Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina

Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from... GENOME ANNOUNCEMENT The Burkholderia genus comprises >80 validly described species, isolated from diverse niches in nature. Species within the Burkholderia cepacia complex (Bcc) are mainly recognized as opportunistic pathogens of cystic fibrosis or immunocompromised patients ( 1 , 2 ). However, several Burkholderia species have also been isolated from diverse ecological niches, such as agricultural soils, root nodules, the gut microbiota of insects, contaminated soils, endophytes of leaves or plant roots, and the interior of spores or fungi mycelia, indicating the wide versatility of this genus ( 3 – 12 ). The whole-genome shotgun sequencing of Burkholderia cordobensis type strain LMG 27620, isolated from an agricultural soil in Córdoba Province, Argentina, was performed ( 13 ). Genomic DNA was extracted from tryptone soybean agar cultures using the method of Pitcher et al. ( 14 ). The genome was sequenced by Macrogen, Inc. (Geumcheon-gu, Seoul, Republic of Korea) using an Illumina HiSeq 2000 sequencing platform. A total of 1,002,545,392 reads were obtained, with a G+C content of 62.5%. Paired-end reads (2 × 100 bp) were trimmed and assembled de novo using the A5 pipeline, obtaining 69 scaffolds (longest scaffold, 1,508,897 bp; N 50 , 70,128 bp) with 105× coverage ( 15 ). Scaffolds were ordered in Mauve ( 16 ) with the genome of B. cordobensis YI23 as a reference. The genome consists of 9,044,501 bp. Automatic gene prediction and functional annotation were carried out by using the RAST server ( 17 ), revealing 8,556 protein-coding sequences, 55 tRNAs, 3 rRNAs, and 43 ribosomal proteins. Several Burkholderia species are able to degrade xenobiotic compounds. In fact, phylogenetically closely related strains, such as B. cordobensis YI23, Burkholderia sp. SJ98, Burkholderia jiangsuensis MP-1, and Burkholderia zhejiangensis OP-1, have been isolated from polluted environments ( 18 – 20 ). It was previously shown that B. cordobensis YI23 and Burkholderia sp. SJ98 share a gene cluster involved in chemotaxis toward compounds that they degrade, such as chloronitroaromatic compounds ( 21 , 22 ). B. cordobensis LMG 27620 also harbors the same cluster of chemotaxis genes. In addition, several genes of biotechnological interest were detected. Phenol monooxygenase genes and its regulator genes and paraquat-induced proteins were also found in the LMG 27620 genome. In addition, genes involved in biocontrol process were present, as chitinases and N -acetylglucosamine utilization were observed. Overall, the evidence presented here turns this strain into a biotechnological potential microorganism to be involved in pest biological control and biodegradation of pollutants in contaminated environments. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LGRC00000000 . The version described in this paper is version LGRC01000000. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Genome Announcements PubMed Central

Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina

Genome Announcements, Volume 3 (5) – Oct 22, 2015

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Publisher
PubMed Central
Copyright
Copyright © 2015 Draghi et al.
eISSN
2169-8287
D.O.I.
10.1128/genomeA.01238-15
Publisher site
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Abstract

GENOME ANNOUNCEMENT The Burkholderia genus comprises >80 validly described species, isolated from diverse niches in nature. Species within the Burkholderia cepacia complex (Bcc) are mainly recognized as opportunistic pathogens of cystic fibrosis or immunocompromised patients ( 1 , 2 ). However, several Burkholderia species have also been isolated from diverse ecological niches, such as agricultural soils, root nodules, the gut microbiota of insects, contaminated soils, endophytes of leaves or plant roots, and the interior of spores or fungi mycelia, indicating the wide versatility of this genus ( 3 – 12 ). The whole-genome shotgun sequencing of Burkholderia cordobensis type strain LMG 27620, isolated from an agricultural soil in Córdoba Province, Argentina, was performed ( 13 ). Genomic DNA was extracted from tryptone soybean agar cultures using the method of Pitcher et al. ( 14 ). The genome was sequenced by Macrogen, Inc. (Geumcheon-gu, Seoul, Republic of Korea) using an Illumina HiSeq 2000 sequencing platform. A total of 1,002,545,392 reads were obtained, with a G+C content of 62.5%. Paired-end reads (2 × 100 bp) were trimmed and assembled de novo using the A5 pipeline, obtaining 69 scaffolds (longest scaffold, 1,508,897 bp; N 50 , 70,128 bp) with 105× coverage ( 15 ). Scaffolds were ordered in Mauve ( 16 ) with the genome of B. cordobensis YI23 as a reference. The genome consists of 9,044,501 bp. Automatic gene prediction and functional annotation were carried out by using the RAST server ( 17 ), revealing 8,556 protein-coding sequences, 55 tRNAs, 3 rRNAs, and 43 ribosomal proteins. Several Burkholderia species are able to degrade xenobiotic compounds. In fact, phylogenetically closely related strains, such as B. cordobensis YI23, Burkholderia sp. SJ98, Burkholderia jiangsuensis MP-1, and Burkholderia zhejiangensis OP-1, have been isolated from polluted environments ( 18 – 20 ). It was previously shown that B. cordobensis YI23 and Burkholderia sp. SJ98 share a gene cluster involved in chemotaxis toward compounds that they degrade, such as chloronitroaromatic compounds ( 21 , 22 ). B. cordobensis LMG 27620 also harbors the same cluster of chemotaxis genes. In addition, several genes of biotechnological interest were detected. Phenol monooxygenase genes and its regulator genes and paraquat-induced proteins were also found in the LMG 27620 genome. In addition, genes involved in biocontrol process were present, as chitinases and N -acetylglucosamine utilization were observed. Overall, the evidence presented here turns this strain into a biotechnological potential microorganism to be involved in pest biological control and biodegradation of pollutants in contaminated environments. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LGRC00000000 . The version described in this paper is version LGRC01000000.

Journal

Genome AnnouncementsPubMed Central

Published: Oct 22, 2015

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