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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

MRA00620-21
10.1128/MRA.00620-21
mra.00620-21
Genome Sequences
bacteriologyBacteriologyComplete Genome Sequence of Dickeya dadantii subsp. dieffenbachiae Strain S3-1, Isolated from a White-Flowered Calla Lily in Taiwan
https://orcid.org/0000-0003-4964-9620
Lee Yung-An a christinacabrera@example.com

Chen Kuan-Pei a
a Department of Life Science, Fu Jen Catholic University, Xin-zhuang District, New Taipei City, Taiwan, Republic of China
Editor Baltrus David A. University of Arizona

Citation Lee Y-A, Chen K-P. 2021. Complete genome sequence of Dickeya dadantii subsp. dieffenbachiae strain S3-1, isolated from a white-flowered calla lily in Taiwan. Microbiol Resour Announc 10:e00620-21. https://doi.org/10.1128/MRA.00620-21.

16 9 2021
9 2021
16 9 2021
10 37 e00620-2117 6 2021
23 8 2021
Copyright © 2021 Lee and Chen.
2021
Lee and Chen.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Erwinia chrysanthemi S3-1 is a bacterial soft rot pathogen of the white-flowered calla lily. The complete genome sequence of the strain was determined and used to reclassify the strain as Dickeya dadantii subsp. dieffenbachiae. The sequence will be useful to study plant host-driven speciation in strains of D. dadantii.

Council of Agriculture (COA) https://doi.org/10.13039/100007841 100AS-5.4.2-BQ-B6 Lee Yung-An cover-dateSeptember 2021
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pmcANNOUNCEMENT

Erwinia chrysanthemi S3-1 is a bacterial pathogen with a higher virulence on white-flowered calla lily (Zantedeschia aethiopica) than other E. chrysanthemi strains (1, 2). E. chrysanthemi strains have been reclassified into the genus Dickeya, which contains 12 species (3–11). In this study, the genome sequence of strain S3-1 was determined and used to identify the strain to the species level of Dickeya based on the average nucleotide identity (ANI) (12) and in silico DNA-DNA hybridization (isDDH) (13) values.

The genome of strain S3-1 was sequenced using both Illumina MiSeq short-read and Oxford Nanopore Technologies (ONT) long-read sequencing methods. A single colony was cultured overnight at 28°C in Miller's Luria-Bertani broth medium (Neogen, Lansing, MI), and genomic DNA was extracted using the Genomic-tip 20/G kit (Qiagen, Valencia, CA). The extracted DNA was fragmented and a sequencing library constructed using the Celero EZ DNA-Seq library preparation kit (Tecan Genomics, San Carlos, CA) for Illumina sequencing (MiSeq sequencer; 2 × 300-bp base-paired reads) (Illumina, San Diego, CA). The raw data contained 4,138,542 reads (300 bp each read; N50, 300 bp) with a total of 1,245.7 Mb. For the long-read sequencing, the short DNA fragments of the same DNA preparation were removed using the short-read eliminator kit (Circulomics, Baltimore, MD), and a sequencing library was prepared using the native barcoding expansion kit 1-12 (EXP-NBD104; ONT) and the ligation sequencing kit (SQK-LSK109; ONT). Sequencing was performed on an ONT MinION device (MIN-101B) with FLO-MIN106 flow cells. In total, 1,663,872 reads (lengths ranging from 2,889 bp to 233 kbp; N50, 16,136 bp) were generated, comprising 4,807.2 Mb, and trimmed to remove the adapters, low-quality sequences (<Q20), and ambiguous bases using CLC Genomics Workbench v10 (CLC bio, Cambridge, MA). The Nanopore reads were base called, demultiplexed, and adapter trimmed using GridION MinKNOW v21.02.5 software with Guppy v4.3.4 high-accuracy mode. The Illumina trimmed reads and Nanopore reads were used to perform de novo assembly using the SPAdes v3.13.0 program (14).

The assembled genome is a 5,065,613-bp circular chromosome (G+C content, 56.5%) and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v5.2 (15). The chromosome contains 4,337 predicted coding sequences. The ANI and isDDH values were calculated by comparing the genome sequence of strain S3-1 with that of each type species of Dickeya, using the ANI Calculator (OAU v1.2) with the OrthoANIu algorithm (16) and a pipeline (http://ggdc.dsmz.de/) for isDDH (13). The species threshold was set to 96% for ANI and 70% for isDDH (12, 13).

The ANI and isDDH values between strain S3-1 and species of Dickeya range from 84.64 to 96.74% and 23.4 to 72%, respectively. ANI values above 96% were calculated only with D. dadantii strains, and an isDDH value above 70% was calculated only with D. dadantii subsp. dieffenbachiae NCPPB 2976T (Table 1). Accordingly, strain S3-1 was identified as D. dadantii subsp. dieffenbachiae. Both strains S3-1 and NCPPB 2976T were isolated from Araceae plants. Plant host specificity may exist, and the genome sequence of strain S3-1 will be useful to study host-driven speciation in D. dadantii strains.

TABLE 1 Average nucleotide identity and in silico DNA-DNA hybridization values of strain S3-1 compared with the genome sequences of other D. dadantii strains

Strain	GenBank accession no.	Host	ANI (%)	isDDH (%)	
D. dadantii S3-1	CP076386	Zantedeschia aethiopica (Araceae)			
D. dadantii subsp. dieffenbachiae NCPPB 2976T	CM001978.1	Dieffenbachia sp. (Araceae)	96.74	72	
D. dadantii NCPPB 3537	CM001982.1	Solanum tuberosum (Solanaceae)	96.46	68.8	
D. dadantii NCPPB 3937	CP002038.1	Saintpaulia ionantha (Gesneriaceae)	96.34	68.4	
D. dadantii subsp. dadantii NCPPB 898T	CM001976.1	Pelargonium capitatum (Geraniaceae)	96.30	67.4	

Data availability.

The sequence reported here was submitted to the NCBI database under accession no. CP076386, and the raw reads are available in the Sequence Read Archive (SRA) under accession no. SRX11062135 (Illumina MiSeq) and accession no. SRX11062136 (Oxford Nanopore [MinION]), under BioProject accession no. PRJNA734702.

ACKNOWLEDGMENT

This research was supported by grants from the Council of Agriculture (100AS-5.4.2-BQ-B6), Taiwan, Republic of China.
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