Complete genome sequence of a Chinese Pseudomonas syringae pv. actinidiae strain Yunnan3.2

TL;DR

This paper presents the full genome sequence of a Pseudomonas syringae strain causing kiwifruit disease in China.

Contribution

The study provides the complete genome sequence of a new Pseudomonas syringae pv. actinidiae strain from China.

Findings

The genome consists of a 6,564,315-bp chromosome with 58.41% GC content.

A circular plasmid of 74,466 bp was also identified.

Abstract

Here, we report the complete genome sequence for Pseudomonas syringae pv. actinidiae strain Yunnan3.2, which was isolated from diseased kiwifruit grown in Yunnan province, China. The complete genome of Yunnan3.2 comprises a 6,564,315-bp chromosome with a GC content of 58.41% and a circular plasmid (74,466 bp).

Figures

Phylogenetic tree of Pseudomonas syringae pv. actinidiae strain Yunnan3.2. The phylogenetic analysis was performed by the Type Strain Genome Server (TYGS) based on genome blast distance phylogeny (GBDP) distances calculated from genome sequences. The complete genome sequences of 10 Pseudomonas species were automatically deposited by TYGS. The genome sequences of the other 11 Psa strains were downloaded from the GenBank database. Notably, Yunnan3.2 strain is highlighted in red. The numbers below branches represent GBDP pseudo-bootstrap support values from 100 replications. Leaf labels are annotated according to (1) species cluster, (2) subspecies cluster, (3) percent G + C, (4) delta statistics, (5) genome size (in bp), and (6) protein count, respectively.

Tables

TABLE 1. Genome annotation statistics of Yunnan3.2

Characteristic	Yunnan3.2a
Total bases (bp)	6,564,315
GC (%)	58.41
Genes	6,001
CDSs	5,918
Complete rRNAs (5S, 16S, 23S)	6, 5, 5
tRNA	63
ncRNA	4
Pseudo genes	480
CRISPR	44

Full text

ANNOUNCEMENT

Pseudomonas syringae pv. actinidiae (Psa) causes bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis), one of the most devastating bacterial diseases of kiwifruit (1). Since Psa was first isolated in Japan (2), it has been found in several countries, including Korea, Italy, France, New Zealand, and Spain (1, 3–7). In China, this disease has been reported in multi-provinces including Sichuan, Hunan, Anhui, and Shaanxi (8–10). Here, we presented a high-quality, complete genome sequence of Psa strain Yunnan3.2.

Psa strain was isolated from diseased kiwifruit branches grown in Zhaotong (N27°, E103°), Yunnan province, China. Branch tissues were sterilized using 70% ethanol and ground with sterile water. The diluted solution was plated onto Luria-Bertani (LB) agar plate (11) and incubated at 28°C. Multiple single colonies were identified as Psa strain through PCR amplification using specific primer pair Psa-F/Psa-R (12). Among them, Yunnan3.2 strain was chosen for sequencing. A single colony of Yunnan3.2 strain was cultured in LB liquid medium for 12 h, and 5 mL of the bacterial suspension was centrifuged to collect bacterial cells. Then, the bacterial cells were submitted to Beijing Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), for sequencing. Genomic DNA was extracted using STE method (13) and quantified with Qubit fluorometer (Thermo Scientific, USA). The whole genome of Yunnan3.2 was sequenced on both the PacBio platform and Illumina PE150 platform, using SMRT bell TM Template kit (version 2.0) and NEBNextUltra DNA Library Prep Kit for Illumina (NEB, USA), respectively. Low-quality reads were filtered using SMRT Link v8.0, and the filtered reads were assembled by software Canu (https://github.com/marbl/canu/, version 2.0) (14). A total of 762,396 reads with an N50 length of 7,919 bp and average read length of 4,972 bp were obtained through PacBio sequencing, which provided approximately 570-fold genome coverage. For Illumina sequencing, paired-end reads (2 × 150 bp), totaling 7,573,333 reads covering a total of 2.272 Gb clean data (Q20, 97.61; Q30, 93.43) with 424-fold genome coverage, were obtained. Pilon v1.23 was employed to correct the assembled genome using Illumina sequence data, resulting in a final genome with high accuracy (15). BLASTN was employed to assess the genomic loops (overlap >2 kb), and the overlapping parts were cut off (16). GeneMarkS was employed to predict and filter genes of the genome (17), while the publicly accessible version of the genome was annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (18). All tools were run with default parameters unless otherwise specified.

The genomic features for strain Yunnan3.2 are summarized in Table 1. The genome-based classification of strain Yunnan3.2 was conducted using the Type Strain Genome Server (TYGS) web server (19). Phylogenetic analysis revealed that Yunnan3.2 clustered together with two New Zealand Psa strains ICMP18708 (GenBank: CP012179) (20) and ICMP18884 (GenBank: CP011972) (21) (Fig. 1). The average nucleotide identity (ANI) values between strain Yunnan3.2 and ICMP18708, Yunnan3.2 and ICMP18884, and Yunnan3.2 and a Chinese Psa strain Shannxi_M228 (GenBank: CP048810) (22) were 99.95, 99.95, and 99.75, respectively. The analysis of ANI was performed by using EzBioCloud (https://www.ezbiocloud.net/tools/ani) (23).

Phylogenetic tree of Pseudomonas syringae pv. actinidiae strain Yunnan3.2. The phylogenetic analysis was performed by the Type Strain Genome Server (TYGS) based on genome blast distance phylogeny (GBDP) distances calculated from genome sequences. The complete genome sequences of 10 Pseudomonas species were automatically deposited by TYGS. The genome sequences of the other 11 Psa strains were downloaded from the GenBank database. Notably, Yunnan3.2 strain is highlighted in red. The numbers below branches represent GBDP pseudo-bootstrap support values from 100 replications. Leaf labels are annotated according to (1) species cluster, (2) subspecies cluster, (3) percent G + C, (4) delta statistics, (5) genome size (in bp), and (6) protein count, respectively.