The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.
ABSTRACT
The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.
ANNOUNCEMENT
Streptomyces species are soil-dwelling bacteria that harbor large linear chromosomes (1). We report here the genome sequences of 11 sympatric Streptomyces strains belonging to the same species. In order to select conspecifics, we sampled soil grains at the cubic milliliter scale from a French forest (maximal distance of 8 cm from each other). After dissolution in sterile water and spreading of serial dilutions on Streptomyces isolation medium (SIM) (2), the 16S rRNA sequences of the strains were determined and analyzed using BLAST (3), and their phylogenetic relationships were characterized by multilocus sequence analysis (MLSA) using the Molecular Evolutionary Genetics Analysis version 7 (MEGA7) software (4). After growth in liquid Hickey-Tresner medium at 30°C for 30 h, DNA purification was performed using the salting-out method (5), followed by chloroform extraction. The targeted genes (rRNA gene and the MLSA genes) were amplified using universal (16S rRNA gene [6]) and specific (MLSA [7]) primers. The 11 strains selected showed identical 16S rRNA gene sequences and minimal MLSA divergence. These strains are related to Streptomyces olivochromogenes (strain DSM40451), with an average identity of 99.93% for the 16S rRNA gene sequences (8). A hybrid assembly using Oxford Nanopore technology for scaffolding and Illumina technology for sequence improvement was performed (Table 1). Base calling of these sequences was performed using the Oxford Nanopore base callers Albacore (v0.8.4 or v2.0.2) or Guppy (v0.3.0). Nanopore reads (minimum quality mean, 7) were generated on minION or gridION systems. When strains were multiplexed, Porechop (v0.2.4, using default settings) was used for demultiplexing (and adaptor trimming). The coverage ranged from 41× to 344×. The Illumina paired-end libraries were created using the Illumina Nextera kit, except for RLB1-8 and RLB1-9, for which sonication (Covaris) and adaptor ligation (Illumina TruSeq) were used instead. Paired reads were generated using a MiSeq reagent kit v3 (150 cycles) and the Genome Analyzer system (Illumina). The minimum read size was set to 10 bp, and adaptor trimming was performed using Cutadapt (v1.15, using default settings). The coverages of the paired-end reads (length, 75 to 300 bp) ranged from 58× to 320×. The hybrid assembly was performed using Unicycler (9) v0.4.2 or v0.4.3 (using default settings) to assemble 1 to 19 large contigs covering the whole genome of each strain, enabling the acquisition of each linear chromosome in one scaffold and the identification of extrachromosomal elements when present. One or two extrachromosomal linear or circular replicons were identified in 5 of the 11 strains by in silico prediction or pulsed-field gel electrophoresis experiments (10). The total genome sizes ranged from 11.76 to 12.45 Mb, positioning these strains among the largest bacterial genomes (Table 1).
TABLE 1.
Genome features, sequencing statistics, and accession numbers of the 11 conspecific Streptomyces strains
| Strain or replicon | Illumina sequencing information |
Oxford Nanopore sequencing information |
Replicon size (bp)c | Genome size (bp) | Total no. of CDSa | G+C content (%) | TIRb (kb) | GenBank accession no. | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of reads (approx coverage [×]) | SRA accession no. | No. of reads (approx coverage [×]) | N50 of raw reads (kb) | Flow cell type(s) | Sequencing kit(s) | Base caller | SRA accession no. | |||||||
| RLB1-8 | 15,381,622 (320) | SRR9661592 | 655,482 (150) | 4.3 | FAH18893 (9.5), FAH18988 (9.5), FAH24488 (9.5) | sqk-lsk308 | albacore_2.0.2 | SRR9710048 | 11,765,340 | 11,765,340 | 10,635 | 70.2 | 357 | CP041650 |
| RLB1-9 | 18,329,970 (115) | SRR9661591 | 88,694 (41) | 7.6 | FAF19789 (9.4) | sqk-lsk308 | albacore_0.8.4 | SRR9710047 | 11,940,408 | 12,200,709 | 10,838 | 70.2 | 311 | CP041654 |
| pRLB1-9.1 | 154,158C | 175 | 69,0 | CP041653 | ||||||||||
| pRLB1-9.2 | 106,143L | 111 | 68.7 | 24 | CP041652 | |||||||||
| RLB3-5 | 3,196,108 (67) | SRR9661590 | 144,521 (56) | 7.1 | FAH24352 (9.5), FAH29240 (9.4) | sqk-lsk308, sqk-lsk108 | albacore_2.0.2 | SRR9710050 | 11,898,970 | 11,898,970 | 10,731 | 70.2 | 365 | CP041651 |
| RLB3-6 | 3,274,272 (68) | SRR9661589 | 299,155 (52) | 4.6 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710049 | 12,338,263 | 12,448,281 | 11,255 | 70.1 | 587 | CP041602 |
| pRLB3-6.1 | 110,314C | 101 | 70.6 | CP041601 | ||||||||||
| RLB3-17 | 3,976,622 (83) | SRR9661596 | 202,455 (50) | 5.6 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710052 | 12,023,175 | 12,023,175 | 10,934 | 70.2 | 451 | CP041610 |
| S1A1-3 | 3,243,184 (68) | SRR9661595 | 198,567 51) | 5.2 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710051 | 12,042,091 | 12,042,091 | 10,920 | 70.2 | 393 | CP041611 |
| S1A1-7 | 3,504,210 (73) | SRR9661594 | 533,299 (73) | 2.8 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710054 | 11,713,151 | 12,005,504 | 10,580 | 70.3 | 513 | CP041604 |
| pS1A1-7.1 | 292,353C | 252 | 69.7 | CP041603 | ||||||||||
| S1A1-8 | 3,191,318 (66) | SRR9661593 | 780,962 (53) | 1.1 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710053 | 12,036,971 | 12,036,971 | 10,918 | 70.2 | 394 | CP041612 |
| S1D4-14 | 2,794,454 (58) | SRR9661598 | 2,066,754 (344) | 3.2 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710056 | 11,723,487 | 11,934,498 | 10,591 | 70.2 | 369 | CP041607 |
| pS1D4-14.1 | 112,196L | 118 | 68.7 | 0 | CP041605 | |||||||||
| pS1D4-14.2 | 98,815C | 138 | 69.1 | CP041606 | ||||||||||
| S1D4-20 | 3,327,172 (69) | SRR9661597 | 1,424,402 (255) | 4.1 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710055 | 11,851,257 | 12,245,276 | 10,742 | 70.2 | 373 | CP041609 |
| pS1D4-20.1 | 394,019L | 329 | 69.1 | 68 | CP041608 | |||||||||
| S1D4-23 | 3,543,760 (74) | SRR9661599 | 400,348 (61) | 3.5 | FAF19789 (9.4) | sqk-lsk308 | guppy_0.3.0 | SRR9710057 | 12,057,712 | 12,057,712 | 10,971 | 70.2 | 421 | CP041613 |
As determined through automatic annotation by the NCBI Prokaryotic Genome Annotation Pipeline. CDS, coding sequences.
TIR, terminal inverted repeat.
L/C, linear (L) or circular (C) replicon configuration, as predicted by the assembler and tested by pulsed-field gel electrophoresis (not shown).
Data availability.
Genome sequences and raw sequence reads are available from GenBank and the NCBI Sequence Read Archive under the accession numbers shown in Table 1.
ACKNOWLEDGMENTS
This work was funded by the French National Research Agency (grants ANR LABEX ARBRE and ANR-11-LABX-0002-01), by the French National Institute for Agricultural Research (INRA), and by Région Lorraine (now called Région Grand Est).
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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
Genome sequences and raw sequence reads are available from GenBank and the NCBI Sequence Read Archive under the accession numbers shown in Table 1.