Table 1.
List of genomes sequenced on PacBio RS II on the Okinawa genome projects
| Sample name | Methods | Replicon name | Genome length (b) | G+C content (%) | Hard-to-sequence regions | Accession no. | Published year [Ref.] |
|---|---|---|---|---|---|---|---|
| Mycobacterium tuberculosis Kurono (ATCC35812) | PacBio | Chromosome | 4,415,078 | 65.60 | G+C content of 80% region (2,000 bp), 117 sets of >1000-bp identical sequence pairs | AP014573 | 2015 [17] |
| Multidrug-resistant Acinetobacter baumannii IOMTU433 | PacBio | Chromosome | 4,000,970 | 39.15 | 41 sets of >1000-bp identical sequence pairs (5355-bp maximum) | AP014649 | 2015 [18] |
| Plasmid | 189,354 | 39.53 | AP014650 | ||||
| Multidrug-resistant Pseudomonas aeruginosa NCGM1984 | PacBio | Chromosome | 6,850,954 | 65.96 | 6 sets of >10,000-bp identical sequence pairs (27,239-bp maximum) | AP014646 | 2016 [19] |
| Leptospira interrogans serovar Manilae strain UP-MMC-NIID 1 | PacBio | Chromosome 1 | 4,238,972 | 35.00 | Plasmid, methylation | CP011931 | 2015 [20] |
| Chromosome 2 | 358,378 | 34.91 | CP011932 | ||||
| Plasmid pLIMLP1 | 70,055 | 34.54 | CP011933 | ||||
| L. interrogans serovar Manilae strain UP-MMC-NIID 67 | Chromosome 1 | 4,238,922 | 35.00 | CP011934 | |||
| Chromosome 2 | 358,377 | 34.91 | CP011935 | ||||
| Plasmid pLIMLP1 | 70,055 | 34.54 | CP011936 | ||||
| Helicobacter pylori Oki102 | PacBio | Chromosome | 1,633,212 | 38.81 | 8227-bp identical pair, methylation | CP006820 | 2014 [21] |
| H. pylori Oki112 | Chromosome | 1,637,925 | 38.81 | CP006821 | |||
| H. pylori Oki128 | Chromosome | 1,553,826 | 38.97 | CP006822 | |||
| H. pylori Oki154 | Chromosome | 1,599,700 | 38.80 | G+C content of 28.7% region (2000 bp) | CP006823 | ||
| H. pylori Oki422 | Chromosome | 1,634,852 | 38.83 | CP006824 | |||
| H. pylori Oki673 | Chromosome | 1,595,058 | 38.82 | CP006825 | |||
| H. pylori Oki828 | Chromosome | 1,600,345 | 38.80 | CP006826 | |||
| H. pylori Oki898 | Chromosome | 1,634,875 | 38.83 | CP006827 | |||
| Influenza virus Okinawa strain | PacBio | cDNA | Data not published | Data not published | Full-length sequencing of all eight segments without assembly or resequencing | Data not published | This article |
| Streptomyces versipellis 4083-SVS6, vst gene cluster | PacBio | BAC | 124,623 | 70.74 | G+C content of 76.2% region (2000 bp) | LC006086 | 2014 [30] |
| Actinomadura fulva subsp. indica ATCC 53714, flv gene cluster | PacBio | Not opened | Not opened | Not opened | Not opened | LC095592 | 2015 [31] |
| Lactobacillus curvatus FBA2 | PacBio | Chromosome | 1,848,756 | 42.1 | 43 sets of >1000-bp identical sequence pairs (3118-bp maximum), G+C content of 26.9% region | CP016028 | 2016 [32] |
| Dehalococcoides. mccartyi IBARAKI | PacBio, SOLiD3 | Chromosome | 1,451,062 | 47.00 | 39 sets of >1000-bp identical sequence pairs | NZ-AP014563 | 2014 [33] |
| Endosymbiont of Bathymodiolus septemdierum str. Myojin Knoll | PacBio, 454, Sanger, Illumina | Chromosome | 1,469,434 | 38.70 | Subpopulation | AP013042 | 2015 [34] |
| Bacterial symbiont “TC1” of Trimyema compressum | PacBio | Chromosome | 1,586,453 | 32.8 | 207 sets of >1000-bp identical sequence pairs, G+C content of 23.5% region | CP014606 | 2016 [36] |
| Plasmid | 35,795 | 29.7 | CP014607 | ||||
| Vigna. angularis cv. ‘Shumari’ | PacBio, Illumina | 11 Chromosome | All scaffolds Total 522,761,097 (cover 95%) Anchored scaffolds Total 471,245,712 (cover 85.6%) |
– | Repetitive regions (50.6% of genome) | AP015034-AP017294 | 2015 [37] |
| Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311 | PacBio | Chromosome | 4,793,299 | 52.20 | 5420-bp identical sequence pair | CP009102 | 2014 [41] |
| Plasmid | 38,457 | 40.70 | CP009103 | ||||
| Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231T) | PacBio | Chromosome | 2,755,072 | 32.86 | 29 sets of >1000-bp identical sequence pairs (,063-bp maximum), tandem repeats (384 bp × 5 copies) | CP011526 | 2015 [42] |
| Plasmid | 27,490 | 30.69 | CP011527 | ||||
| Pseudomonas aeruginosa DSM 50071T | PacBio | Chromosome | 6,317,050 | 66.52 | 5288-bp identical pair, 183 tandem repeats (246 bp × 20.7 copies) | CP012001 | 2015 [43] |
| Clostridium sporogenes DSM 795T | PacBio | Chromosome | 4,142,990 | 27.98 | 86 sets of >1000-bp identical sequence pairs (4911-bp maximum), 380 tandem repeats (369 bp × 8.5 copies maximum), variable number tandem repeat | CP011663 | 2015 [44] |
| CM-SJS/TEN-associated IKZF1 SNPs region of Japanese reference, Japanese SJS, and healthy subjects | PacBio | Targeted long amplicon | Data not published | Data not published | Targeted region (17 kb) of diploid genome | Data not published | This article |