Stella species are unique star-shaped alphaproteobacteria found in various environments. We report the complete genome sequences of three Stella strains, Stella humosa ATCC 43930, Stella vacuolata ATCC 43931, and Stella species ATCC 35155. These are the first complete genome sequences of members of the genus Stella.
ABSTRACT
Stella species are unique star-shaped alphaproteobacteria found in various environments. We report the complete genome sequences of three Stella strains, Stella humosa ATCC 43930, Stella vacuolata ATCC 43931, and Stella species ATCC 35155. These are the first complete genome sequences of members of the genus Stella.
ANNOUNCEMENT
Although bacteria have a wide variety of cell shapes, the mechanisms underlying the generation of the complex morphology and evolution of shape diversity remain unknown. In this study, we report the first complete genome sequences of three Stella strains which have a unique star-shape morphology. Stella species are flat, six-pronged, star-shaped bacteria found in various environments, e.g., freshwater, soil, and sewage (1). The genus Stella comprises Gram-negative alphaproteobacteria belonging to the order Rhodospirillales in the family Rhodospirillaceae (2). These unique star-shaped bacteria were isolated first in Russia, and three species are currently deposited with the American Type Culture Collection (ATCC). Stella humosa ATCC 43930 and Stella vacuolata ATCC 43931 were isolated from a soil sample in Krasnodar and in horse manure, respectively (1). Eleven additional strains have also been isolated (3), and we deposited the third Stella species strain, ATCC 35155. This strain was isolated from brackish water in the Baltic Sea, and the ATCC has termed this strain Stella aquatica ATCC 35155.
S. humosa, S. vacuolata, and Stella sp. strain ATCC 35155 cells were grown in ATCC medium 1298 (brackish Prosthecomicrobium; https://www.atcc.org/~/media/BCF4A47455D44063A66771F94C62AF54.ashx) at 30°C and 150 rpm for 8, 3, and 6 days, respectively, and then pelleted. DNA was extracted from the cells with Wizard genomic DNA purification kits (Promega) according to the manufacturer’s instructions. Long-read library preparation for Nanopore sequencing was performed with a 1D2 sequencing kit (SQK-LSK308; Nanopore) without fragmentation. The libraries were then sequenced on a MinION device with a 1D2 flow cell (FLO-MIN107; Nanopore) and base called with Guppy v2.3.5 (Nanopore). Short-read libraries for paired-end sequencing (2 × 300 bp) were prepared using a Nextera XT kit (Illumina) without preceding fragmentation, such as ultrasonic shearing, and sequenced on an Illumina MiSeq platform with the MiSeq reagent kit v3 for 600 cycles. The number of short reads and the number and the average length of long reads for each sample are summarized in Table 1.
TABLE 1.
General features of Stella species genomes and a summary of their sequencing data
| ATCC no. | Bacterial species | No. of Illumina paired reads | Nanopore reads |
Total coverage (×) | Genome size (bp) | GC content (%) | No. of CDSs | Accession no. | |
|---|---|---|---|---|---|---|---|---|---|
| No. | Avg length (bp) | ||||||||
| ATCC 43930 | Stella humosa | 2,446,912 | 25,819 | 3,340.4 | 140 | 5,832,650 | 69.8 | 5,556 | AP019700 |
| ATCC 43931 | Stella vacuolata | 3,290,870 | 203,511 | 4,874.2 | 330 | 5,834,761 | 70.9 | 5,515 | AP019702 |
| ATCC 35155 | Stella sp. | 4,069,690 | 186,264 | 3,717.6 | 310 | 5,339,096 | 70.6 | 5,058 | AP019701 |
For S. humosa, the long-read assembly was performed with Canu v1.8 (4), including a read correction step. The resulting contig was then circularized with Circlator v1.5.5 (5) and polished with short reads by Pilon v1.2.3 (6). These software tools were used with default parameters. For S. vacuolata and Stella sp. ATCC 35155, hybrid assembly of long and short reads was performed with Unicycler v0.4.8 (7), with default parameters, including a built-in read correction step and a polishing step with Pilon. The resulting circular contigs were additionally polished with short reads by Pilon. A single contiguous circularized sequence was obtained for each of the three species. The Stella chromosomes were 5.3 to 5.8 Mbp and were GC rich (∼70% GC content; Table 1). Automatic annotation using the DDBJ Fast Annotation and Submission Tool (DFAST) pipeline (8) detected more than 5,000 coding sequences (CDSs) on each chromosome (Table 1).
Data availability.
The whole-genome sequences of the three Stella strains were deposited with DDBJ/GenBank under accession numbers AP019700 to AP019702 (Table 1). The fastq files of raw reads were deposited in the DDBJ Sequence Read Archive (DRA)/NCBI SRA under the accession number DRA008500. The versions described in this paper are the first versions.
ACKNOWLEDGMENTS
This work was supported, in part, by a Grant-in-Aid for Scientific Research on Innovative Areas (grant 17H06389) from MEXT and the RIKEN Special Postdoctoral Researcher Program.
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Data Availability Statement
The whole-genome sequences of the three Stella strains were deposited with DDBJ/GenBank under accession numbers AP019700 to AP019702 (Table 1). The fastq files of raw reads were deposited in the DDBJ Sequence Read Archive (DRA)/NCBI SRA under the accession number DRA008500. The versions described in this paper are the first versions.