ABSTRACT
The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.
ANNOUNCEMENT
Bifidobacteria are often used as probiotics due to their health-promoting effects (1). Bifidobacterium animalis subsp. lactis BB-12 (2) has been associated with positive effects in areas such as immune function (3–5), gastrointestinal health (6), and the respiratory system (7, 8). Here, we present a second version of the BB-12 genome, generated through state-of-the-art sequencing technologies using both Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms.
BB-12 (DSM 15954) was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) (Braunschweig, Germany) in April 2004 and stored at −80°C. Cells were grown anaerobically at 37°C in MRS broth containing 0.05% l-cysteine hydrochloride monohydrate. Genomic DNA was extracted with the DNeasy blood and tissue kit on a QiaCube system (Qiagen, Germany). Sequencing libraries were generated using a KAPA HyperPlus library preparation kit and KAPA dual-indexed adapters (Roche, Switzerland), and AMPure XP beads (Beckman Coulter, USA) were used for library cleanup steps, following the manufacturers’ protocols. DNA concentrations were measured on a Qubit 3.0 fluorimeter using Qubit double-stranded DNA (dsDNA) broad-range and Qubit 1X dsDNA high-sensitivity (HS) assays (Thermo Fisher Scientific, USA). The average dsDNA library size distribution was determined using the Agilent HS next-generation sequencing (NGS) fragment (1 to 6,000 bp) kit on an Agilent fragment analyzer. Libraries were sequenced with the 600-cycle MiSeq reagent kit v3 on a MiSeq platform (Illumina Inc., USA) with a paired-end protocol and read lengths of 301 nucleotides (nt). Short-read sequencing yielded 686,356 read pairs with a total length of 255,784,736 nt. The reads were trimmed for quality using AdapterRemoval v2.2.4 (9) with parameters --minquality 20 --minlength 30 --trimqualities --trimns --trim5p 15.
For long-read sequencing, genomic DNA was extracted with a Genomic Maxi AX gravity column-based kit (A&A Biotechnology, Poland), prepared using a rapid barcoding sequencing kit (SQK-RBK004; ONT), and sequenced on a MinION flow cell (R9.4.1 FLO-MIN106; ONT) for 48 h. This yielded 72,175 reads with a total length of 374,342,567 nt and an N50 value of 10,185 nt. Base calling was performed with the Guppy base caller v3.2.10, and adapters were trimmed using ONT MinKNOW software.
The complete genome sequence of BB-12 was assembled using the long and short sequencing reads with Unicycler v0.4.7 (10) in conservative mode, resulting in one 1,944,152-bp circular chromosome with a G+C content of 60.5%. The genome sequence was annotated with Prokaryotic Genome Annotation Pipeline (PGAP) v4.13 (11), resulting in 1,615 genes.
To assess whether the genome sequenced here differs from the previously available BB-12 genome (GenBank accession number NC_017214.1), breseq v0.35.5 (12) with default settings was used to map Illumina reads from this work to both genome sequences. Mapping of Illumina reads to the genome sequence produced in this work did not yield any variants, while mapping to the previously available genome sequence resulted in 74 single-nucleotide differences and 235 small indels (Table 1).
TABLE 1.
Overview of the genetic differences identified by comparing the newly generated reads to the previously available BB12 genome sequence (GenBank accession number NC_017214.1)a
| Nucleotide position | Mutation | Annotation | Gene(s) |
|---|---|---|---|
| 469 | C→A | Q49K (CAA→AAG) | BIF_00469 → |
| 471 | A→G | Q49K (CAA→AAG) | BIF_00469 → |
| 21536 | +A | Coding (867/927 nt) | BIF_02142 → |
| 21540 | 3 bp→12 bp | Coding (871–873/927 nt) | BIF_02142 → |
| 28398 | +C | Intergenic (+28/−48) | BIF_00002 → / → BIF_02140 |
| 28414 | A→T | Intergenic (+44/−32) | BIF_00002 → / → BIF_02140 |
| 28417 | 4 bp→18 bp | Intergenic (+47/−26) | BIF_00002 → / → BIF_02140 |
| 45995 | +TGGAATTCCACGGGCCT | Intergenic (+95/+86) | BIF_01763 → / ← BIF_01079 |
| 93265 | +CG | Intergenic (+43/+6) | BIF_01365 → / ← BIF_02171 |
| 93267 | +AACC | Intergenic (+45/+4) | BIF_01365 → / ← BIF_02171 |
| 93268 | T→A | Intergenic (+46/+3) | BIF_01365 → / ← BIF_02171 |
| 93270 | +AT | Intergenic (+48/+1) | BIF_01365 → / ← BIF_02171 |
| 103949 | 4 bp→22 bp | Intergenic (+18/+56) | BIF_01186 → / ← BIF_02012 |
| 103961 | C→A | Intergenic (+30/+47) | BIF_01186 → / ← BIF_02012 |
| 103963 | Δ1 bp | Intergenic (+32/+45) | BIF_01186 → / ← BIF_02012 |
| 112686 | +25 bp | Intergenic (−226/+31) | BIF_00107 ← / ← BIF_00801 |
| 132978 | 5 bp→19 bp | Intergenic (+14/−185) | BIF_01865 → / → BIF_02174 |
| 132990 | +G | Intergenic (+26/−177) | BIF_01865 → / → BIF_02174 |
| 132999 | +C | Intergenic (+35/−168) | BIF_01865 → / → BIF_02174 |
| 152141 | 21 bp→37 bp | Intergenic (+39/+16) | BIF_01884 → / ← BIF_00858 |
| 156687 | +23 bp | Intergenic (+51/+2) | BIF_00548 → / ← BIF_00217 |
| 174620 | +G | Coding (9/300 nt) | BIF_02178 → |
| 174628 | +G | Coding (17/300 nt) | BIF_02178 → |
| 174796 | 3 bp→25 bp | Coding (185–187/300 nt) | BIF_02178 → |
| 174847 | +G | Coding (236/300 nt) | BIF_02178 → |
| 174849 | G→C | A80P (GCC→CCC) | BIF_02178 → |
| 226865 | +A | Coding (974/1,167 nt) | BIF_00004 ← |
| 226867 | G→C | S324S (TCC→TCG) | BIF_00004 ← |
| 303227 | +GGTGG | Intergenic (+30/+242) | BIF_01290 → / ← BIF_00983 |
| 332638 | +GCATGCGGCGA | Intergenic (+65/+62) | BIF_00009 → / ← BIF_01572 |
| 332642 | G→C | Intergenic (+69/+58) | BIF_00009 → / ← BIF_01572 |
| 348109 | 9 bp→32 bp | Intergenic (+13/+31) | BIF_01159 → / ← BIF_02184 |
| 374215 | +32 bp | Intergenic (−158/+189) | BIF_00055 ← / ← BIF_01897 |
| 374264 | +G | Intergenic (−207/+140) | BIF_00055 ← / ← BIF_01897 |
| 374286 | 2 bp→GC | Intergenic (−229/+117) | BIF_00055 ← / ← BIF_01897 |
| 395152 | 49 bp→66 bp | Intergenic (+77/+63) | BIF_01176 → / ← BIF_00941 |
| 395195 | 7 bp→19 bp | Intergenic (+120/+62) | BIF_01176 → / ← BIF_00941 |
| 412279 | +CTGAGCACACGGGGGCCG | Intergenic (+8/−75) | BIF_01519 → / → BIF_01115 |
| 412281 | G→T | Intergenic (+10/−73) | BIF_01519 → / → BIF_01115 |
| 412292 | +A | Intergenic (+21/−62) | BIF_01519 → / → BIF_01115 |
| 412906 | +54 bp | Intergenic (+25/+20) | BIF_01115 → / ← BIF_01114 |
| 416028 | +C | Intergenic (+371/+25) | BIF_01112 → / ← BIF_02188 |
| 416031 | +GA | Intergenic (+374/+22) | BIF_01112 → / ← BIF_02188 |
| 423866 | 1 bp→GG | Intergenic (+45/+26) | BIF_00671 → / ← BIF_00700 |
| 423877 | 1 bp→18 bp | Intergenic (+56/+15) | BIF_00671 → / ← BIF_00700 |
| 426071 | +GGCGCCACACGCGAA | Intergenic (−149/+31) | BIF_00700 ← / ← BIF_01226 |
| 426073 | +C | Intergenic (−151/+29) | BIF_00700 ← / ← BIF_01226 |
| 442719 | Δ1 bp | Intergenic (−50/+31) | BIF_01320 ← / ← BIF_00999 |
| 442725 | 6 bp→19 bp | Intergenic (−56/+20) | BIF_01320 ← / ← BIF_00999 |
| 458009 | +45 bp | Coding (13/132 nt) | BIF_02190 ← |
| 479759 | A→G | Intergenic (+44/+44) | BIF_01252 → / ← BIF_01632 |
| 512389 | 2 bp→GC | Coding (58–59/180 nt) | BIF_02194 ← |
| 512406 | +C | Coding (42/180 nt) | BIF_02194 ← |
| 512414 | +C | Coding (34/180 nt) | BIF_02194 ← |
| 515142 | 2 bp→AA | Coding (116–117/2,316 nt) | BIF_02061 → |
| 515145 | G→A | W40* (TGG→TAG) | BIF_02061 → |
| 515153 | G→C | V43L (GTA→CTA) | BIF_02061 → |
| 544458 | A→G | T524T (ACA→ACG) | BIF_01621 → |
| 544491 | 20 bp→35 bp | Coding (1,605–1,624/1,653 nt) | BIF_01621 → |
| 551925 | 3 bp→17 bp | Coding (31–33/1,518 nt) | BIF_02058 → |
| 551931 | Δ1 bp | Coding (37/1,518 nt) | BIF_02058 → |
| 555527 | 62 bp→77 bp | Intergenic (+44/+177) | BIF_00496 → / ← BIF_01682 |
| 574023 | +AACCCGCCC | Intergenic (−880/+30) | BIF_16SrRNA12 ← / ← BIF_01549 |
| 601285 | Δ1 bp | Coding (2/771 nt) | BIF_00943 ← |
| 607329 | +AC | Coding (148/159 nt) | BIF_02197 → |
| 607331 | G→C | A50P (GCG→CCC) | BIF_02197 → |
| 627558 | Δ1 bp | Intergenic (+54/−170) | BIF_01669 → / → BIF_02198 |
| 627563 | +CCCGCCGGC | Intergenic (+59/−165) | BIF_01669 → / → BIF_02198 |
| 631554 | +C | Intergenic (−383/+213) | BIF_00740 ← / ← BIF_00658 |
| 631589 | +A | Intergenic (−418/+178) | BIF_00740 ← / ← BIF_00658 |
| 631599 | Δ1 bp | Intergenic (−428/+168) | BIF_00740 ← / ← BIF_00658 |
| 631605 | 11 bp→48 bp | Intergenic (−434/+152) | BIF_00740 ← / ← BIF_00658 |
| 632722 | +24 bp | Intergenic (−212/+219) | BIF_00658 ← / ← BIF_01209 |
| 632782 | +G | Intergenic (−272/+159) | BIF_00658 ← / ← BIF_01209 |
| 690916 | 7 bp→28 bp | Intergenic (+28/+71) | BIF_01558 → / ← BIF_01474 |
| 795160 | (G)8→9 | Coding (834/1,299 nt) | BIF_01420 → |
| 803347 | +AGGTGGGG | Coding (433/435 nt) | BIF_02002 ← |
| 803348 | +AT | Coding (432/435 nt) | BIF_02002 ← |
| 803350 | A→C | S144A (TCG→GCA) | BIF_02002 ← |
| 805769 | +AGCA | Intergenic (−41/+271) | BIF_00477 ← / ← BIF_02124 |
| 813756 | +C | Intergenic (+67/−63) | BIF_01190 → / → BIF_02126 |
| 889981 | 48 bp→76 bp | Intergenic (+42/+30) | BIF_01494 → / ← BIF_00763 |
| 890037 | +G | Intergenic (+98/+21) | BIF_01494 → / ← BIF_00763 |
| 899064 | +A | Intergenic (+234/−448) | BIF_01023 → / → BIF_01805 |
| 899066 | C→A | Intergenic (+236/−446) | BIF_01023 → / → BIF_01805 |
| 899080 | +G | Intergenic (+250/−432) | BIF_01023 → / → BIF_01805 |
| 899096 | C→A | Intergenic (+266/−416) | BIF_01023 → / → BIF_01805 |
| 927296 | +GGG | Intergenic (+878/+33) | BIF_01509 → / ← BIF_01083 |
| 980962 | +G | Intergenic (−141/+180) | BIF_00863 ← / ← BIF_01247 |
| 996014 | 1 bp→CG | Intergenic (+36/−287) | BIF_02104 → / → BIF_01142 |
| 1054723 | +29 bp | Intergenic (+134/−290) | BIF_00088 → / → BIF_02096 |
| 1054848 | 2 bp→21 bp | Intergenic (+259/−164) | BIF_00088 → / → BIF_02096 |
| 1054883 | 2 bp→GT | Intergenic (+294/−129) | BIF_00088 → / → BIF_02096 |
| 1151595 | +C | Intergenic (+39/+27) | BIF_02003 → / ← BIF_tRNA28 |
| 1203020 | (C)6→5 | Intergenic (−170/−29) | BIF_02234 ← / → BIF_00647 |
| 1203058 | (G)6→5 | Coding (10/2,550 nt) | BIF_00647 → |
| 1249797 | 15 bp→34 bp | Coding (32–46/126 nt) | BIF_02237 → |
| 1254633 | T→C | K65R (AAG→AGG) | BIF_00633 ← |
| 1270898 | +T | Intergenic (+15/+58) | BIF_00472 → / ← BIF_00205 |
| 1270906 | +TGTGGGGCCCTACGG | Intergenic (+23/+50) | BIF_00472 → / ← BIF_00205 |
| 1270910 | +C | Intergenic (+27/+46) | BIF_00472 → / ← BIF_00205 |
| 1283590 | +TTCGGG | Intergenic (+24/−367) | BIF_00825 → / → BIF_00906 |
| 1283592 | +CC | Intergenic (+26/−365) | BIF_00825 → / → BIF_00906 |
| 1291704 | 2 bp→11 bp | Intergenic (−1,307/+149) | BIF_01039 ← / ← BIF_00316 |
| 1291708 | +T | Intergenic (−1,311/+146) | BIF_01039 ← / ← BIF_00316 |
| 1291709 | G→C | Intergenic (−1,312/+145) | BIF_01039 ← / ← BIF_00316 |
| 1309076 | +C | Coding (128/1,077 nt) | BIF_01009 ← |
| 1309114 | A→G | C30C (TGT→TGC) | BIF_01009 ← |
| 1333145 | +CC | Intergenic (+76/+16) | BIF_01182 → / ← BIF_00625 |
| 1333149 | +ACGCA | Intergenic (+80/+12) | BIF_01182 → / ← BIF_00625 |
| 1333151 | +A | Intergenic (+82/+10) | BIF_01182 → / ← BIF_00625 |
| 1333153 | +C | Intergenic (+84/+8) | BIF_01182 → / ← BIF_00625 |
| 1345841 | +A | Intergenic (+107/+54) | BIF_01862 → / ← BIF_00279 |
| 1345851 | 3 bp→18 bp | Intergenic (+117/+42) | BIF_01862 → / ← BIF_00279 |
| 1345877 | +G | Intergenic (+143/+18) | BIF_01862 → / ← BIF_00279 |
| 1345918 | +G | Coding (517/540 nt) | BIF_00279 ← |
| 1345930 | +T | Coding (505/540 nt) | BIF_00279 ← |
| 1347684 | +ACC | Intergenic (−32/−35) | BIF_02123 ← / → BIF_00396 |
| 1347686 | +C | Intergenic (−34/−33) | BIF_02123 ← / → BIF_00396 |
| 1347687 | +C | Intergenic (−35/−32) | BIF_02123 ← / → BIF_00396 |
| 1352581 | G→A | Intergenic (+158/+131) | BIF_00072 → / ← BIF_00341 |
| 1352652 | +ACAGAAGGGCGGT | Intergenic (+229/+60) | BIF_00072 → / ← BIF_00341 |
| 1352657 | C→G | Intergenic (+234/+55) | BIF_00072 → / ← BIF_00341 |
| 1352659 | A→C | Intergenic (+236/+53) | BIF_00072 → / ← BIF_00341 |
| 1360042 | 19 bp→35 bp | Intergenic (+28/+7) | BIF_00368 → / ← BIF_01760 |
| 1376069 | 14 bp→33 bp | Intergenic (+38/+27) | BIF_01846 → / ← BIF_00467 |
| 1414041 | C→A | A373D (GCC→GAC) | BIF_00934 → |
| 1414072 | Δ1 bp | Coding (1,149/1,152 nt) | BIF_00934 → |
| 1414079 | +G | Intergenic (+4/+74) | BIF_00934 → / ← BIF_00718 |
| 1414090 | 8 bp→28 bp | Intergenic (+15/+56) | BIF_00934 → / ← BIF_00718 |
| 1419213 | +G | Intergenic (+37/+331) | BIF_00332 → / ← BIF_02065 |
| 1419441 | T→G | Intergenic (+265/+103) | BIF_00332 → / ← BIF_02065 |
| 1419443 | C→T | Intergenic (+267/+101) | BIF_00332 → / ← BIF_02065 |
| 1419447 | 40 bp→53 bp | Intergenic (+271/+58) | BIF_00332 → / ← BIF_02065 |
| 1419488 | T→G | Intergenic (+312/+56) | BIF_00332 → / ← BIF_02065 |
| 1419490 | +TG | Intergenic (+314/+54) | BIF_00332 → / ← BIF_02065 |
| 1419492 | 1 bp→AC | Intergenic (+316/+52) | BIF_00332 → / ← BIF_02065 |
| 1419499 | 2 bp→GC | Intergenic (+323/+44) | BIF_00332 → / ← BIF_02065 |
| 1419504 | +C | Intergenic (+328/+40) | BIF_00332 → / ← BIF_02065 |
| 1424409 | 4 bp→36 bp | Intergenic (+52/−47) | BIF_00028 → / → BIF_00780 |
| 1429003 | 1 bp→16 bp | Intergenic (+54/−44) | BIF_00776 → / → BIF_01792 |
| 1429006 | T→G | Intergenic (+57/−41) | BIF_00776 → / → BIF_01792 |
| 1429008 | C→T | Intergenic (+59/−39) | BIF_00776 → / → BIF_01792 |
| 1435740 | 10 bp→24 bp | Intergenic (+33/+22) | BIF_00308 → / ← BIF_00385 |
| 1435753 | C→A | Intergenic (+46/+18) | BIF_00308 → / ← BIF_00385 |
| 1442201 | +G | Intergenic (+56/+22) | BIF_00264 → / ← BIF_01752 |
| 1444091 | 1 bp→35 bp | Intergenic (−135/+100) | BIF_01751 ← / ← BIF_01116 |
| 1444149 | +C | Intergenic (−193/+42) | BIF_01751 ← / ← BIF_01116 |
| 1444153 | +C | Intergenic (−197/+38) | BIF_01751 ← / ← BIF_01116 |
| 1459986 | 14 bp→30 bp | Intergenic (+38/+3) | BIF_00179 → / ← BIF_00879 |
| 1466361 | +TTGCGTTCCC | Intergenic (−140/+28) | BIF_01803 ← / ← BIF_00130 |
| 1466364 | +C | Intergenic (−143/+25) | BIF_01803 ← / ← BIF_00130 |
| 1466365 | G→T | Intergenic (−144/+24) | BIF_01803 ← / ← BIF_00130 |
| 1469891 | +G | Intergenic (+56/−504) | BIF_00011 → / → BIF_02078 |
| 1469893 | +G | Intergenic (+58/−502) | BIF_00011 → / → BIF_02078 |
| 1470155 | A→C | Intergenic (+320/−240) | BIF_00011 → / → BIF_02078 |
| 1470159 | T→C | Intergenic (+324/−236) | BIF_00011 → / → BIF_02078 |
| 1470162 | +C | Intergenic (+327/−233) | BIF_00011 → / → BIF_02078 |
| 1470165 | T→C | Intergenic (+330/−230) | BIF_00011 → / → BIF_02078 |
| 1470171 | G→C | Intergenic (+336/−224) | BIF_00011 → / → BIF_02078 |
| 1470174 | G→C | Intergenic (+339/−221) | BIF_00011 → / → BIF_02078 |
| 1470177 | +C | Intergenic (+342/−218) | BIF_00011 → / → BIF_02078 |
| 1470183 | 1 bp→CC | Intergenic (+348/−212) | BIF_00011 → / → BIF_02078 |
| 1470187 | +C | Intergenic (+352/−208) | BIF_00011 → / → BIF_02078 |
| 1470190 | T→C | Intergenic (+355/−205) | BIF_00011 → / → BIF_02078 |
| 1470192 | T→C | Intergenic (+357/−203) | BIF_00011 → / → BIF_02078 |
| 1470195 | T→C | Intergenic (+360/−200) | BIF_00011 → / → BIF_02078 |
| 1470204 | T→C | Intergenic (+369/−191) | BIF_00011 → / → BIF_02078 |
| 1470206 | A→T | Intergenic (+371/−189) | BIF_00011 → / → BIF_02078 |
| 1470216 | G→C | Intergenic (+381/−179) | BIF_00011 → / → BIF_02078 |
| 1470227 | 2 bp→GC | Intergenic (+392/−167) | BIF_00011 → / → BIF_02078 |
| 1470235 | G→T | Intergenic (+400/−160) | BIF_00011 → / → BIF_02078 |
| 1470237 | T→C | Intergenic (+402/−158) | BIF_00011 → / → BIF_02078 |
| 1470245 | T→C | Intergenic (+410/−150) | BIF_00011 → / → BIF_02078 |
| 1470253 | A→C | Intergenic (+418/−142) | BIF_00011 → / → BIF_02078 |
| 1470256 | T→C | Intergenic (+421/−139) | BIF_00011 → / → BIF_02078 |
| 1470259 | T→C | Intergenic (+424/−136) | BIF_00011 → / → BIF_02078 |
| 1470276 | T→C | Intergenic (+441/−119) | BIF_00011 → / → BIF_02078 |
| 1470279 | 4 bp→CATT | Intergenic (+444/−113) | BIF_00011 → / → BIF_02078 |
| 1470308 | 4 bp→CCG | Intergenic (+473/−84) | BIF_00011 → / → BIF_02078 |
| 1470314 | T→C | Intergenic (+479/−81) | BIF_00011 → / → BIF_02078 |
| 1470322 | A→C | Intergenic (+487/−73) | BIF_00011 → / → BIF_02078 |
| 1470328 | T→C | Intergenic (+493/−67) | BIF_00011 → / → BIF_02078 |
| 1474821 | +G | Coding (7/2,349 nt) | BIF_00363 → |
| 1474832 | +C | Coding (18/2,349 nt) | BIF_00363 → |
| 1494471 | +TGAAGCGGC | Intergenic (+15/+59) | BIF_00354 → / ← BIF_02081 |
| 1494477 | T→G | Intergenic (+21/+53) | BIF_00354 → / ← BIF_02081 |
| 1494479 | 1 bp→TG | Intergenic (+23/+51) | BIF_00354 → / ← BIF_02081 |
| 1507139 | 7 bp→21 bp | Intergenic (+39/+35) | BIF_00355 → / ← BIF_00882 |
| 1516347 | Δ1 bp | Intergenic (+37/−88) | BIF_01797 → / → BIF_tRNA37 |
| 1516350 | +TC | Intergenic (+40/−85) | BIF_01797 → / → BIF_tRNA37 |
| 1533794 | C→A | Intergenic (−79/+25) | BIF_00836 ← / ← BIF_00445 |
| 1533800 | 3 bp→15 bp | Intergenic (−85/+17) | BIF_00836 ← / ← BIF_00445 |
| 1537535 | G→A | Intergenic (+448/−131) | BIF_01766 → / → BIF_02245 |
| 1537566 | C→G | Intergenic (+479/−100) | BIF_01766 → / → BIF_02245 |
| 1537568 | G→C | Intergenic (+481/−98) | BIF_01766 → / → BIF_02245 |
| 1537618 | C→T | Intergenic (+531/−48) | BIF_01766 → / → BIF_02245 |
| 1537650 | 2 bp→AT | Intergenic (+563/−15) | BIF_01766 → / → BIF_02245 |
| 1537653 | 1 bp→CG | Intergenic (+566/−13) | BIF_01766 → / → BIF_02245 |
| 1537688 | A→C | N8T (AAC→ACC) | BIF_02245 → |
| 1537694 | A→T | E10V (GAG→GTG) | BIF_02245 → |
| 1537708 | C→T | P15S (CCT→TCC) | BIF_02245 → |
| 1537710 | T→C | P15S (CCT→TCC) | BIF_02245 → |
| 1537719 | 2 bp→GC | Coding (54–55/99 nt) | BIF_02245 → |
| 1537727 | Δ1 bp | Coding (62/99 nt) | BIF_02245 → |
| 1537733 | +TG | Coding (68/99 nt) | BIF_02245 → |
| 1537743 | G→C | M26I (ATG→ATC) | BIF_02245 → |
| 1541799 | Δ1 bp | Coding (970/1,029 nt) | BIF_02111 → |
| 1541804 | 69 bp→84 bp | [BIF_02111] | |
| 1541874 | +C | Intergenic (+16/−107) | BIF_02111 → / → BIF_01915 |
| 1576870 | +C | Intergenic (+277/+73) | BIF_00659 → / ← BIF_00506 |
| 1576890 | 2 bp→10 bp | Intergenic (+297/+52) | BIF_00659 → / ← BIF_00506 |
| 1589406 | +ATGCGCCTGAC | Intergenic (−86/+44) | BIF_01830 ← / ← BIF_00522 |
| 1593487 | 2 bp→GC | Intergenic (−92/+36) | BIF_02016 ← / ← BIF_02017 |
| 1593511 | +C | Intergenic (−116/+13) | BIF_02016 ← / ← BIF_02017 |
| 1593523 | +G | Intergenic (−128/+1) | BIF_02016 ← / ← BIF_02017 |
| 1593561 | +T | Coding (242/279 nt) | BIF_02017 ← |
| 1595922 | 12 bp→22 bp | Intergenic (+63/+15) | BIF_00337 → / ← BIF_01744 |
| 1595936 | +GA | Intergenic (+77/+12) | BIF_00337 → / ← BIF_01744 |
| 1595981 | Δ1 bp | Coding (846/879 nt) | BIF_01744 ← |
| 1595984 | +AC | Coding (843/879 nt) | BIF_01744 ← |
| 1595988 | +C | Coding (839/879 nt) | BIF_01744 ← |
| 1602531 | 3 bp→13 bp | Intergenic (+9/−74) | BIF_00963 → / → BIF_00287 |
| 1602535 | 1 bp→CC | Intergenic (+13/−72) | BIF_00963 → / → BIF_00287 |
| 1610137 | Δ2 bp | Intergenic (−9/+26) | BIF_01901 ← / ← BIF_00277 |
| 1634778 | +C | Intergenic (+137/−53) | BIF_01000 → / → BIF_00897 |
| 1657183 | 12 bp→30 bp | Intergenic (−58/+30) | BIF_01871 ← / ← BIF_00406 |
| 1671395 | 8 bp→29 bp | Intergenic (+22/+60) | BIF_00122 → / ← BIF_00441 |
| 1676721 | +CGGGAGCCTTCCCATATCAA | Intergenic (+49/+5) | BIF_00162 → / ← BIF_00129 |
| 1685544 | 12 bp→38 bp | Intergenic (+9/+81) | BIF_00244 → / ← BIF_01784 |
| 1685646 | Δ1 bp | Coding (515/525 nt) | BIF_01784 ← |
| 1691786 | 2 bp→16 bp | Intergenic (−152/+40) | BIF_00694 ← / ← BIF_00758 |
| 1704247 | +G | Intergenic (+37/+72) | BIF_00639 → / ← BIF_01823 |
| 1704249 | 38 bp→61 bp | Intergenic (+39/+33) | BIF_00639 → / ← BIF_01823 |
| 1704394 | +G | Coding (414/489 nt) | BIF_01823 ← |
| 1714609 | +ATACGAAGAGGCCC | Intergenic (+15/+75) | BIF_02095 → / ← BIF_02255 |
| 1714612 | A→G | Intergenic (+18/+72) | BIF_02095 → / ← BIF_02255 |
| 1714619 | 2 bp→TG | Intergenic (+25/+64) | BIF_02095 → / ← BIF_02255 |
| 1714622 | G→C | Intergenic (+28/+62) | BIF_02095 → / ← BIF_02255 |
| 1720652 | 14 bp→29 bp | [BIF_02256] | |
| 1735437 | 17 bp→34 bp | Intergenic (−31/+299) | BIF_01975 ← / ← BIF_00492 |
| 1747481 | Δ1 bp | Intergenic (+38/+25) | BIF_00693 → / ← BIF_00329 |
| 1747488 | +A | Intergenic (+45/+18) | BIF_00693 → / ← BIF_00329 |
| 1747489 | +CCCCTCACATTT | Intergenic (+46/+17) | BIF_00693 → / ← BIF_00329 |
| 1755127 | C→G | M12I (ATG→ATC) | BIF_00612 ← |
| 1755177 | +C | Coding (2,001/2,019 nt) | BIF_00102 ← |
| 1755247 | 2 bp→GC | Coding (1,930–1,931/2,019 nt) | BIF_00102 ← |
| 1756978 | +G | Coding (200/2,019 nt) | BIF_00102 ← |
| 1757068 | 1 bp→GT | Coding (110/2,019 nt) | BIF_00102 ← |
| 1757069 | +C | Coding (109/2,019 nt) | BIF_00102 ← |
| 1759022 | +A | Intergenic (−66/+70) | BIF_tRNA49 ← / ← BIF_00125 |
| 1759023 | +ATGGGGTGT | Intergenic (−67/+69) | BIF_tRNA49 ← / ← BIF_00125 |
| 1759024 | +C | Intergenic (−68/+68) | BIF_tRNA49 ← / ← BIF_00125 |
| 1759026 | G→T | Intergenic (−70/+66) | BIF_tRNA49 ← / ← BIF_00125 |
| 1759057 | +C | Intergenic (−101/+35) | BIF_tRNA49 ← / ← BIF_00125 |
| 1770206 | 7 bp→20 bp | Intergenic (+28/+64) | BIF_01817 → / ← BIF_01834 |
| 1770224 | G→C | Intergenic (+46/+52) | BIF_01817 → / ← BIF_01834 |
| 1787741 | 18 bp→50 bp | Intergenic (+6/+30) | BIF_02258 → / ← BIF_00170 |
| 1790308 | Δ1 bp | Intergenic (+24/+44) | BIF_01753 → / ← BIF_01191 |
| 1790315 | +GGGCCCGCGAACAC | Intergenic (+31/+37) | BIF_01753 → / ← BIF_01191 |
| 1790322 | Δ1 bp | Intergenic (+38/+30) | BIF_01753 → / ← BIF_01191 |
| 1790332 | +G | Intergenic (+48/+20) | BIF_01753 → / ← BIF_01191 |
| 1799928 | 6 bp→16 bp | Intergenic (+109/−49) | BIF_02068 → / → BIF_00066 |
| 1800775 | 2 bp→TA | Intergenic (+95/+64) | BIF_00066 → / ← BIF_01169 |
| 1800778 | A→C | Intergenic (+98/+62) | BIF_00066 → / ← BIF_01169 |
| 1800781 | Δ1 bp | Intergenic (+101/+59) | BIF_00066 → / ← BIF_01169 |
| 1800786 | +C | Intergenic (+106/+54) | BIF_00066 → / ← BIF_01169 |
| 1800822 | +AG | Intergenic (+142/+18) | BIF_00066 → / ← BIF_01169 |
| 1800824 | 6 bp→14 bp | Intergenic (+144/+11) | BIF_00066 → / ← BIF_01169 |
| 1800831 | +CC | Intergenic (+151/+9) | BIF_00066 → / ← BIF_01169 |
| 1805672 | 13 bp→37 bp | Intergenic (−25/+12) | BIF_01167 ← / ← BIF_02259 |
| 1806026 | +G | Coding (2,837/2,883 nt) | BIF_00729 ← |
| 1809002 | Δ1 bp | Coding (192/1,608 nt) | BIF_00491 → |
| 1809008 | +G | Coding (198/1,608 nt) | BIF_00491 → |
| 1809045 | 25 bp→59 bp | Coding (235–259/1,608 nt) | BIF_00491 → |
| 1815438 | +GGAAGGGGC | Intergenic (−7/+29) | BIF_00256 ← / ← BIF_00796 |
| 1815443 | A→C | Intergenic (−12/+24) | BIF_00256 ← / ← BIF_00796 |
| 1815446 | Δ1 bp | Intergenic (−15/+21) | BIF_00256 ← / ← BIF_00796 |
| 1815449 | Δ1 bp | Intergenic (−18/+18) | BIF_00256 ← / ← BIF_00796 |
| 1824017 | +26 bp | Intergenic (+34/+19) | BIF_00792 → / ← BIF_01147 |
| 1832709 | T→A | R51W (AGG→TGG) | BIF_02260 ← |
| 1832733 | Δ1 bp | Coding (127/180 nt) | BIF_02260 ← |
| 1832760 | Δ1 bp | Coding (100/180 nt) | BIF_02260 ← |
| 1850719 | 3 bp→13 bp | Intergenic (−100/+17) | BIF_00078 ← / ← BIF_01879 |
| 1851378 | +T | Coding (71/711 nt) | BIF_01879 ← |
| Coding (163/216 nt) | BIF_02261 ← | ||
| 1853256 | Δ1 bp | Coding (63/195 nt) | BIF_02082 ← |
| 1885096 | 10 bp→24 bp | Intergenic (+17/+55) | BIF_01746 → / ← BIF_01789 |
| 1885634 | 2 bp→GC | Coding (1,865–1,866/2,340 nt) | BIF_01789 ← |
| 1885679 | 2 bp→CT | Coding (1,820–1,821/2,340 nt) | BIF_01789 ← |
| 1885686 | +G | Coding (1,814/2,340 nt) | BIF_01789 ← |
| 1885711 | +G | Coding (1,789/2,340 nt) | BIF_01789 ← |
| 1885722 | +A | Coding (1,778/2,340 nt) | BIF_01789 ← |
| 1885787 | 2 bp→GC | Coding (1,712–1,713/2,340 nt) | BIF_01789 ← |
| 1885792 | +C | Coding (1,708/2,340 nt) | BIF_01789 ← |
| 1885854 | Δ1 bp | Coding (1,646/2,340 nt) | BIF_01789 ← |
| 1893674 | 2 bp→TGC | Coding (2,445–2,446/2,673 nt) | BIF_00866 → |
| 1893713 | +G | Coding (2,484/2,673 nt) | BIF_00866 → |
| 1893740 | +G | Coding (2,511/2,673 nt) | BIF_00866 → |
| 1893947 | A→C | Intergenic (+45/+15) | BIF_00866 → / ← BIF_00684 |
| 1893952 | 3 bp→26 bp | Intergenic (+50/+8) | BIF_00866 → / ← BIF_00684 |
| 1903558 | 34 bp→73 bp | Intergenic (+2/+61) | BIF_00971 → / ← BIF_01033 |
| 1913433 | C→T | Intergenic (+33/+59) | BIF_02085 → / ← BIF_01409 |
| 1914632 | +AAGGGGCGCCG | Coding (60/1,200 nt) | BIF_01409 ← |
| 1914636 | A→G | V19A (GTA→GCA) | BIF_01409 ← |
| 1932289 | +G | Intergenic (+61/+53) | BIF_02266 → / ← BIF_00333 |
| 1932291 | +T | Intergenic (+63/+51) | BIF_02266 → / ← BIF_00333 |
| 1932292 | +G | Intergenic (+64/+50) | BIF_02266 → / ← BIF_00333 |
| 1932294 | 1 bp→GC | Intergenic (+66/+48) | BIF_02266 → / ← BIF_00333 |
| 1932295 | +CA | Intergenic (+67/+47) | BIF_02266 → / ← BIF_00333 |
| 1932335 | +CGCCT | Intergenic (+107/+7) | BIF_02266 → / ← BIF_00333 |
a
The nucleotide position column indicates the nucleotide position in GenBank accession number NC_017214.1, the mutation column indicates the genetic variant, the annotation column shows the effect of a variant on a gene (for intergenic variants, the numbers in parentheses indicate the variant’s position relative to the flanking genes, with positive numbers indicating that the variant is downstream and negative numbers indicating that the variant is upstream; for coding variants, the numbers in parentheses indicate the variant’s position in the affected gene and the gene's length), and the gene(s) column shows the locus tag(s) of the gene(s) in which or between which the variant occurs.
Data availability.
The genome sequence has been deposited in NCBI GenBank with accession number CP001853.2. The raw reads have been deposited in the SRA under BioProject number PRJNA42883 with accession numbers SRX9857028 (MiSeq) and SRX9857029 (MinION).
ACKNOWLEDGMENT
This work was funded by Chr. Hansen A/S.
Contributor Information
Kristian Jensen, Email: dkkrje@chr-hansen.com.
Julie C. Dunning Hotopp, University of Maryland School of Medicine
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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
The genome sequence has been deposited in NCBI GenBank with accession number CP001853.2. The raw reads have been deposited in the SRA under BioProject number PRJNA42883 with accession numbers SRX9857028 (MiSeq) and SRX9857029 (MinION).