PROKARYOTES
crossm Complete Genome Sequence of Arcobacter sp. Strain LFT 1.7 Isolated from Great Scallop (Pecten maximus) Larvae A. L. Diéguez,
J. L. Romalde
Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
ABSTRACT Arcobacter sp. strain LFT 1.7 was isolated from great scallop (Pecten max-
imus) larvae. Analysis of the 16S rRNA gene sequence showed that strain LFT 1.7 formed an independent lineage in the genus Arcobacter. The draft genome of LFT 1.7 was sequenced to determine the taxonomic position and ecological function of this strain.
T
he genus Arcobacter was described by Vandamme et al. in 1991 (1) to accommodate two species of Campylobacter—namely, C. nitrofigilis and C. cryaerophila. This genus presents a global distribution and it has been associated with a great diversity of environments and hosts. Some members of Arcobacter are considered emergent enteropathogens and zoonotic agents (2), responsible for diarrhea and peritonitis in humans (3) or abortions and mastitis in animals (4). Consumption of contaminated water or food is considered the principal transmission route, but this is not clear. So, numerous studies have been carried out to estimate the prevalence of Arcobacter spp. in diverse environments and hosts such as water or mollusks. Due to these studies, the number of known species within this genus considerably increased in the past decade (http://www.bacterio.net/arcobacter.html). The genome sequence of strain LFT 1.7 was obtained by Sistemas Genómicos (Valencia, Spain) using Illumina paired-end sequencing technology. The quality of the reads was analyzed using Trimmomatic version 0.32 (5). Genome assembly was performed using SPAdes version 3.6.1 (6), and QUAST (7). The resulting genome for LFT 1.7 consists of 451 contigs (⬎200 bp) of 3,617,612 bp and has a G⫹C content of 28.7%. The N50 contig size was 343,594 bp, with the largest contig being 1,211,507 bp. Automatic gene annotation was carried out by the Rapid Annotations using Subsystems Technology (RAST) server (8), and tRNAs were identified by tRNAscan-SE version 1.21 (9). The genome of LFT 1.7 contains 3,350 protein-encoding genes and 69 tRNAs. The annotation of the genome revealed 36 encoding regions of resistance to antibiotics, including beta-lactamase, and resistance to fluoroquinolones, as well as toxic compounds such as arsenic. This genome contains 74 genes related to nitrogen metabolism. Among them, 33 genes are involved in denitrification, with gene clusters encoding nitric oxide reductase, nitrous oxide reductase, and nitrite reductase. The other 41 genes are implicated in nitrate and nitrite ammonification, ammonia assimilation, dissimilatory nitrite reductase, or nitrosative stress. Also, 48 genes encoding bacterial hemoglobins and one flavohemoglobin were detected in the LFT 1.7 genome. These proteins confer protection from nitric oxide and nitrosative stress. The genome sequence of this strain will help in the study of the heterogeneity of the genus Arcobacter and the ecological function of this bacterium in different environments. Volume 5 Issue 6 e01617-16
Received 1 December 2016 Accepted 6 December 2016 Published 9 February 2017 Citation Diéguez AL, Romalde JL. 2017. Complete genome sequence of Arcobacter sp. strain LFT 1.7 isolated from great scallop (Pecten maximus) larvae. Genome Announc 5:e01617-16. https://doi.org/10.1128/ genomeA.01617-16. Copyright © 2017 Diéguez and Romalde. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to J. L. Romalde, [email protected].
genomea.asm.org 1
Diéguez and Romalde
Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MKCO00000000. The version described in this paper is the first version, MKCO01000000. ACKNOWLEDGMENTS This work was supported in part by project 245119 (REPROSEED) from KBBE-2009/ 1/2-11 Subprogram of the 7th Framework Programme (FP7), European Commission, and grant AGL2013-42628-R from the Ministerio de Economía y Competitividad (Spain).
REFERENCES 1. Vandamme P, Falsen E, Rossau R, Hoste B, Segers P, Tytgat R, De Ley J. 1991. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol 41:88 –103. https://doi.org/ 10.1099/00207713-41-1-88. 2. Ho HTK, Lipman LJA, Gaastra W. 2006. Arcobacter, what is known and unknown about a potential foodborne zoonotic agent! Vet Microbiol 115:1–13. https://doi.org/10.1016/j.vetmic.2006.03.004. 3. Vandenberg O, Dediste A, Houf K, Ibekwem S, Souayah H, Cadranel S, Douat N, Zissis G, Butzler JP, Vandamme P. 2004. Arcobacter species in humans. Emerg Infect Dis 10:1863–1867. https://doi.org/10.3201/ eid1010.040241. 4. Logan EF, Neill SD, Mackie DP. 1982. Mastitis in dairy cows associated with an aerotolerant campylobacter. Vet Rec 110:229 –230. https://doi.org/ 10.1136/vr.110.10.229. 5. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114 –2120. https://doi.org/ 10.1093/bioinformatics/btu170.
Volume 5 Issue 6 e01617-16
6. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714 –737. https://doi.org/ 10.1089/cmb.2013.0084. 7. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https:// doi.org/10.1093/bioinformatics/btt086. 8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 9. Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964. https://doi.org/10.1093/nar/25.5.0955.
genomea.asm.org 2
crossm Complete Genome Sequence of Arcobacter sp. Strain LFT 1.7 Isolated from Great Scallop (Pecten maximus) Larvae A. L. Diéguez,
J. L. Romalde
Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
ABSTRACT Arcobacter sp. strain LFT 1.7 was isolated from great scallop (Pecten max-
imus) larvae. Analysis of the 16S rRNA gene sequence showed that strain LFT 1.7 formed an independent lineage in the genus Arcobacter. The draft genome of LFT 1.7 was sequenced to determine the taxonomic position and ecological function of this strain.
T
he genus Arcobacter was described by Vandamme et al. in 1991 (1) to accommodate two species of Campylobacter—namely, C. nitrofigilis and C. cryaerophila. This genus presents a global distribution and it has been associated with a great diversity of environments and hosts. Some members of Arcobacter are considered emergent enteropathogens and zoonotic agents (2), responsible for diarrhea and peritonitis in humans (3) or abortions and mastitis in animals (4). Consumption of contaminated water or food is considered the principal transmission route, but this is not clear. So, numerous studies have been carried out to estimate the prevalence of Arcobacter spp. in diverse environments and hosts such as water or mollusks. Due to these studies, the number of known species within this genus considerably increased in the past decade (http://www.bacterio.net/arcobacter.html). The genome sequence of strain LFT 1.7 was obtained by Sistemas Genómicos (Valencia, Spain) using Illumina paired-end sequencing technology. The quality of the reads was analyzed using Trimmomatic version 0.32 (5). Genome assembly was performed using SPAdes version 3.6.1 (6), and QUAST (7). The resulting genome for LFT 1.7 consists of 451 contigs (⬎200 bp) of 3,617,612 bp and has a G⫹C content of 28.7%. The N50 contig size was 343,594 bp, with the largest contig being 1,211,507 bp. Automatic gene annotation was carried out by the Rapid Annotations using Subsystems Technology (RAST) server (8), and tRNAs were identified by tRNAscan-SE version 1.21 (9). The genome of LFT 1.7 contains 3,350 protein-encoding genes and 69 tRNAs. The annotation of the genome revealed 36 encoding regions of resistance to antibiotics, including beta-lactamase, and resistance to fluoroquinolones, as well as toxic compounds such as arsenic. This genome contains 74 genes related to nitrogen metabolism. Among them, 33 genes are involved in denitrification, with gene clusters encoding nitric oxide reductase, nitrous oxide reductase, and nitrite reductase. The other 41 genes are implicated in nitrate and nitrite ammonification, ammonia assimilation, dissimilatory nitrite reductase, or nitrosative stress. Also, 48 genes encoding bacterial hemoglobins and one flavohemoglobin were detected in the LFT 1.7 genome. These proteins confer protection from nitric oxide and nitrosative stress. The genome sequence of this strain will help in the study of the heterogeneity of the genus Arcobacter and the ecological function of this bacterium in different environments. Volume 5 Issue 6 e01617-16
Received 1 December 2016 Accepted 6 December 2016 Published 9 February 2017 Citation Diéguez AL, Romalde JL. 2017. Complete genome sequence of Arcobacter sp. strain LFT 1.7 isolated from great scallop (Pecten maximus) larvae. Genome Announc 5:e01617-16. https://doi.org/10.1128/ genomeA.01617-16. Copyright © 2017 Diéguez and Romalde. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to J. L. Romalde, [email protected].
genomea.asm.org 1
Diéguez and Romalde
Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MKCO00000000. The version described in this paper is the first version, MKCO01000000. ACKNOWLEDGMENTS This work was supported in part by project 245119 (REPROSEED) from KBBE-2009/ 1/2-11 Subprogram of the 7th Framework Programme (FP7), European Commission, and grant AGL2013-42628-R from the Ministerio de Economía y Competitividad (Spain).
REFERENCES 1. Vandamme P, Falsen E, Rossau R, Hoste B, Segers P, Tytgat R, De Ley J. 1991. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol 41:88 –103. https://doi.org/ 10.1099/00207713-41-1-88. 2. Ho HTK, Lipman LJA, Gaastra W. 2006. Arcobacter, what is known and unknown about a potential foodborne zoonotic agent! Vet Microbiol 115:1–13. https://doi.org/10.1016/j.vetmic.2006.03.004. 3. Vandenberg O, Dediste A, Houf K, Ibekwem S, Souayah H, Cadranel S, Douat N, Zissis G, Butzler JP, Vandamme P. 2004. Arcobacter species in humans. Emerg Infect Dis 10:1863–1867. https://doi.org/10.3201/ eid1010.040241. 4. Logan EF, Neill SD, Mackie DP. 1982. Mastitis in dairy cows associated with an aerotolerant campylobacter. Vet Rec 110:229 –230. https://doi.org/ 10.1136/vr.110.10.229. 5. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114 –2120. https://doi.org/ 10.1093/bioinformatics/btu170.
Volume 5 Issue 6 e01617-16
6. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714 –737. https://doi.org/ 10.1089/cmb.2013.0084. 7. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https:// doi.org/10.1093/bioinformatics/btt086. 8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 9. Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964. https://doi.org/10.1093/nar/25.5.0955.
genomea.asm.org 2
