Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively.
ABSTRACT
Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively.
ANNOUNCEMENT
Chlamydiae are Gram-negative bacteria distributed worldwide in humans, livestock, companion animals, and free-living animals (1–3). The genus Chlamydia includes 14 characterized species (4–7) and 4 candidate species (8–11). C. abortus is a cause of abortion and fetal loss in ruminants and other mammals, while C. psittaci is an etiological agent of avian chlamydiosis in birds (12, 13). Both of them are known to be associated with zoonotic potential, thus posing a threat to human health (14, 15). Recently, the occurrence of C. abortus was noted in nonmammalian hosts (16, 17). Novel strains originating from wild birds were provisionally named avian C. abortus (17). Considering the worldwide distribution of these strains in diverse bird families, avian C. abortus strains should be considered epidemiologically relevant (17–20).
Here, we present the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie. Molecular analysis based on multilocus sequence typing (MLST) performed in our previous study clearly classified these isolates within the C. abortus species (17).
Avian C. abortus strains representing genotypes G2 and 1V were isolated from cloacal swab samples originating from mallard and magpie on Buffalo green monkey (BGM) cell culture with UltraMDCK serum-free medium (Lonza Cologne, Germany). The medium was renewed after 18 h. Cultures were propagated in T25 flasks and incubated at 37°C with 5% CO2 in a fully humidified cabinet for 72 h (17). After three passages, cell culture was used for DNA extraction using a QIAamp DNA minikit (Qiagen, Germany) following the manufacturer’s instructions. Host DNA was removed using a NEBNext microbiome DNA enrichment kit (New England Biolabs, USA). Genomic libraries were constructed using a Nextera XT DNA library preparation kit and a Nextera XT index kit (Illumina, USA). Sequencing was performed on a MiSeq sequencer (Illumina) with the 2 × 300-bp paired-end protocol. The raw read quality was evaluated based on FastQC 0.1.18 (21), followed by adapter and quality trimming using Trimmomatic 0.36 (22). Nonchlamydial reads originating from host DNA were identified through mapping against the African green monkey genome using the Burrows-Wheeler Aligner MEM algorithm (BWA-MEM) 0.7.15 (23) and discarded. The total numbers of filtered reads of strains 15-49d3 and 15-58d44 were 172,095 (43,895,761 bp) and 619,570 (148,956,163 bp), respectively. Trimmed and filtered reads were assembled using SPAdes 3.11.1 (24). The coverage cutoff was set at 10× and 500-bp length, which resulted in 2 contigs (15-49d3) and 5 contigs (15-58d44). The lengths of the total genome assemblies of strains 15-49d3 and 15-58d44 were 1,140,139 bp and 1,158,207 bp, respectively. The N50 value for strain 15-58d44 was 776,426 bp. The draft genome sequences were annotated using the Rapid Annotations using Subsystems Technology (RAST) pipeline (25). Detailed properties of the genomes are presented in Table 1. Default parameters were used for all software unless otherwise specified.
TABLE 1.
Genome properties of avian Chlamydia abortus genotype G2 strain 15-49d3 and genotype 1V strain 15-58d44
| Featurea | Value | % of total | Accession no. |
|---|---|---|---|
| 15-49d3 | |||
| Chromosome | |||
| No. of contigs | 1 | ||
| Length (bp) | 1,132,456 | ||
| Scaffold 1 (bp) | 1,132,456 | LS450956 | |
| Avg read coverage (×) | ∼37.5 | ||
| DNA coding (bp) | 1,007,970 | 89.01 | |
| DNA G+C content (%) | 39.6 | ||
| No. of genes | |||
| Total | 1,089 | 100 | |
| Protein coding genes | 1,048 | 96.24 | |
| RNA genes | 41 | 3.76 | |
| Pseudogenes | |||
| Genes with functional prediction | 750 | 68.87 | |
| Genes assigned to COGs | 497 | 45.64 | |
| Genes with Pfam domains | 753 | 69.15 | |
| Genes with signal peptides | 52 | 4.78 | |
| Genes with transmembrane helices | 234 | 21.49 | |
| Plasmid | |||
| No. of contigs | 1 | ||
| Length (bp) | 7,683 | ||
| Scaffold 2 (bp) | 7,683 | LS450957 | |
| Avg read coverage (×) | ∼102.5 | ||
| DNA G+C content (%) | 32.6 | ||
| No. of CDS | 8 | ||
| 15-58d44 | |||
| Chromosome | |||
| No. of contigs | 4 | ||
| Total length (bp) | 1,150,527 | ||
| Scaffold 1 (bp) | 776,426 | CAJHTZ010000001 | |
| Scaffold 2 (bp) | 372,709 | CAJHTZ010000002 | |
| Scaffold 4 (bp) | 870 | CAJHTZ010000004 | |
| Scaffold 5 (bp) | 522 | CAJHTZ010000005 | |
| Avg read coverage (×) | ∼76.38 | ||
| DNA coding (bp) | 1,028,907 | 89.43 | |
| DNA G+C content (%) | 39.9 | ||
| No. of genes | |||
| Total genes | 1,080 | 100 | |
| Protein coding genes | 1,039 | 96.20 | |
| RNA genes | 41 | 3.80 | |
| Pseudogenes | |||
| Genes with functional prediction | 710 | 65.74 | |
| Genes assigned to COGs | 500 | 46.30 | |
| Genes with Pfam domains | 764 | 70.74 | |
| Genes with signal peptides | 57 | 5.28 | |
| Genes with transmembrane helices | 257 | 23.80 | |
| Plasmid | |||
| No. of contigs | 1 | ||
| Length (bp) | 7,680 | ||
| Scaffold 3 (bp) | 7,680 | CAJHTZ010000003 | |
| Avg read coverage (×) | ∼304.5 | ||
| DNA G+C content (%) | 33.0 | ||
| No. of CDS | 8 | ||
CDS, coding DNA sequences; COG, clusters of orthologous groups.
Data availability.
The genome sequences of strain 15-49d3 have been deposited at ENA/GenBank/DDBJ under the accession numbers LS450956 and LS450957, and the raw reads under number ERS2484025. The genome sequences of strain 15-58d44 have been deposited at ENA/GenBank/DDBJ under the accession numbers CAJHTZ010000001, CAJHTZ010000002, CAJHTZ010000003, CAJHTZ010000004, and CAJHTZ010000005, and the raw reads have been deposited under SRA number ERS2484027. The BioProject accession number is PRJEB26715.
ACKNOWLEDGMENTS
This research was funded by the KNOW (Leading National Research Centre) Scientific Consortium “Healthy Animal—Safe Food,” decision of Ministry of Science and Higher Education number 05-1/KNOW2/2015.
We thank Agata Mitura from the Department of Cattle and Sheep Diseases (NVRI, Puławy, Poland) for excellent technical assistance in preparation of the DNA samples. Christiane Schnee (FLI, Jena, Germany), Karine Laroucau (ANSES, Maisons Alfort, France), and their coworkers are acknowledged for help with isolation of the strains and useful suggestions. We are grateful to Arkadiusz Bomba and coworkers from the Department of Omics Analysis (NVRI, Puławy, Poland) for valuable technical assistance and continuous support.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequences of strain 15-49d3 have been deposited at ENA/GenBank/DDBJ under the accession numbers LS450956 and LS450957, and the raw reads under number ERS2484025. The genome sequences of strain 15-58d44 have been deposited at ENA/GenBank/DDBJ under the accession numbers CAJHTZ010000001, CAJHTZ010000002, CAJHTZ010000003, CAJHTZ010000004, and CAJHTZ010000005, and the raw reads have been deposited under SRA number ERS2484027. The BioProject accession number is PRJEB26715.