacteriochlorophyll a Aerobic anoxygenic phototrophic bacteria South China Sea Genome sequence
a b s t r a c t
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1. Introduction
28 29
Aerobic anoxygenic phototrophic bacteria (AAPB) represent an important and widespread functional bacterial group defined by their obligate aerobic and facultative photoheterotrophic abilities in the ocean (Kolber et al., 2001; Jiao et al., 2007, 2010). They could utilize the light as energy supplementary for microbial metabolism and growth. The energy from the bacteriochlorophyll (BChl) a -based photosynthesis could be up to 20–30% of total energy requirements (Kolber et al., 2001). The abundance of AAPB takes up 1% to 15% in marine euphotic zone (Kolber et al., 2001; Jiao et al., 2007). AAPB are thought to play significant roles in the carbon and energy cycles in the upper oceans. Marine cultured AAPB are usually classified into Proteobacteria, including Alpha- and Gammaproteobacteria. The first isolate of marine AAPB established Erythrobacter genus (Alphaproteobacteria), Erythrobacter longus strain DSM 6997 (Shiba, 1984). Here we report the draft genome of AAPB strain Erythrobacter sp. JL475 (=MCCC 1F00069) isolated from the South China Sea. The draft genomes of strain JL475 were obtained by Illumina pair-end sequencing technology. Two libraries with average sizes of 150 and 500 bps were constructed, respectively. Mate-paired reads of average 100-bp length were assembled using Velvet software (v1.2.03) and total read size of ~ 2.5 Gbp was obtained (Zerbino and Birney, 2008). Total contig size of ~3.26 Mbp with an average of 780× coverage was obtained. The overall G + C content of strain JL475 was 61.7% (Table 1).
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Erythrobacter sp. JL475 is a bacteriochlorophyll a-containing aerobic anoxygenic photo-heterotrophic bacterium. Here, we report the draft genome sequence of Erythrobacter sp. JL475 isolated from the South China Sea. It comprises ~3.26 Mbp in 7 contigs with the G + C content of 61.7%. A total of 3042 protein-coding genes were obtained, and one complete photosynthetic gene cluster (~38 Kbp) was found. © 2015 Published by Elsevier B.V.
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Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea
2Q2
⁎ Corresponding authors. E-mail addresses: [email protected] (Q. Zheng), [email protected] (N. Jiao).
The open reading frames (ORFs) were analyzed using Glimmer 3.02 software (Delcher et al., 2007). tRNAscan-SE (v1.21) was used to identify the tRNA genes (Lowe and Eddy, 1997), and rRNA identification performed by RNAmmer 1.2 software (Lagesen et al., 2007). A total of 3042 protein-coding genes was obtained (Table 1). 3 rRNAs and 44 tRNAs existed in the genome (Table 1). The predicted ORFs were annotated through comparisons with the NCBI-nr database and KEGG protein database (Kanehisa et al., 2008). The functional genes were then identified by association with clusters of orthologous groups' (COGs) classification against the conserved domains' database (Marchler-Bauer et al., 2013) and the KEGG pathway collection (Moriya et al., 2007). 2168 proteins matched to known functions in the genome. There were 2314 proteins and 1427 proteins that were classified to COG categories and KEGG orthologs respectively. One complete photosynthesis gene cluster (PGC) was found in the genome of strain JL475, and it consisted of two typical subclusters: bchIDO-
51 52
Table 1 General genomic features of Erythrobacter sp. JL475 and NAP1.
t1:1 Q1 t1:2
Assembly size (bp) G + C content (%) Contigs Protein-coding genes 5S rRNA genes 16S rRNA genes 23S rRNA genes tRNA genes
53 54 55 56 57 58 59 60 61 62 63 64 65 66
Erythrobacter sp. JL475
Erythrobacter sp. NAP1
t1:3
3,263,324 61.7 7 3042 1 1 1 44
3,266,173 60.9 4 3177 1 1 1 45
t1:4 t1:5 t1:6 t1:7 t1:8 t1:9 t1:10 t1:11
http://dx.doi.org/10.1016/j.margen.2015.02.006 1874-7787/© 2015 Published by Elsevier B.V.
Please cite this article as: Zheng, Q., et al., Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.02.006
2
Q. Zheng et al. / Marine Genomics xxx (2015) xxx–xxx
Fig. 1. The structure and composition of PGC in Erythrobacter sp. JL475. Green, bch genes; red, puf and regulators genes; pink, puh genes; orange, crt genes. The horizontal arrows represent putative transcripts. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
90
Acknowledgments
91
This work was supported by the 973 program (2013CB955700) and the SOA project (GASI-03-01-02-05) to NJ, and the NSFC project (41306126) and Fundamental Research Funds for the Central Universities (2013121051) to QZ.
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The data from this whole-genome shotgun project have been deposited at DDBJ/EMBL/GenBank under accession number JMIV00000000. The version described in this paper is the first version, with accession number JMIV01000000.
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Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Jiao, N., Zhang, Y., Zeng, Y., Hong, N., Liu, R., Chen, F., Wang, P., 2007. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ. Microbiol. 9, 3091–3099. Jiao, N., Zhang, F., Hong, N., 2010. Significant roles of bacteriochlorophyll a supplemental to chlorophyll a in the ocean. ISME J. 4, 595–597. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y., 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484. Koblížek, M., Béjà, O., Bidigare, R.R., Christensen, S., Benitez-Nelson, B., Vetriani, C., Kolber, M.K., Falkowski, P.G., Kolber, Z.S., 2003. Isolation and characterization of Erythrobacter sp. strains from the upper ocean. Arch. Microbiol. 180, 327–338. Koblížek, M., Janouškovec, J., Oborník, M., Johnson, J.H., Ferriera, S., Falkowski, P.G., 2011. Genome sequence of the marine photoheterotrophic bacterium Erythrobacter sp. strain NAP1. J Bacteriol 193, 5881–5882. Kolber, Z.S., Gerald, F., Lang, A.S., Beatty, J.T., Blankenship, R.E., VanDover, C.L., Vetriani, C., Koblizek, M., Rathgeber, C., Falkowski, P.G., 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292, 2492–2495. Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35, 3100–3108. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Marchler-Bauer, A., Zheng, C., Chitsaz, F., Derbyshire, M.K., Geer, L.Y., Geer, R.C., Gonzales, N.R., Gwadz, M., Hurwitz, D.I., Lanczycki, C.J., Lu, F., Lu, S., Marchler, G.H., Song, J.S., Thanki, N., Yamashita, R.A., Zhang, D., Bryant, S.H., 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41, 348–352. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, 182–185. Shiba, T., 1984. Utilization of light energy by the strictly aerobic bacterium Erythrobacter sp. OCh 114. J. Gen. Appl. Microbiol. 30, 239–244. Zerbino, D.R., Birney, E., 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829. Zheng, Q., Zhang, R., Koblížek, M., Boldareva, E.N., Yurkov, V., Yan, S., Jiao, N., 2011. Diverse arrangement of photosynthetic gene clusters in aerobic anoxygenic phototrophic bacteria. PLoS One 6, e25050. http://dx.doi.org/10.1371/journal.pone.0025050. Zheng, Q., Koblížek, M., Beatty, J.T., Jiao, N., 2013. Evolutionary divergence of marine aerobic anoxygenic phototrophic bacteria as seen from diverse organizations of their photosynthesis gene clusters. In: Thomas Beatty, J. (Ed.), Advances in Botanical Research, pp. 359–383.
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2. Nucleotide sequence accession numbers
71 72
95
P
85
69 70
References
D
83 84
crtCDF-bchCXYZ-pufBALM and bchFNBHLM-lhaA-puhABC (Fig. 1). The PGC organization in strain JL475 was almost identical to Erythrobacter sp. NAP1 in terms of gene arrangement and composition (Koblížek et al., 2003, 2011). The PGC arrangement in strain JL475 belonged to type III (forward crtF-bchCXYZ-puf plus forward bchFNBHLM-LhaA-puh) (Zheng et al., 2011, 2013). There were less crt genes in the PGC of strain JL475, that was consistent with the relatively small sizes of its genome and PGC compared to AAPB in Roseobacters. However, some crt genes were found out of the PGC in the chromosome. In addition, genes coding for flagellum formation were present as revealed by a detailed inspection of the genome sequence. An integrative conjugative element was detected in the genome, which was a selftransmissible mobile genetic element that mediated lateral gene transfer between prokaryotes. Type IV secretion system was also identified, and it contained one seven-gene cluster: virB2B3B4-virB6-virB9B10B11. The genomic data of strain JL475 would contribute to the increasing scope and depth of AAPB genomes' database, and to clarify their evolutionary history and environmental adaption mechanism in the future.
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Please cite this article as: Zheng, Q., et al., Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.02.006
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
1
Genomics/technical resources
4Q3
Qiang Zheng ⁎, Yanting Liu, Jia Sun, Nianzhi Jiao ⁎
5
State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
6
a r t i c l e
7 8 9 10 11
Article history: Received 28 January 2015 Received in revised form 7 February 2015 Accepted 8 February 2015 Available online xxxx
12 13 14 15 16 17
Keywords: Erythrobacter Bacteriochlorophyll a Aerobic anoxygenic phototrophic bacteria South China Sea Genome sequence
a b s t r a c t
E T C
25
1. Introduction
28 29
Aerobic anoxygenic phototrophic bacteria (AAPB) represent an important and widespread functional bacterial group defined by their obligate aerobic and facultative photoheterotrophic abilities in the ocean (Kolber et al., 2001; Jiao et al., 2007, 2010). They could utilize the light as energy supplementary for microbial metabolism and growth. The energy from the bacteriochlorophyll (BChl) a -based photosynthesis could be up to 20–30% of total energy requirements (Kolber et al., 2001). The abundance of AAPB takes up 1% to 15% in marine euphotic zone (Kolber et al., 2001; Jiao et al., 2007). AAPB are thought to play significant roles in the carbon and energy cycles in the upper oceans. Marine cultured AAPB are usually classified into Proteobacteria, including Alpha- and Gammaproteobacteria. The first isolate of marine AAPB established Erythrobacter genus (Alphaproteobacteria), Erythrobacter longus strain DSM 6997 (Shiba, 1984). Here we report the draft genome of AAPB strain Erythrobacter sp. JL475 (=MCCC 1F00069) isolated from the South China Sea. The draft genomes of strain JL475 were obtained by Illumina pair-end sequencing technology. Two libraries with average sizes of 150 and 500 bps were constructed, respectively. Mate-paired reads of average 100-bp length were assembled using Velvet software (v1.2.03) and total read size of ~ 2.5 Gbp was obtained (Zerbino and Birney, 2008). Total contig size of ~3.26 Mbp with an average of 780× coverage was obtained. The overall G + C content of strain JL475 was 61.7% (Table 1).
38 39 40Q6 41 42 43 44 45 46 47 48 49 50
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N C O
36 37 Q5
U
34 35 Q4
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18 19 20 21 22
D
P
Erythrobacter sp. JL475 is a bacteriochlorophyll a-containing aerobic anoxygenic photo-heterotrophic bacterium. Here, we report the draft genome sequence of Erythrobacter sp. JL475 isolated from the South China Sea. It comprises ~3.26 Mbp in 7 contigs with the G + C content of 61.7%. A total of 3042 protein-coding genes were obtained, and one complete photosynthetic gene cluster (~38 Kbp) was found. © 2015 Published by Elsevier B.V.
26 24 23
30 31
O
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i n f o
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Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea
2Q2
⁎ Corresponding authors. E-mail addresses: [email protected] (Q. Zheng), [email protected] (N. Jiao).
The open reading frames (ORFs) were analyzed using Glimmer 3.02 software (Delcher et al., 2007). tRNAscan-SE (v1.21) was used to identify the tRNA genes (Lowe and Eddy, 1997), and rRNA identification performed by RNAmmer 1.2 software (Lagesen et al., 2007). A total of 3042 protein-coding genes was obtained (Table 1). 3 rRNAs and 44 tRNAs existed in the genome (Table 1). The predicted ORFs were annotated through comparisons with the NCBI-nr database and KEGG protein database (Kanehisa et al., 2008). The functional genes were then identified by association with clusters of orthologous groups' (COGs) classification against the conserved domains' database (Marchler-Bauer et al., 2013) and the KEGG pathway collection (Moriya et al., 2007). 2168 proteins matched to known functions in the genome. There were 2314 proteins and 1427 proteins that were classified to COG categories and KEGG orthologs respectively. One complete photosynthesis gene cluster (PGC) was found in the genome of strain JL475, and it consisted of two typical subclusters: bchIDO-
51 52
Table 1 General genomic features of Erythrobacter sp. JL475 and NAP1.
t1:1 Q1 t1:2
Assembly size (bp) G + C content (%) Contigs Protein-coding genes 5S rRNA genes 16S rRNA genes 23S rRNA genes tRNA genes
53 54 55 56 57 58 59 60 61 62 63 64 65 66
Erythrobacter sp. JL475
Erythrobacter sp. NAP1
t1:3
3,263,324 61.7 7 3042 1 1 1 44
3,266,173 60.9 4 3177 1 1 1 45
t1:4 t1:5 t1:6 t1:7 t1:8 t1:9 t1:10 t1:11
http://dx.doi.org/10.1016/j.margen.2015.02.006 1874-7787/© 2015 Published by Elsevier B.V.
Please cite this article as: Zheng, Q., et al., Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.02.006
2
Q. Zheng et al. / Marine Genomics xxx (2015) xxx–xxx
Fig. 1. The structure and composition of PGC in Erythrobacter sp. JL475. Green, bch genes; red, puf and regulators genes; pink, puh genes; orange, crt genes. The horizontal arrows represent putative transcripts. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
90
Acknowledgments
91
This work was supported by the 973 program (2013CB955700) and the SOA project (GASI-03-01-02-05) to NJ, and the NSFC project (41306126) and Fundamental Research Funds for the Central Universities (2013121051) to QZ.
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The data from this whole-genome shotgun project have been deposited at DDBJ/EMBL/GenBank under accession number JMIV00000000. The version described in this paper is the first version, with accession number JMIV01000000.
75 76
96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136
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Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Jiao, N., Zhang, Y., Zeng, Y., Hong, N., Liu, R., Chen, F., Wang, P., 2007. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ. Microbiol. 9, 3091–3099. Jiao, N., Zhang, F., Hong, N., 2010. Significant roles of bacteriochlorophyll a supplemental to chlorophyll a in the ocean. ISME J. 4, 595–597. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y., 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484. Koblížek, M., Béjà, O., Bidigare, R.R., Christensen, S., Benitez-Nelson, B., Vetriani, C., Kolber, M.K., Falkowski, P.G., Kolber, Z.S., 2003. Isolation and characterization of Erythrobacter sp. strains from the upper ocean. Arch. Microbiol. 180, 327–338. Koblížek, M., Janouškovec, J., Oborník, M., Johnson, J.H., Ferriera, S., Falkowski, P.G., 2011. Genome sequence of the marine photoheterotrophic bacterium Erythrobacter sp. strain NAP1. J Bacteriol 193, 5881–5882. Kolber, Z.S., Gerald, F., Lang, A.S., Beatty, J.T., Blankenship, R.E., VanDover, C.L., Vetriani, C., Koblizek, M., Rathgeber, C., Falkowski, P.G., 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292, 2492–2495. Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35, 3100–3108. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Marchler-Bauer, A., Zheng, C., Chitsaz, F., Derbyshire, M.K., Geer, L.Y., Geer, R.C., Gonzales, N.R., Gwadz, M., Hurwitz, D.I., Lanczycki, C.J., Lu, F., Lu, S., Marchler, G.H., Song, J.S., Thanki, N., Yamashita, R.A., Zhang, D., Bryant, S.H., 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41, 348–352. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, 182–185. Shiba, T., 1984. Utilization of light energy by the strictly aerobic bacterium Erythrobacter sp. OCh 114. J. Gen. Appl. Microbiol. 30, 239–244. Zerbino, D.R., Birney, E., 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829. Zheng, Q., Zhang, R., Koblížek, M., Boldareva, E.N., Yurkov, V., Yan, S., Jiao, N., 2011. Diverse arrangement of photosynthetic gene clusters in aerobic anoxygenic phototrophic bacteria. PLoS One 6, e25050. http://dx.doi.org/10.1371/journal.pone.0025050. Zheng, Q., Koblížek, M., Beatty, J.T., Jiao, N., 2013. Evolutionary divergence of marine aerobic anoxygenic phototrophic bacteria as seen from diverse organizations of their photosynthesis gene clusters. In: Thomas Beatty, J. (Ed.), Advances in Botanical Research, pp. 359–383.
R O
2. Nucleotide sequence accession numbers
71 72
95
P
85
69 70
References
D
83 84
crtCDF-bchCXYZ-pufBALM and bchFNBHLM-lhaA-puhABC (Fig. 1). The PGC organization in strain JL475 was almost identical to Erythrobacter sp. NAP1 in terms of gene arrangement and composition (Koblížek et al., 2003, 2011). The PGC arrangement in strain JL475 belonged to type III (forward crtF-bchCXYZ-puf plus forward bchFNBHLM-LhaA-puh) (Zheng et al., 2011, 2013). There were less crt genes in the PGC of strain JL475, that was consistent with the relatively small sizes of its genome and PGC compared to AAPB in Roseobacters. However, some crt genes were found out of the PGC in the chromosome. In addition, genes coding for flagellum formation were present as revealed by a detailed inspection of the genome sequence. An integrative conjugative element was detected in the genome, which was a selftransmissible mobile genetic element that mediated lateral gene transfer between prokaryotes. Type IV secretion system was also identified, and it contained one seven-gene cluster: virB2B3B4-virB6-virB9B10B11. The genomic data of strain JL475 would contribute to the increasing scope and depth of AAPB genomes' database, and to clarify their evolutionary history and environmental adaption mechanism in the future.
E
67 68
U
N
C
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137
Please cite this article as: Zheng, Q., et al., Genome sequence of aerobic anoxygenic phototrophic bacterium Erythrobacter sp. JL475, isolated from the South China Sea, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.02.006
