Draft genome sequences of 28 strains of Microbacteriaceae from plants infested by plant-parasitic nematodes were obtained using Illumina technology. The sequence data will provide useful baseline information for the development of comparative genomics and systematics of Microbacteriaceae and facilitate understanding of molecular mechanisms involved in interactions between plants and nematode-associated bacterial complexes.
ABSTRACT
Draft genome sequences of 28 strains of Microbacteriaceae from plants infested by plant-parasitic nematodes were obtained using Illumina technology. The sequence data will provide useful baseline information for the development of comparative genomics and systematics of Microbacteriaceae and facilitate understanding of molecular mechanisms involved in interactions between plants and nematode-associated bacterial complexes.
ANNOUNCEMENT
Members of the family Microbacteriaceae (class Actinobacteria) inhabit various terrestrial and aquatic ecosystems and often occur in plants as endophytes and pathogens (1, 2). Plant-pathogenic species of the genus Rathayibacter belonging to this family are transmitted to their host plants by gall-forming nematodes of the genus Anguina (Anguinidae) (3, 4). Along with Rathayibacter, some other Microbacteriaceae, including members of the genera Agreia, Leifsonia, Microbacterium, and Plantibacter, were recovered from plant galls induced by Anguinidae and from leaf tissues of Tanacetum vulgare infested by Aphelenchoides fragariae (1, 5–8).
Novel nematode-associated strains of Microbacteriaceae were isolated from plant galls induced by different anguinids and from plant tissues affected by Aphelenchoides species (Table 1). The air-dried plant samples were soaked in distilled water for 1 h, washed twice with sterile distilled water, placed in 0.85% NaCl solution, and milled. One drop of the obtained suspension was plated onto modified Corynebacterium agar (9) or Reasoner’s 2A (R2A) agar (Fluka Analytical, USA) and incubated for 1 to 3 weeks at room temperature (18 to 24°C). The isolated strains were identified on the basis of matrix-assisted laser desorption ionization (MALDI) mass spectra and 16S rRNA gene sequences as described previously (10, 11) and deposited in the All-Russian Collection of Microorganisms (VKM; http://www.vkm.ru).
TABLE 1.
Characteristics and DDBJ/ENA/GenBank accession numbers of genome sequences
| Organism | Plant | Nematode | Geography | No. of reads | Coverage (×) | No. of scaffolds | Scaffold N50 (bp) | Genome size (Mbp) | G+C content (%) | No. of proteins | SRA accession no. | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Agreia pratensis VKM Ac-2874 | Poa annua | Anguina pacificae | San Francisco, CA, USA | 7,950,938 | 304 | 13 | 1,078,817 | 3.8 | 65.2 | 3,532 | SRR13176583 | JADKRN000000000 |
| Clavibacter michiganensis subsp. michiganensis VKM Ac-1790 | Agrostis sp. | Anguina agrostis | Sakhalin Island, Russia | 16,949,770 | 737 | 9 | 808,662 | 3.3 | 72.7 | 3,036 | SRR13176582 | JADKRO000000000 |
| Clavibacter michiganensis subsp. phaseoli VKM Ac-2886 | Sambucus racemosa | Aphelenchoides ritzemabosi | Moscow Region, Russia | 18,464,076 | 785 | 21 | 2,249,679 | 3.4 | 73.2 | 3,186 | SRR13176571 | JADKRP000000000 |
| Clavibacter sp. strain VKM Ac-2542 | Elymus repens | Anguina agropyri | Moscow Region, Russia | 15,327,488 | 656 | 5 | 1,206,839 | 3.3 | 73.0 | 3,103 | SRR13176562 | JADKRQ000000000 |
| Clavibacter sp. strain VKM Ac-2872 | Poa annua | Anguina pacificae | San Francisco, CA, USA | 16,543,808 | 675 | 12 | 2,167,218 | 3.5 | 72.7 | 3,276 | SRR13176561 | JADKRR000000000 |
| Clavibacter sp. strain VKM Ac-2873 | Agrostis capillaris | Anguina agrostis | Washington, USA | 17,375,186 | 751 | 14 | 534,200 | 3.3 | 73.2 | 3,064 | SRR13176560 | JADKRS000000000 |
| Curtobacterium flaccumfaciens VKM Ac-1386 | Agrostis sp. | Anguina agrostis | Iturup Island, Russia | 12,378,592 | 457 | 18 | 376,811 | 3.9 | 70.9 | 3,687 | SRR13176559 | JADKRT000000000 |
| Curtobacterium flaccumfaciens VKM Ac-1795 | Agrostis sp. | Anguina agrostis | Sakhalin Island, Russia | 11,498,758 | 417 | 36 | 428,105 | 3.9 | 70.7 | 3,692 | SRR13176558 | JADKRU000000000 |
| Curtobacterium sp. strain VKM Ac-1376 | Poa annua | Subanguina radicicola | Moscow Region, Russia | 9,503,968 | 362 | 61 | 195,312 | 3.8 | 70.4 | 3,507 | SRR13176557 | JADKRV000000000 |
| Curtobacterium sp. strain VKM Ac-1393 | Calamagrostis sp. | Heteroanguina graminophila | Kunashir Island, Russia | 12,098,310 | 438 | 20 | 491,012 | 3.9 | 70.5 | 3,681 | SRR13176556 | JADKRW000000000 |
| Curtobacterium sp. strain VKM Ac-1395 | Festuca rubra | Anguina graminis | Moscow Region, Russia | 9,679,080 | 355 | 18 | 628,495 | 3.9 | 71.1 | 3,670 | SRR13176581 | JADKRX000000000 |
| Curtobacterium sp. strain VKM Ac-1796 | Centaurea sp. | Mesoanguina picridis | North Caucasus, Russia | 12,573,324 | 503 | 9 | 630,474 | 3.6 | 71.0 | 3,364 | SRR13176580 | JADKRY000000000 |
| Curtobacterium sp. strain VKM Ac-2865 | Agrostis capillaris | Anguina agrostis | Washington, USA | 13,029,810 | 500 | 15 | 428,310 | 3.7 | 71.4 | 3,461 | SRR13176579 | JADKRZ000000000 |
| Curtobacterium sp. strain VKM Ac-2884 | Agrostis capillaris | Anguina agrostis | Washington, USA | 9,597,106 | 354 | 15 | 694,950 | 3.9 | 70.9 | 3,646 | SRR13176578 | JADKSA000000000 |
| Curtobacterium sp. strain VKM Ac-2887 | Agrostis capillaris | Anguina agrostis | Moscow Region, Russia | 12,452,164 | 427 | 57 | 242,003 | 4.2 | 70.6 | 3,952 | SRR13176577 | JADKSB000000000 |
| Curtobacterium sp. strain VKM Ac-2889 | Agrostis sp. | Anguina agrostis | Kunashir Island, Russia | 11,453,674 | 457 | 9 | 940,853 | 3.6 | 71.0 | 3,357 | SRR13176576 | JADKSC000000000 |
| Frigoribacterium sp. strain VKM Ac-1396 | Festuca rubra | Anguina graminis | Moscow Region, Russia | 11,568,590 | 486 | 8 | 1,115,953 | 3.4 | 71.7 | 3,088 | SRR13176575 | JADKSD000000000 |
| Frigoribacterium sp. strain VKM Ac-2530 | Tanacetum vulgare | Aphelenchoides fragariae | Moscow Region, Russia | 19,836,426 | 834 | 5 | 1,902,771 | 3.4 | 72.7 | 3,110 | SRR13176574 | JADKSE000000000 |
| Frondihabitans sp. strain VKM Ac-2883 | Fagus sp. | Litylenchus sp. | New York State, USA | 6,461,938 | 253 | 24 | 417,102 | 3.7 | 67.3 | 3,391 | SRR13176573 | JADKSF000000000 |
| Herbiconiux sp. strain VKM Ac-1786 | Elymus repens | Anguina agropyri | Moscow Region, Russia | 16,964,600 | 622 | 4 | 2,263,567 | 3.9 | 71.1 | 3,649 | SRR13176572 | JADKSG000000000 |
| Microbacterium sp. strain VKM Ac-2870 | Poa annua | Anguina pacificae | San Francisco, CA, USA | 11,489,968 | 526 | 12 | 704,918 | 3.1 | 68.3 | 2,905 | SRR13176570 | JADKSH000000000 |
| Plantibacter sp. strain VKM Ac-2876 | Poa annua | Anguina pacificae | San Francisco, CA, USA | 9,413,878 | 338 | 7 | 1,281,621 | 4.0 | 69.5 | 3,702 | SRR13176569 | JADKSI000000000 |
| Plantibacter sp. strain VKM Ac-2880 | Klasea latifolia | Mesoanguina picridis | Iran | 11,839,552 | 422 | 7 | 2,540,737 | 4.0 | 69.4 | 3,765 | SRR13176568 | JADKSJ000000000 |
| Plantibacter sp. strain VKM Ac-2885 | Festuca rubra | Anguina graminis | Moscow Region, Russia | 12,004,120 | 410 | 4 | 2,630,716 | 4.2 | 69.2 | 3,853 | SRR13176567 | JADKSK000000000 |
| Pseudoclavibacter sp. strain VKM Ac-2867 | Agrostis capillaris | Anguina agrostis | Washington, USA | 10,413,762 | 357 | 47 | 195,216 | 4.2 | 68.2 | 3,812 | SRR13176566 | JADKSL000000000 |
| Pseudoclavibacter sp. strain VKM Ac-2888 | Tanacetum vulgare | Aphelenchoides fragariae | Moscow Region, Russia | 11,942,026 | 409 | 7 | 3,268,120 | 4.2 | 68.5 | 3,851 | SRR13176565 | JADKSM000000000 |
| Rathayibacter sp. strain VKM Ac-2878 | Danthonia californica | Anguina danthoniae | Fort Ross, CA, USA | 11,690,574 | 569 | 9 | 860,400 | 2.9 | 69.9 | 2,692 | SRR13176564 | JADKSN000000000 |
| Rathayibacter sp. strain VKM Ac-2879 | Danthonia californica | Anguina danthoniae | Fort Ross, CA, USA | 9,176,840 | 448 | 9 | 860,400 | 2.9 | 69.9 | 2,690 | SRR13176563 | JADKSO000000000 |
For genome sequencing, DNA was extracted with a QIAamp DNA minikit (Qiagen, Germany) from biomass grown in liquid peptone-yeast medium as described previously (7) or using cells incubated on R2A agar for 2 to 3 days at 28°C. DNA library construction and sequencing were conducted by Novogene Co., Ltd., using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s recommendations. Pooled DNA libraries were sequenced on an Illumina NovaSeq 6000 instrument to obtain 150-bp paired-end reads.
Default parameters were used for all software unless otherwise specified. The quality of the reads was checked with FastQC 0.11.8 (12). Adapter sequences and low-quality regions in raw reads were cut with Trimmomatic 0.39 (13) with the following options: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; SLIDINGWINDOW:4:20; MINLEN:50. Trimmed reads were assembled using SPAdes 3.14.1 (14) with the following options: --cov-cutoff, auto, and --isolate. The quality of assembly was assessed with QUAST 5.0.2 (15). Assemblies were annotated with NCBI PGAP (16) and the RAST Web server (17, 18).
Additional comparative phenotypic study of the sequenced strains, along with genome-wide analyses of phylogenetically closely related plant endophytes and pathogens, will facilitate understanding of their role in bacterial-nematode complexes, including mechanisms of molecular interactions between members of these complexes and plants.
Data availability.
These whole-genome shotgun projects have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENT
This work was sponsored by the United States Department of Agriculture Animal and Plant Health Inspection Service according to the research project AP18PPQS&T00C159 (18-0422-000-FR) “Enhancing Diagnostics of Plant Pathogenic Bacteria of the Genus Rathayibacter” (principal investigator [PI], S.A.S.).
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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
These whole-genome shotgun projects have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.