Draft genome sequences of 11 bacteria belonging to the family Microbacteriaceae were obtained using Illumina technology. The genomes of these strains have sizes from 3.14 to 4.30 Mb with their genomic DNA characterized as having high G+C contents (above 65%).
ABSTRACT
Draft genome sequences of 11 bacteria belonging to the family Microbacteriaceae were obtained using Illumina technology. The genomes of these strains have sizes from 3.14 to 4.30 Mb with their genomic DNA characterized as having high G+C contents (above 65%). These genomic data will be useful for natural taxonomy and comparative genomic studies of bacterial strains of the family Microbacteriaceae.
ANNOUNCEMENT
The family Microbacteriaceae Park et al. 1995 emend. Stackebrandt et al. 1997 emend. Zhi et al. 2009 comprises a large group of predominantly aerobic Gram-positive bacteria with high G+C contents in their genomic DNA that are distinguished from other actinobacteria by a combination of their unusual group B cell wall peptidoglycan and unsaturated respiratory menaquinones (1, 2). Currently, the family comprises 51 recognized genera and about 275 recognized species (http://www.bacterio.net/microbacteriaceae.html). There are about 80 sequenced genomes for type strains of the family Microbacteriaceae (https://www.ezbiocloud.net/taxon?tn=Microbacteriaceae). Efforts to obtain complete genome sequences of all type strains belonging to the family Microbacteriaceae are critical to the future microbial systematics of this group and for constructing the unified tree of life.
The type strains of six known species of the genera Agreia, Clavibacter, Okibacterium, Plantibacter, and Rathayibacter were isolated from various sources associated with plants (Table 1) (3–7). In addition, the novel strains Agreia sp. VKM Ac-1783, Agreia sp. VKM Ac-2052, Plantibacter sp. VKM Ac-1784, Plantibacter sp. VKM Ac-1787, and Rathayibacter oskolensis VKM Ac-2121T were isolated from plant galls induced by nematodes and from the healthy plant without any symptoms of disease (Table 1) (8–10). All strains were deposited in the All-Russian Collection of Microorganisms (http://www.vkm.ru/Catalogue.htm).
TABLE 1.
Genome sequence statistical information and DDBJ/ENA/GenBank accession numbers
| Organism | Plant source | Nematode | Total no. of reads post-trimming |
Total size post-trimming (Mb) |
No. of contigs (scaffolds) |
Coverage (×) |
N50 (bp) | Genome size (Mb) |
G+C content (%) |
No. of proteins |
SRA no. | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
A. pratensis VKM Ac-2510T |
Phyllosphere of grasses |
No | 5,153,882 | 773.1 | 10 | 214 | 860,306 | 3.58 | 65.4 | 3,418 | SRR5832269 | FXAY00000000 |
| Agreia sp. VKM Ac-1783 | Elymus repens |
Anguina agropyri |
5,567,834 | 835.2 | 7 | 220 | 1,002,356 | 3.76 | 65.8 | 3,551 | SRR5832516 | FXWI00000000 |
| Agreia sp. VKM Ac-2052 |
Calamagrostis neglecta |
Heteroanguina graminophila |
7,310,900 | 1,096.6 | 19 | 280 | 442,588 | 3.88 | 65.2 | 3,654 | SRR5832511 | FUYG00000000 |
|
C. michiganensis subsp. michiganensis VKM Ac-1403T |
Lycopersicon esculentum |
No | 6,669,630 | 993.8 | 14 (13) | 300 | 2,018,315 | 3.30 | 72.7 | 3,045 | SRR5216688 | FVZG00000000 |
| O. fritillariae VKM Ac-2059T | Fritillaria ruthenica | No | 5,278,668 | 791.8 | 4 | 250 | 2,068,692 | 3.14 | 67.8 | 2,808 | SRR5832512 | FUZP00000000 |
| P. flavus VKM Ac-2504T | Phyllosphere of grasses |
No | 4,884,328 | 732.6 | 12 (11) | 169 | 544,526 | 4.30 | 69.1 | 4,002 | SRR5832515 | FXAP00000000 |
| Plantibacter sp. VKM Ac-1784 | E. repens | A. agropyri | 5,096,142 | 764.4 | 8 | 184 | 674,883 | 4.12 | 69.2 | 3,829 | SRR5832517 | FXWJ00000000 |
| Plantibacter sp. VKM Ac-1787 |
Cousinia onopordioides |
Mesoanguina picridis |
5,710,806 | 850.9 | 5 | 211 | 2,657,854 | 4.02 | 69.5 | 3,719 | SRR5832510 | FUZO00000000 |
| R. rathayi VKM Ac-1601T | Dactylis glomerata | Anguina sp. | 5,193,410 | 779.0 | 46 (45) | 244 | 321,699 | 3.22 | 69.3 | 3,126 | SRR5832513 | OCNL00000000 |
| R. iranicus VKM Ac-1602T | Triticum aestivum | A. tritici | 5,315,024 | 797.3 | 50 (49) | 236 | 188,097 | 3.38 | 67.2 | 3,268 | SRR5832514 | QGDV00000000 |
| R. oskolensis VKM Ac-2121T |
Androsace koso-poljanskii |
No | 5,903,488 | 879.6 | 5 | 222 | 1,280,863 | 3.95 | 71.6 | 3,628 | SRR5832669 | FXBM00000000 |
Biomass for DNA extraction was obtained after growth in liquid peptone-yeast medium (11) at 28°C for 18 to 20 h on a rotary shaker. The genomic DNA was extracted using guanidinium thiocyanate and Triton X-100, followed by purification with Cleanup Standard BC022 (Evrogen, Russia). The draft genome sequences of the strains were generated at the DOE Joint Genome Institute (JGI) (Walnut Creek, CA, USA). The Illumina shotgun libraries with an insert size of 262 to 287 bp were constructed and sequenced using the Illumina HiSeq 2000 platform to produce 2 × 150-bp paired-end reads. All raw Illumina sequence data were filtered using BBDuk (http://sourceforge.net/projects/bbmap), which removes known Illumina artifacts and PhiX sequences. Reads with more than one N, quality scores (before trimming) averaging less than 8, or reads shorter than 51 bp (after trimming) were discarded. The remaining reads were mapped to masked versions of human, cat, and dog references using BBMAP (http://sourceforge.net/projects/bbmap) and discarded if their identities exceeded 95%. Sequence masking was performed with BBMask (http://sourceforge.net/projects/bbmap). The following steps were then performed for assembly: (i) artifact-filtered Illumina reads were assembled using SPAdes version 3.6.2 (with the parameters “--cov-cutoff auto --phred-offset 33 -t 8 -m 40 --careful -k 25,55,95 --12”) (12); and (2) assembly contigs with lengths of <1 kb were discarded. The genome was annotated using the JGI Microbial Genome Annotation Pipeline (13). Statistical information for the draft genome sequences is given in Table 1.
Further genome-wide comparative analyses of these strains and phylogenetically closely related bacteria belonging to the family Microbacteriaceae will enhance an understanding of the borderlines of prokaryotic species and facilitate insight into the molecular mechanisms involved in interactions between plants and bacteria.
Data availability.
The whole-genome shotgun projects reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions reported here are the first versions.
ACKNOWLEDGMENTS
These sequence data were produced by the U.S. Department of Energy Joint Genome Institute (DOE JGI) (http://www.jgi.doe.gov) in collaboration with the All-Russian Collection of Microorganisms (VKM) (http://www.vkm.ru/index.htm) in the frame of the Genomic Encyclopedia of Bacteria and Archaea Project Phase III (GEBA III) (14). The employees of DOE JGI, VKM, and the Department of Microbiology, University of Georgia, are acknowledged for their support of this global project.
The genome sequencing was supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. The reported study was also partially funded by RFBR through research project 16-34-01048mol_a (N.V.P.) and the Russian Federation Federal Agency of Scientific Organizations’ Bioresource Collections Program (L.I.E.).
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Associated Data
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Data Availability Statement
The whole-genome shotgun projects reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions reported here are the first versions.