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. 2015 Jun 14;5:241–253. doi: 10.1016/j.gdata.2015.06.010

Draft genome sequence of Paenibacillus dauci sp. nov., a carrot-associated endophytic actinobacteria

Qian Wu a,1, Liying Zhu c,1, Ling Jiang b,⁎, Xian Xu a, Qing Xu a, Zhidong Zhang d, He Huang a
PMCID: PMC4583675  PMID: 26484263

Abstract

Paenibacillus dauci sp. nov., a new kind of endophytic actinobacteria, is separated from the inner tissues of carrot sample, which forms intimated associations with carrot acting as biological control agents. Here we report a 5.37-Mb assembly of its genome sequence and other useful information, including the coding sequences (CDSs) responsible for biological processes such as antibiotic metabolic process, antimicrobial metabolism, anaerobic regulation and the biosynthesis of vitamin B and polysaccharide. This novel strain can be a potential source of novel lead products for exploitation in the field of pharmaceutical, agriculture and industry.

Keywords: Paenibacillus dauci, Endophytic actinobacteria, Genome analysis

Specifications
Organism/cell/tissue Paenibacillus dauci sp. nov.
Strain H9T
Sequencer or array type Illumina Hiseq 2000
Data format Raw and processed
Experimental factors DNA extracted from a wild-type strain, no treatment
Experimental features Draft genome sequencing of Paenibacillus dauci, assembly and annotation
Consent N/A
Sample source location A carrot sample from Xinjiang Uyghur Autonomous Region (China)
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1. Direct link to deposited data

Deposited data can be found here: http://www.ncbi.nlm.nih.gov/nuccore/LAQQ00000000.

Endophytic actinobacteria have a capacity to produce numerous secondary metabolites with a mass of biological activity, such as antibiotics, antitumor and anti-infection agents, plant growth promoters and enzymes, and may promote plant establishment under adverse environmental stresses [1]. Introducing such bacterial strains to plant tissues can result in increased plant growth, usually due to suppression of plant pathogenic microorganisms [2]. It seems to be pivotal for obtaining a healthy microfloral balance within plants, soil appearing to be an important and moderating source of bacterial endophytes [3]. Recently, our group has isolated from a carrot sample from Xinjiang Uyghur Autonomous Region (China) a novel species of Paenibacillus dauci sp. nov. (= CGMCC 100608T = JCM30283T), which can produce potential antimicrobial substances playing the part of endophytic actinobacteria [4]. Comparisons with 16S rRNA gene sequences as shown in Fig. 1 revealed that the novel strain had the highest similarity to Paenibacillus hunanensis FeL05T (97%). However, the phylogenetic distances from recognized species (Fig. 2) indicated that P. dauci sp. nov. is not affiliated to any of these recognized species. We can therefore conclude that this strain represents a novel species of the genus Paenibacillus. What's more, high nitrogenase activity, strong antagonism against plant pathogenic fungi, extensive carbon source utilization, and stress resistance were also uncovered. In consequence, investigation of the genetic information and characteristics of P. dauci is desired to further investigate its mechanism of metabolic regulation. Knowledge of the genome sequence and bioinformatics will be of great help in this regard.

Fig. 1.

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Multiple sequence alignment of Paenibacillus (taichungen: Paenibacillus taichungen strain JN1; dauci: Paenibacillus dauci; polymyxa: Paenibacillus polymyxa strain YRL13; wulumuqien: Paenibacillus wulumuqiensis; FeL05: Paenibacillus hunanensis strain FeL05; FeL11: Paenibacillus hunanensis strain FeL11; IHB: Paenibacillus sp. IHB B2283; Ch380: Paenibacillus sp. Ch380; SG3: Paenibacillus sp. SG3; B17a: Paenibacillus sp. B17a; pabuli: Paenibacillus pabuli; HA39: Paenibacillus sp. HA39; HA62: Paenibacillus sp. HA62; p33: Paenibacillus sp. P33; CH-3: Paenibacillus sp. CH-3; hunanensis: Paenibacillus hunanensis strain Y22; BD3526: Paenibacillus sp. BD3526; YQ1: Paenibacillus sp. YQ1).

Fig. 2.

Fig. 2

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Phylogenetic tree analysis of Paenibacillus dauci sp. nov. in this study and other strains belonging to the genus Paenibacillus (MEGA 3.1).

Here we present the draft genome sequence of strain P. dauci H9T obtained using the Illumina Hiseq 2000 system, which was performed by Shenzhen BGI. Tech. Co., Ltd. The reads were assembled with SOAPdenovo [5], [6], the version is 2.04, and the sequence was annotated using the RAST annotation server (Fig. 3) [7]. A library containing 500-bp inserts was constructed. Sequencing was performed based on the paired-end strategy of 473 reads to produce 790 Mb of filtered sequences, representing a 126-fold coverage of the genome. The sequence of Paenibacillus algorifonticola XJ259T is 5,449,237 bases with a G + C content of 46.5%, which was assembled into 26 contigs and 19 scaffolds. It contains 4766 open reading frames (ORFs), 77 tRNA genes, and 1 rRNA gene (Table 1) identified by Glimmer 3.02 [8], Genemark [9], tRNAscan-SE [10], and RNAmmer [11].

Fig. 3.

Fig. 3

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COG function classification of Paenibacillus dauci sp. nov. (B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolite biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms).

Table 1.

General features of Paenibacillus dauci sp. nov. draft genome.

Specifications
Organism/cell/tissue Paenibacillus dauci sp. nov.
Strain H9T
Sequencer or array type Illumina Hiseq 2000
Data format Raw and processed
Experimental factors DNA extracted from a wild-type strain, no treatment
Experimental features Draft genome sequencing of Paenibacillus dauci, assembly and annotation
Consent N/A
Sample source location a carrot sample from Xinjiang Uyghur Autonomous Region (China)
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According to the genomic analysis of strain P. dauci, we analyzed 36 ORFs related to antibiotic metabolic process. 10 ORFs related to the antimicrobial peptide transport system. 4 ORFs about plant growth promoting (PGP) were found. Additionally, 12 ORFs were also discovered related to trehalose, which makes us believe that it could be related to the shock-resistant mechanism since the trehalose is regarded as a molecular chaperone. What's more, the biosynthesis of vitamin B was annotated in the strain P. dauci as there were 19 ORFs related to vitamin B12 production and vitamin B6 metabolism. Further studies will be performed to confirm their functions, and a complete genome sequence will be included in the future to reveal the unique molecular characteristics of strain P. dauci.

2. Nucleotide sequence accession numbers

This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number LAQQ00000000. The version described in this paper is the first version, with accession number LAQQ01000000.

Conflict of interest

The authors declare that there is no conflict of interest on any work published in this paper.

Acknowledgments

This work was supported by the National Science Foundation for Young Scholars of China (21225626, 21406111), the National High Technology Research and Development Program of China (2012AA022101, 2012AA021700), the Natural Science Foundation of Jiangsu Province (BK20131406, BK20130917), and the Natural Science Foundation for Colleges and Universities in Jiangsu Province (14KJB530003).

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