Table 1.
Paenibacillus larvae strains and respective reference name, accession number, genome sequencing method and coverage, genotype classification, GC content, genome size, number of contigs, and respective sizes.
| Host | Strain | Reference strain | Accession no. | Sequencing method | Genome coverage | ERIC genotype | GC% | Size (Mbp) | No. of contigs | Size range of contigs (Kbp) | Prophages (validated) | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Intact | Defective | |||||||||||
| 3* | DSM 25719 | DSM 25719 | NZ_ADFW00000000.1 | Sanger dideoxy sequencing; 454; Illumina | 94 | I | 44.1 | 4.58 | 8 | 8.1–3,664 | 21 | 8 | 13 |
| 5a | MEX14 | NZ_LAWY00000000 | 454 | 50 | I | 44.0 | 4.19 | 139 | 0.5–213.6 | 17 | 3 | 14 | |
| 6 | ATCC 9545 | ATCC 9545 | NZ_CP019687.1 | PacBio | 147.4 | I | 44.2 | 4.29 | NA | NA | 13 | 5 | 8 |
| 7 | ATCC 13537 | ATCC 13537 | NZ_CP019794.1 | PacBio | 56.4 | IV | 44.3 | 4.41 | NA | NA | 16 | 3 | 13 |
| 8 | CCM 38 | CCUG 7429 | NZ_CP020327.1 | PacBio | 150.8 | IV | 44.3 | 4.33 | NA | NA | 15 | 5 | 10 |
| 9* | SAG 10367 | SAG 10367 | NZ_CP020557.1 | PacBio | 214.2 | II | 44.1 | 4.67 | NA | NA | 18 | 7 | 11 |
| 10 | ERIC_I | DSM 7030 | NZ_CP019651.1 | PacBio; Illumina HiSeq2500 | 193 | I | 44.2 | 4.29 | NA | NA | 15 | 5 | 10 |
| 11* | ERIC_III | LMG 16252 | NZ_CP019655.1 | PacBio; Illumina HiSeq2500 | 114 | III | 44.2 | 4.49 | NA | NA | 18 | 7 | 11 |
| 12 | ERIC_IV | LMG 16247 | NZ_CP019659.1 | PacBio; Illumina HiSeq2500 | 113 | IV | 44.3 | 4.27 | NA | NA | 15 | 3 | 12 |
| 13 | DSM 25430; ERIC_II | DSM 25430 | NZ_CP019652.1 | PacBio; Illumina HiSeq2500 | 153 | II | 45.0 | 4.02 | NA | NA | 12 | 1 | 11 |
| 14* | ERIC_V | DSM 106052 | CP019717.1 | PacBio; Illumina HiSeq2500 | 257 | V | 44.1 | 4.67 | NA | NA | 21 | 8 | 13 |
| Average GC content | 44.3 | Total validated | 181 | 55 | 126 | ||||||||
| Host (Excluded) | Strain | Reference strain | Accession no. | Sequencing method | Genome coverage | ERIC genotype | GC% | Size (Mbp) | No. of contigs | Size range of contigs (Kbp) | Prophages (excluded) | ||
| Total | Intact | Defective | |||||||||||
| 1b | BRL-230010 | NZ_AARF00000000.1 | 454 | 50 | I | 44.1 | 3.98 | 646 | 0.25–58.6 | 23 | 0 | 23 | |
| 2b | B-3650 | LMG 16245 | NZ_ADZY00000000.3 | Sanger; Illumina | 1; 100 | I | 44.1 | 4.35 | 353 | 0.05–331.7 | 9 | 0 | 9 |
| 4c | DSM 25430 | DSM 25430 | NC_023134.1 | Sanger dideoxy sequencing; 454; Illumina | 64 | II | 45 | 4.05 | NA | NA | 8 | 0 | 8 |
The last three columns refer to the number of total, intact and defective prophages present in each strain, after manual validation. *Hosts with genome size >4.49 Mbp and with ≥7 no. of intact prophages. The second table details data from strains excluded from the analysis.
Host 5 (MEX14) classified as ERIC I without experimental validation; homology and position in the ERIC I branch of phylogenetic tree available on NCBI database.
The high number of contigs available restricted an accurate analysis.
Sequence reported by Djukic et al. (2014), identical to the obtained latter (re-sequenced) by Beims et al. (2020). NA, not applicable.