ABSTRACT
We report the complete genome sequence and annotation of Escherichia coli DGF-298, a genome-reduced E. coli strain with interesting properties for systems and synthetic biology. DGF-298 has a single circular chromosome of 2,991,126 bp and 2,831 genes, including 2,691 coding sequences, with a mean G + C content of ~51%.
KEYWORDS: Escherichia coli, DGF-298, whole-genome sequencing, synthetic biology, systems biology, reduced genome
ANNOUNCEMENT
Genome-reduced organisms such as Escherichia coli DGF-298 constitute interesting cell chassis for synthetic biology (1 – 5). DGF-298 was generated from E. coli W3110 by deleting non-essential genes, prophages, and other undesirable elements using λ-Red recombination and P1 transduction (2, 3). Approximately 36% of the chromosome was removed while preserving a growth comparable to W3110 (1, 2, 5). We proceeded to the whole-genome sequencing of E. coli DGF-298 using Illumina sequencing and Oxford Nanopore Technology (ONT).
DGF-298 (DGF-298W100::rev234::SC) was acquired from the KHK Collection of the SHIGEN National Institute of Genetics. DGF-298 genomic DNA (gDNA) was isolated from an overnight culture grown in LB medium at 37°C using the Quick-gDNA MiniPrep kit (Zymo Research) according to the manufacturer’s specifications. To prepare an ONT sequencing library, 1.5 µg of gDNA was sheared at ~20 kbp using a Covaris g-TUBE by centrifuging twice at 1,650 × g for 1 min. No further size selection was performed. Sequencing adaptors were ligated using the R9 SQK-NSK007 ONT Ligation Sequencing Kit, and sequencing was performed on a MinION Mk1B device equipped with an R9 flow cell. Live base-calling was performed using MinKNOW software v1.1.21. A total of 1,614 reads passed MinKNOW default quality filter, corresponding to 14,978,836 bp with an N 50 of 13,742 bp. For Illumina sequencing, DNA was sheared and prepared using the QIAseq FX DNA Library Kit (QIAGEN) with 100 ng of the same gDNA preparation according to the manufacturer’s specifications, with the following modifications: (i) 2 min fragmentation time, (ii) provided adaptors and primers replaced by custom oligonucleotides, (iii) library amplification using the VeraSeq 2.0 DNA polymerase (Enzymatics), and (iv) final library purification and size selection using 0.7× AMPure XP beads (Agencourt). Library quality was assessed on a 2100 Bioanalyzer instrument (Agilent). Paired-end Illumina sequencing (2 × 125 bp) was performed on an Illumina HiSeq 2000 system at the McGill University and Génome Québec Innovation Centre (Montréal, Canada). 1,308,045 paired-end reads were obtained, corresponding to a genome coverage of ~100×. Illumina read quality was evaluated with FastQC v0.11.9, revealing an average Phred score of 35 for the forward and reverse reads. DGF-298 genome was de novo assembled using quality-filtered ONT reads and Newbler 2.6 RunAssembly, generating a single scaffold of 2,966,096 bp comprising seven contigs. Gaps were filled and circular conformation was confirmed by performing local mapping of ONT and Illumina reads using Newbler 2.6 RunMapping. Adapters were trimmed using Newbler 2.6 vt option. Genome assembly was error-corrected by alignment of the Illumina reads using BWA sampe v0.7.15 (6). DGF-298 chromosome was manually rotated to match E. coli W3110 (AP009048.1) start and end coordinates. Genome annotations were transferred from E. coli W3110 to the corrected sequence with RATT 1.0 (7), and mutations were identified using MUMmer v3.23 (8) (Table 1). Annotations were manually curated according to the detected mutations and deleted regions present in DGF-298 (2, 3).
TABLE 1.
Complete genomic changes between E. coli DGF-298 and W3110
| Mutation type a | Start position DGF-298 b | End position DGF-298 b | Length (bp) | Start position W3110 c | End position W3110 c | Length (bp) | Nucleotide change d | Deleted gene(s) e | Partially affected gene(s) | Protein mutation type(s) | Protein mutation(s) | Notes f |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Deletion | 15445 | 15445 | 0 | 15445 | 16903 | 1,459 | n/a | insL; hokC | mokC | Deletion | p.Met20_Glu69del | mokC is now annotated as pseudo |
| Deletion | 18187 | 18187 | 0 | 19646 | 20508 | 863 | n/a | insB; insA | - | - | - | - |
| Deletion | 63535 | 63535 | 0 | 65857 | 78797 | 12,941 | n/a | araD; araA; araB; araC; yabI; thiQ; thiP; tbpA; sgrR; sgrS; setA | - | - | - | - |
| Insertion | 63540 | 63542 | 3 | 78802 | 78802 | 0 | n/a | - | Intergenic | - | - | - |
| Substitution | 140203 | 140203 | 1 | 155463 | 155463 | 1 | A > T | - | ecpD | Extension | p.*247Glyext*11 | Mutation in stop codon, ecpD is now annotated as pseudo |
| Deletion | 152141 | 152141 | 0 | 167401 | 173315 | 5,915 | n/a | fhuA; fhuC; fhuD | fhuB | Deletion | p.Met1_Gly618del | fhuB is now annotated as pseudo |
| Deletion | 223125 | 223125 | 0 | 244301 | 253746 | 9,446 | n/a | yafJ; yafK; yafQ; dinJ; yafL; yafM; fhiA; mbhA; dinB; yafN; yafO; yafP; ykfJ | prfH | Deletion | p.Met1_Ser15del | prfH is now annotated as pseudo |
| Substitution | 223627 | 223627 | 1 | 254249 | 254249 | 1 | A > T | - | Intergenic | - | - | - |
| Deletion | 231678 | 231678 | 0 | 262300 | 387867 | 125,568 | n/a | ykfI; yafW; ykfH; ykfG; yafX; ykfF; ykfB; yafY; yafZ; ykfA; perR; insN; insI; insO; ykfC; insH; mmuP; mmuM; afuC; afuB; insB; insA; ykgN; yagB; yagA; yagE; yagF; yagG; yagH; yagI; argF; insB; insA; yagJ; yagK; yagL; yagM; yagN; intF; yagP; yagQ; yagR; yagS; yagT; yagU; ykgJ; yagV; yagW; yagX; yagY; yagZ; ykgK; ykgL; ykgM; eaeH; insE; insF; ykgA; ykgB; ykgI; ykgC; ykgD; ykgE; ykgF; ykgG; ykgH; betA; betB; betI; betT; yahA; yahB; yahC; yahD; yahE; yahF; yahG; yahH; yahI; yahJ; yahK; yahL; yahM; yahN; yahO; prpR; prpB; prpC; prpD; prpE; codB; codA; cynR; cynT; cynS; cynX; lacA; lacY; lacZ; lacI; mhpR; mhpA; mhpB; mhpC; mhpD; mhpF; mhpE; mhpT; yaiL; frmB; frmA; frmR; yaiO; yaiX; insC; insD; yaiF; yaiP; yaiS; tauA; tauB; tauC; tauD | - | - | - | - |
| Substitution | 232635 | 232635 | 1 | 388825 | 388825 | 1 | C > T | - | hemB | Missense | p.Asp43Asn | - |
| Substitution | 232901 | 232901 | 1 | 389091 | 389091 | 1 | T > C | - | Intergenic | - | - | - |
| Deletion | 233285 | 233285 | 0 | 389475 | 404039 | 14,565 | n/a | yaiT; insF; insE; yaiU; yaiV; ampH; sbmA; yaiW; yaiY; yaiZ; ddlA; yaiB; phoA; psiF; yaiC | - | - | - | - |
| Substitution | 327386 | 327386 | 1 | 498141 | 498141 | 1 | T > C | - | hemH | Missense | p.Phe288Ser | - |
| Deletion | 347612 | 347612 | 0 | 518367 | 533048 | 14,682 | n/a | tesA; ybbA; ybbP; rhsD; ybbC; ylbH; ybbD; ylbG; ybbB; ybbS; allA; allR | ybbO | Deletion | p.Met1_His3del | ybbO is now annotated as pseudo |
| Substitution | 349124 | 349124 | 1 | 534561 | 534561 | 1 | T > C | - | gcl | Silent | p.Ala474Ala | - |
| Substitution | 349960 | 349960 | 1 | 535397 | 535397 | 1 | T > C | - | hyi | Missense | p.Leu155Pro | - |
| Substitution | 350279 | 350279 | 1 | 535716 | 535716 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 350336 | 350336 | 1 | 535773 | 535773 | 1 | T > C | - | Intergenic | - | - | - |
| Deletion | 350404 | 350404 | 0 | 535841 | 550551 | 14,711 | n/a | ybbV; ybbW; allB; ybbY; glxK; ylbA; allC; allD; fdrA; ylbE; ylbF; ybcF | glxR | Deletion | p.Met11_Ala292del | glxR is now annotated as pseudo |
| Substitution | 356710 | 356710 | 1 | 556858 | 556858 | 1 | A > T | - | folD | Missense | p.Leu36Gln | - |
| Deletion | 364129 | 364129 | 0 | 564277 | 608454 | 44,178 | n/a | ybcC; ybcD; insE; insF; renD; emrE; ybcK; ybcL; ybcM; ybcN; ninE; ybcO; rusA; ylcG; ybcQ; insH; nmpC; essD; ybcS; rzpD; rzoD; borD; ybcV; ybcW; nohB; tfaD; ybcY; ylcE; appY; ompT; envY; ybcH; nfrA; nfrB; cusS; cusR; cusC; cusF; cusB; cusA; pheP; ybdG; nfnB; ybdF; ybdJ; ybdK; hokE; insL | intD | Deletion | p.Met1_Asp310del | intD is now annotated as pseudo |
| Substitution | 364131 | 364131 | 1 | 608457 | 608457 | 1 | G > A | - | Intergenic | - | - | - |
| Deletion | 396343 | 396343 | 0 | 640669 | 659192 | 18,524 | n/a | uspG; ybdR; rnk; rna; citT; citG; citX; citF; citE; citD; citC; citA; citB; 'dcuC; insH; dcuC'; crcA; cspE; crcB; ybeH | ybeM | Deletion | p.Met1_Gln172del | ybeM is now annotated as pseudo |
| Substitution | 412090 | 412090 | 1 | 674940 | 674940 | 1 | G > A | - | leuS | Missense | p.Ala89Val | - |
| Substitution | 412492 | 412492 | 1 | 675342 | 675342 | 1 | T > C | - | Intergenic | - | - | - |
| Substitution | 412564 | 412564 | 1 | 675414 | 675414 | 1 | C > A | - | Intergenic | - | - | - |
| Deletion | 412590 | 412590 | 0 | 675440 | 689710 | 14,271 | n/a | ybeL; ybeQ; ybeR; djlB; ybeT; ybeU; djlC; hscC; rihA; gltL; gltK; gltJ; gltI; insH | - | - | - | - |
| Deletion | 452036 | 452036 | 0 | 729157 | 739929 | 10,773 | n/a | kdpF; ybfA; rhsC; ybfB; ybfO; ybfC; ybfQ; ybfL; ybfD; ybgA | phr | Unknown | p.Met1? | Mutation in translation start codon, phr is now annotated as pseudo |
| Deletion | 459251 | 459251 | 0 | 747145 | 753217 | 6,073 | n/a | abrB; ybgO; ybgP; ybgQ; ybgD | nei | Missense and extension | p.His263Gln and p.*264Thrext*9 | Mutation in stop codon, nei is now annotated as pseudo |
| Deletion | 538922 | 538922 | 0 | 832889 | 848426 | 15,538 | n/a | ybiA; dinG; ybiB; ybiC; ybiJ; ybiI; ybiX; fiu; ybiM; ybiN; ybiO; glnQ; glnP; glnH | - | - | - | - |
| Deletion | 558470 | 558470 | 0 | 867975 | 883810 | 15,836 | n/a | yliA; yliB; yliC; yliD; yliE; yliF; yliG; yliH; yliI; yliJ; dacC; deoR; ybjG | - | - | - | - |
| Deletion | 565994 | 565994 | 0 | 891335 | 909716 | 18,382 | n/a | ybjC; nfsA; rimK; ybjN; potF; potG; potH; potI; ybjO; rumB; artJ; artM; artQ; artI; artP; ybjP; ybjQ; ybjR; ybjS; ybjT; ltaE | - | - | - | - |
| Substitution | 705295 | 705295 | 1 | 1049018 | 1049018 | 1 | G > A | - | ymcB | Silent | p.Gly32Gly | - |
| Deletion | 705504 | 705504 | 0 | 1049227 | 1097311 | 48,085 | n/a | ymcD; insA; insB; cspH; cspG; ymcE; gnsA; yccM; torS; torT; torR; torC; torA; torD; cbpM; cbpA; yccE; agp; yccJ; wrbA; ymdF; ycdG; ycdH; ycdI; rarA; ycdK; ycdL; ycdM; ycdC; putA; putP; ycdN; ycdO; ycdB; phoH; ycdP; ycdQ; ycdR; ycdS; ycdT; insF; insE; ymdE; ycdU | ymcC | Deletion | p.Met1_Lys176del | ymcC is now annotated as pseudo |
| Deletion | 706320 | 706320 | 0 | 1098128 | 1117068 | 18,941 | n/a | ycdW; ycdX; ycdY; ycdZ; csgG; csgF; csgE; csgD; csgB; csgA; csgC; insD; insC; ymdA; ymdB; ymdC; mdoC; mdoG; mdoH; yceK; msyB; mdtG | - | - | - | - |
| Substitution | 706680 | 706680 | 1 | 1117429 | 1117429 | 1 | T > C | - | lpxL | Missense | p.Lys244Arg | - |
| Substitution | 720216 | 720216 | 1 | 1130965 | 1130965 | 1 | C > T | - | Intergenic | - | - | - |
| Deletion | 720243 | 720243 | 0 | 1130992 | 1142564 | 11,573 | n/a | flgN; flgM; flgA; flgB; flgC; flgD; flgE; flgF; flgG; flgH; flgI; flgJ; flgK; flgL | - | - | - | - |
| Substitution | 776116 | 776116 | 1 | 1198438 | 1198438 | 1 | A > G | - | Intergenic | - | - | - |
| Deletion | 776122 | 776122 | 0 | 1198444 | 1225484 | 27,041 | n/a | ymfD; ymfE; lit; intE; ymfG; ymfH; ymfI; ymfJ; ymfK; ymfT; ymfL; ymfM; ymfN; ymfR; ymfO; ymfP; ymfQ; ycfK; ymfS; tfaE; stfE; pin; mcrA; icdC; elbA; ycgX; ycgE; ycgF; ycgZ; ymgA; ymgB; ymgC; ycgG; ymgF; ycgH; ymgD; ymgG; ymgH; ycgI | - | - | - | - |
| Deletion | 821463 | 821463 | 0 | 1270827 | 1271361 | 535 | n/a | rdlA; IdrB | ldrA | Unknown | p.Met1? | Mutation in translation start codon, ldrA is now annotated as pseudo |
| Deletion | 846105 | 846105 | 0 | 1296003 | 1308864 | 12,862 | n/a | ychG; adhE; ychE; insC; insD; oppA; oppB; oppC; oppD; oppF; yciU | - | - | - | - |
| Deletion | 896757 | 896757 | 0 | 1359517 | 1368530 | 9,014 | n/a | puuP; puuA; puuD; puuR; puuC; puuB; puuE | - | - | - | - |
| Deletion | 924831 | 924831 | 0 | 1396605 | 1520045 | 123,441 | n/a | ynaI; insH; ynaJ; uspE; fnr; ogt; abgT; abgB; abgA; abgR; isrA; ydaL; ydaM; ydaN; dbpA; ydaO; intR; ydaQ; ydaC; lar; recT; recE; racC; ydaE; kil; sieB; ydaF; ydaG; racR; ydaS; ydaT; ydaU; ydaV; ydaW; rzpR; rzoR; trkG; ynaK; ydaY; ynaA; lomR'; insH; 'lomR; stfR; tfaR; pinR; ynaE; uspF; ompN; micC; ydbK; ydbJ; hslJ; ldhA; ydbH; ynbE; ydbL; feaR; feaB; tynA; maoC; paaA; paaB; paaC; paaD; paaE; paaF; paaG; paaH; paaI; paaJ; paaK; paaX; paaY; ydbA'; insD; insC; insI; 'ydbA; ydbC; ydbD; ynbA; ynbB; ynbC; ynbD; azoR; hrpA; ydcF; aldA; gapC; cybB; ydcA; hokB; mokB; sokB; trg; ydcI; ydcJ; mdoD; ydcH; rimL; ydcK; tehA; tehB; ydcL; yncK; ydcM; ydcO; ydcN; ydcP; yncJ; yncN; ydcQ; ydcR; ydcS; ydcT; ydcU; ydcV; ydcW; ydcX; ydcY; ydcZ | yncA | Extension | p.*173Serext*24 | Mutation in stop codon, yncA is now annotated as pseudo |
| Deletion | 927172 | 927172 | 0 | 1522387 | 1543782 | 21,396 | n/a | yncD; yncE; ansP; yncG; yncH; rhsE; ydcD; yncI; yncM; ydcC; ydcE; yddH; nhoA; yddE; narV; narW; narY | yncC; narZ | Deletion; Deletion | p.Phe138_Arg221del; p.Val175_Lys1246del | yncC and narZ are now annotated as pseudos |
| Substitution | 965844 | 965844 | 1 | 1582455 | 1582455 | 1 | T > A | - | ydeM | Missense | p.Asp17Val | - |
| Deletion | 965946 | 965946 | 0 | 1582557 | 1592251 | 9,695 | n/a | ydeN; ydeO; ydeP; ydeQ; ydeR; ydeS; ydeT; yneL | - | - | - | - |
| Deletion | 966262 | 966262 | 0 | 1592568 | 1599800 | 7,233 | n/a | hipA; hipB; ydeU; ydeK | - | - | - | - |
| Deletion | 974263 | 974263 | 0 | 1607803 | 1607803 | 1 | n/a | Intergenic | Intergenic | - | - | - |
| Deletion | 974283 | 974283 | 0 | 1607823 | 1624231 | 16,409 | n/a | IsrF; lsrG; tam; yneE; uxaB; yneF; yneG; yneH; yneI; yneJ; yneK; ydeA; marC; marR; marA; marB; eamA; ydeE | - | - | - | - |
| Substitution | 974990 | 974990 | 1 | 1624939 | 1624939 | 1 | T > A | - | ydeH | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS |
| Deletion | 975258 | 975258 | 0 | 1625208 | 1625208 | 1 | n/a | - | ydeH | Frameshift | p.Thr120Tyrfs*6 | ydeH is now annotated as pseudo |
| Substitution | 980096 | 980096 | 1 | 1630046 | 1630046 | 1 | T > C | - | Intergenic | - | - | - |
| Deletion | 980104 | 980104 | 0 | 1630054 | 1640180 | 10,127 | n/a | ydfH; ydfZ; ydfI; ydfJ; ydfK; pinQ; tfaQ; stfQ; nohA; ynfO; ydfO; gnsB; ynfN | cspI | Deletion | p.Val68_Leu70del | cspI is now annotated as pseudo |
| Substitution | 980208 | 980208 | 1 | 1640285 | 1640285 | 1 | G > A | - | cspI | Missense | p.His33Tyr | - |
| Insertion | 981683 | 981683 | 1 | 1641759 | 1641759 | 0 | n/a | - | ydfQ | Frameshift | p.Ile5Aspfs*24 | ydfQ is now annotated as pseudo |
| Deletion | 981695 | 981695 | 0 | 1641771 | 1649361 | 7,591 | n/a | ydfR; essQ; cspB; cspF; ydfT; ydfU; rem; hokD; relE; relB; ydfV; flxA; ydfW; ydfX | ydfQ; dicC | Unknown; deletion | p.Met1?; p.Arg69_Ser76del | Mutation in ydfQ start codon; ydfQ and dicC are now annotated as pseudos |
| Deletion | 983841 | 983841 | 0 | 1651508 | 1657863 | 6,356 | n/a | ydfD; ydfE; insD; intQ; ynfP; rspB; rspA; ynfA; ynfB | dicB | Missense and extension | p.Gln62His and p.*63Leuext*5 | Mutation in stop codon, dicB is now annotated as pseudo |
| Substitution | 1036505 | 1036505 | 1 | 1710528 | 1710528 | 1 | A > G | - | rsxC | Silent | p.Ala632Ala | - |
| Substitution | 1179532 | 1179532 | 1 | 1853555 | 1853555 | 1 | C > T | - | ansA | Nonsense | p.Gln328* | New upstream stop codon, ansA is now annotated as pseudo |
| Deletion | 1179557 | 1179557 | 0 | 1853580 | 1864142 | 10,563 | n/a | pncA; ydjE; ydjF; ydjG; ydjH; ydjI; ydjJ; ydjK; ydjL; yeaC; yeaA | ansA | n/a | n/a | Irrelevant mutation, presence of a new upstream stop codon in CDS |
| Deletion | 1190702 | 1190702 | 0 | 1875288 | 1888499 | 13,212 | n/a | yeaK; yoaI; yeaL; yeaM; yeaN; yeaO; yoaF; yeaP; yeaQ; yoaG; yeaR; yeaS; yeaT; yeaU; yeaV; yeaW; yeaX | - | - | - | - |
| Substitution | 1190704 | 1190704 | 1 | 1888502 | 1888502 | 1 | A > G | - | yeaX | n/a | n/a | Irrelevant mutation, presence of another mutation (del) that causes gene deletion |
| Substitution | 1191074 | 1191074 | 1 | 1888872 | 1888872 | 1 | C > A | - | rnd | n/a | n/a | Irrelevant mutation, presence of a new upstream stop codon in CDS |
| Substitution | 1191560 | 1191560 | 1 | 1889358 | 1889358 | 1 | C > T | - | rnd | Nonsense | p.Trp116* | New upstream stop codon, rnd is now annotated as pseudo |
| Substitution | 1250792 | 1250792 | 1 | 1948590 | 1948590 | 1 | C > A | - | ruvC | Silent | p.Leu167Leu | - |
| Deletion | 1265866 | 1265866 | 0 | 1963664 | 1992215 | 28,552 | n/a | yecT; flhE; flhA; flhB; cheZ; cheY; cheB; cheR; tap; tar; cheW; cheA; motB; motA; flhC; flhD; insH; yecG; otsA; otsB; araH; araG; araF; yecI; yecJ; isrB; yecR; ftn; yecH | tyrP | Deletion | p.Met1_Gly133del | tyrP is now annotated as pseudo |
| Deletion | 1269451 | 1269451 | 0 | 1995801 | 2027348 | 31,548 | n/a | uvrY; yecF; sdiA; yecC; yecS; yedO; fliY; fliZ; fliA; fliC; fliD; fliS; fliT; amyA; yedD; yedE; yedF; yedK; yedL; yedN; yedM; intG; fliE; fliF; fliG; fliH; fliI; fliJ; fliK; fliL; fliM; fliN; fliO; fliP; fliQ; fliR; rcsA; dsrB; yodD | uvrC | Deletion | p.Met1_Arg348del | uvrC is now annotated as pseudo |
| Deletion | 1274690 | 1274690 | 0 | 2032588 | 2043515 | 10,928 | n/a | vsr; dcm; yedJ; yedR; yedS; hchA; yedV; yedW; yedX; yedY; yedZ | yedA; yodA | Missenses and extension; Deletion | p.Ser305Arg, p.Glu306Phe, and p.*307Valext*9; p.Met1_Ala2del | yedA and yodA are now annotated as pseudos |
| Substitution | 1274778 | 1274778 | 1 | 2043604 | 2043604 | 1 | A > G | - | yodA | Silent | p.Lys31Lys | - |
| Deletion | 1299463 | 1299463 | 0 | 2068289 | 2081066 | 12,778 | n/a | insH; yoeA; insD; insC; yoeE; yeeP; isrC; flu; yeeR; yeeS; yeeT; yeeU; yeeV; yeeW; yoeF | - | - | - | - |
| Substitution | 1299487 | 1299487 | 1 | 2081091 | 2081091 | 1 | A > G | - | Intergenic | - | - | - |
| Deletion | 1309749 | 1309749 | 0 | 2091353 | 2091607 | 255 | n/a | yoeB | yefM | Deletion | p.Ile82_Glu83del | Deletion of stop codon, yefM is now annotated as pseudo |
| Substitution | 1309751 | 1309751 | 1 | 2091610 | 2091610 | 1 | T > C | - | yefM | Missense | p.Ile81Val | - |
| Substitution | 1309899 | 1309899 | 1 | 2091759 | 2091759 | 1 | C > G | - | yefM | Silent | p.Arg31Arg | - |
| Substitution | 1314255 | 1314255 | 1 | 2096114 | 2096114 | 1 | C > T | - | hisB | Silent | p.His170His | - |
| Deletion | 1321673 | 1321673 | 0 | 2103532 | 2115203 | 11,672 | n/a | 'wbbL; insH; wbbL'; wbbK; wbbJ; wbbI; wbbH; glf; rfbX; rfbC; rfbA; rfbD; rfbB | - | - | - | - |
| Substitution | 1321783 | 1321783 | 1 | 2115314 | 2115314 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 1337480 | 1337480 | 1 | 2131011 | 2131011 | 1 | G > A | - | wcaF | Silent | p.Ser5Ser | - |
| Deletion | 1351872 | 1351872 | 0 | 2145403 | 2186994 | 41,592 | n/a | yegE; alkA; yegD; yegI; yegJ; yegK; yegL; ryeC; ryeD; mdtA; mdtB; mdtC; mdtD; baeS; baeR; yegP; yegQ; ryeE; ogrK; yegZ; yegR; yegS; 'gatR; insE; insF; gatR'; gatD; gatC; gatB; 'gatA; insH; gatA'; gatZ; gatY; fbaB; yegT; yegU; yegV; yegW; yegX | - | - | - | - |
| Deletion | 1364685 | 1364685 | 0 | 2199808 | 2228989 | 29,182 | n/a | molR'; 'molR; yehI; yehK; yehL; yehM; yehP; yehQ; yehR; yehS; yehT; yehU; mlrA; yohO; yehW; yehX; yehY; yehZ; bglX; dld; pbpG; yohC | - | - | - | - |
| Substitution | 1390615 | 1390615 | 1 | 2254920 | 2254920 | 1 | G > A | - | nfo | Silent | p.Gln249Gln | - |
| Deletion | 1390730 | 1390730 | 0 | 2255035 | 2262631 | 7,597 | n/a | yeiI; yeiJ; rihB; yeiL; yeiM; yeiN; yeiC | - | - | - | - |
| Deletion | 1417822 | 1417822 | 0 | 2289724 | 2293603 | 3,880 | n/a | yejO; insH | - | - | - | - |
| Deletion | 1445012 | 1445012 | 0 | 2320795 | 2322130 | 1,336 | n/a | insD; insC | rcsC | CDS fusion | Fusion of rcsC split coding regions (RcsC:p.Met1_Asp791; RcsC:p.Met1_*125) | Deletion of IS2 insertion element and restoration of rcsC found in MG1655 (933 amino acids) |
| Deletion | 1484456 | 1484456 | 0 | 2361574 | 2383930 | 22,357 | n/a | yfaD; ypaA; yfaU; yfaV; yfaW; yfaX; yfaY; yfaZ; yfaO; ais; yfbE; yfbF; yfbG; yfbH; arnT; yfbW; yfbJ; pmrD; menE; menC; menB; yfbB; menD | - | - | - | - |
| Substitution | 1484894 | 1484894 | 1 | 2384368 | 2384368 | 1 | C > T | - | menF | Missense | p.Val316Met | - |
| Deletion | 1485927 | 1485927 | 0 | 2385401 | 2394610 | 9,210 | n/a | elaB; elaA; elaC; elaD; yfbK; yfbL; yfbM; yfbN; yfbO; yfbP | - | - | - | - |
| Substitution | 1486279 | 1486279 | 1 | 2394963 | 2394963 | 1 | C > T | - | nuoN | Missense | p.Ala345Thr | - |
| Substitution | 1502353 | 1502353 | 1 | 2411037 | 2411037 | 1 | A > G | - | IrhA | Missense | p.Leu92Ser | - |
| Deletion | 1502775 | 1502775 | 0 | 2411459 | 2412234 | 776 | n/a | insB; insA | - | - | - | - |
| Substitution | 1502847 | 1502847 | 1 | 2412307 | 2412307 | 1 | T > A | - | Intergenic | - | - | - |
| Substitution | 1513018 | 1513018 | 1 | 2422478 | 2422478 | 1 | C > T | - | Intergenic | - | - | - |
| Substitution | 1513033 | 1513033 | 1 | 2422493 | 2422493 | 1 | A > C | - | Intergenic | - | - | - |
| Deletion | 1513044 | 1513044 | 0 | 2422504 | 2433237 | 10,734 | n/a | yfcC; yfcD; yfcE; yfcF; yfcG; folX; yfcH; yfcI; hisP; hisM; hisQ; hisJ; argT | - | - | - | - |
| Deletion | 1551791 | 1551791 | 0 | 2471986 | 2471986 | 1 | n/a | Intergenic | Intergenic | - | - | - |
| Deletion | 1551796 | 1551796 | 0 | 2471991 | 2481621 | 9,631 | n/a | intS; yfdG; yfdH; yfdI; tfaS; yfdK; yfdL; yfdM; yfdN; yfdO; yfdP; yfdQ; yfdR; yfdS; yfdT | ypdJ | Deletion | p.Met1_Ile28del | ypdJ is now annotated as pseudo |
| Substitution | 1552249 | 1552249 | 1 | 2482075 | 2482075 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 1557415 | 1557415 | 1 | 2487241 | 2487241 | 1 | G > A | - | emrY | Nonsense | p.Gln128* | New upstream stop codon, emrY is now annotated as pseudo |
| Deletion | 1564862 | 1564862 | 0 | 2494688 | 2513688 | 19,001 | n/a | yfdV; oxc; frc; yfdX; ypdI; yfdY; ddg; yfdZ; ypdA; ypdB; ypdC; ypdD; ypdE; ypdF; ypdG; ypdH | - | - | - | - |
| Substitution | 1564887 | 1564887 | 1 | 2513714 | 2513714 | 1 | T > C | - | Intergenic | - | - | - |
| Substitution | 1564912 | 1564912 | 1 | 2513739 | 2513739 | 1 | A > G | - | Intergenic | - | - | - |
| Deletion | 1570891 | 1570891 | 0 | 2519718 | 2523278 | 3,561 | n/a | insL; yfeA | - | - | - | - |
| Deletion | 1647470 | 1647470 | 0 | 2599858 | 2613439 | 13,582 | n/a | hyfA; hyfB; hyfC; hyfD; hyfE; hyfF; hyfG; hyfH; hyfI; hyfJ; hyfR; focB | - | - | - | - |
| Deletion | 1788845 | 1788845 | 0 | 2754815 | 2788618 | 33,804 | n/a | intA; yfjH; alpA; yfjI; yfjJ; yfjK; yfjL; yfjM; yfjN; yfjO; yfjP; yfjQ; yfjR; ypjK; yfjS; yfjT; yfjU; ypjL; yfjV; ypjM; yfjW; yfjX; yfjY; ypjJ; yfjZ; ypjF; ypjA; pinH; ypjB; ypjC; ileY; ygaQ; ygaR; yqaC; yqaD; ygaT | - | - | - | - |
| Substitution | 1789035 | 1789035 | 1 | 2788809 | 2788809 | 1 | C > T | - | ygaF | Missense | p.Pro58Ser | - |
| Substitution | 1789192 | 1789192 | 1 | 2788966 | 2788966 | 1 | C > T | - | ygaF | Missense | p.Ala110Val | - |
| Deletion | 1794538 | 1794538 | 0 | 2794312 | 2800028 | 5,717 | n/a | csiR; ygaU; yqaE; ygaV; ygaP; stpA; ygaW; ygaC; ygaM; nrdH; nrdI | nrdE | Deletion | p.Met1_Leu9del | nrdE is now annotated as pseudo |
| Deletion | 1818961 | 1818961 | 0 | 2824452 | 2829398 | 4,947 | n/a | srlA; srlE; srlB; srlD; gutM; srlR | gutQ | Deletion | p.Met1_Ile310del | gutQ is now annotated as pseudo |
| Substitution | 1826256 | 1826256 | 1 | 2836694 | 2836694 | 1 | A > G | - | hydN | Missense | p.Val23Ala | - |
| Deletion | 1826472 | 1826472 | 0 | 2836910 | 2855462 | 18,553 | n/a | ascG; ascF; ascB; hycI; hycH; hycG; hycF; hycE; hycD; hycC; hycB; hycA; hypA; hypB; hypC; hypD; hypE; fhlA; ygbA | - | - | - | - |
| Substitution | 1837119 | 1837119 | 1 | 2866110 | 2866110 | 1 | T > A | - | Intergenic | - | - | - |
| Deletion | 1847638 | 1847638 | 0 | 2876630 | 2876812 | 183 | n/a | Intergenic | Intergenic | - | - | Highly repeated region |
| Replacement | 1892020 | 1895203 | 3,184 | 2921194 | 2943638 | 22,445 | n/a | yqcA; yqcB; yqcC; csrB; syd; yqcD; ygdH; sdaC; sdaB; exo; fucO; fucA; fucP; fucI; fucK; fucU; fucR; ygdE; ygdD; gcvA; gcvB; ygdI; csdA; ygdK | - | Replacement by a sacB and cmR cassette | - | - |
| Substitution | 1935947 | 1935947 | 1 | 2984382 | 2984382 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 1936037 | 1936037 | 1 | 2984472 | 2984472 | 1 | T > C | - | Intergenic | - | - | - |
| Deletion | 1936063 | 1936063 | 0 | 2984498 | 3032266 | 47,769 | n/a | yqeG; yqeH; yqeI; yqeJ; yqeK; ygeF; ygeG; ygeH; ygeI; pbl; ygeK; ygeL; ygeM; ygeN; ygeO; insD; insC; ygeP; ygeQ; glyU; ygeR; xdhA; xdhB; xdhC; ygeV; ygeW; ygeX; ygeY; hyuA; yqeA; yqeB; yqeC; ygfJ; ygfK; ssnA; ygfM; xdhD; ygfO; guaD; ygfQ; ygfS; ygfT; ygfU; idi | - | - | - | - |
| Deletion | 1961819 | 1961819 | 0 | 3058023 | 3068464 | 10,442 | n/a | yqfE; argP; yliK; argK; ygfG; ygfH; ygfI; yggE; argO; mscS | - | - | - | - |
| Deletion | 1969578 | 1969578 | 0 | 3076224 | 3078055 | 1,832 | n/a | cmtB | cmtA | Deletion | p.Met1_Arg431del | cmtA is now annotated as pseudo |
| Substitution | 1993418 | 1993418 | 1 | 3101896 | 3101896 | 1 | G > A | - | mutY | Silent | p.Leu76Leu | - |
| Deletion | 2000769 | 2000769 | 0 | 3109247 | 3133480 | 24,234 | n/a | yghD; yghE; yghF; yghG; pppA; yghJ; yghK; glcB; glcG; glcF; glcE; glcD; glcC; yghO; insH; yghQ; yghR; yghS; yghT | - | - | - | - |
| Deletion | 2032058 | 2032058 | 0 | 3164770 | 3172081 | 7,312 | n/a | ygiS; ygiT; ygiU; ygiV; ygiW; qseB; qseC; ygiZ; mdaB; ygiN | - | - | - | - |
| Substitution | 2032063 | 2032063 | 1 | 3172087 | 3172087 | 1 | T > A | - | ygiN | n/a | n/a | Irrelevant mutation, presence of another mutation (del) that causes gene deletion |
| Deletion | 2043763 | 2043763 | 0 | 3183787 | 3188521 | 4,735 | n/a | ygiL; insC; insD; yqiG | - | - | - | - |
| Substitution | 2043897 | 2043897 | 1 | 3188656 | 3188656 | 1 | T > C | - | yqiH | Silent | p.Asp40Asp | - |
| Substitution | 2044135 | 2044135 | 1 | 3188894 | 3188894 | 1 | A > T | - | yqiH | Nonsense | p.Lys120* | New upstream stop codon, yqiH is now annotated as pseudo |
| Substitution | 2044622 | 2044622 | 1 | 3189381 | 3189381 | 1 | A > G | - | yqiI | Missense | p.Asn32Asp | - |
| Substitution | 2080125 | 2080125 | 1 | 3224884 | 3224884 | 1 | T > C | - | Intergenic | - | - | - |
| Deletion | 2080131 | 2080131 | 0 | 3224890 | 3240400 | 15,511 | n/a | ygjI; ygjJ; ygjK; fadH; ygjM; ygjN; ygjO; ygjP; ygjQ; ygjR; sraF; alx; sstT; ygjV | - | - | - | - |
| Substitution | 2090850 | 2090850 | 1 | 3251120 | 3251120 | 1 | T > C | - | yhaH | Missense | p.Ile54Thr | - |
| Deletion | 2098089 | 2098089 | 0 | 3258359 | 3269672 | 11,314 | n/a | tdcF; tdcE; insH; tdcD; tdcC; tdcB; tdcA; tdcR; yhaB; yhaC | - | - | - | - |
| Insertion | 2136951 | 2136956 | 6 | 3308534 | 3308534 | 0 | n/a | - | nlpI | Insertion | p.Arg82_Asn83insAsnAsp | - |
| Deletion | 2189503 | 2189503 | 0 | 3361081 | 3370891 | 9,811 | n/a | yhcA; yhcD; yhcE'; insH; 'yhcE; yhcF; yhcG; yhcH; nanK; nanE | gltF | Deletion | p.Ser17_Leu254del | gltF is now annotated as pseudo |
| Substitution | 2229132 | 2229132 | 1 | 3410521 | 3410521 | 1 | C > G | - | dusB | Silent | p.Val129Val | - |
| Deletion | 2230110 | 2230110 | 0 | 3411500 | 3421220 | 9,721 | n/a | yhdJ; yhdU; envR; acrE; acrF; yhdV; yhdW; yhdX | yhdY | Deletion | p.Met1_Ser14del | yhdY is now annotated as pseudo |
| Substitution | 2230111 | 2230111 | 1 | 3421221 | 3421221 | 1 | C > A | - | yhdY | n/a | n/a | Irrelevant mutation, presence of another mutation (del) that causes lost of translation start codon and partial gene deletion |
| Substitution | 2230119 | 2230119 | 1 | 3421229 | 3421229 | 1 | C > T | - | yhdY | n/a | n/a | Irrelevant mutation, presence of another mutation (del) that causes lost of translation start codon and partial gene deletion |
| Deletion | 2295318 | 2295318 | 0 | 3486428 | 3496908 | 10,481 | n/a | yijP; yijO; frwD; pflC; pflD; frwB; frwC | ptsA | Deletion | p.Met1_Ala817del | ptsA is now annotated as pseudo |
| Substitution | 2295319 | 2295319 | 1 | 3496910 | 3496910 | 1 | C > A | - | ptsA | n/a | n/a | Irrelevant mutation, presence of another mutation (del) that causes lost of translation start codon and near complete gene deletion |
| Deletion | 2295581 | 2295581 | 0 | 3497173 | 3497173 | 1 | n/a | - | fsaB | Frameshift | p.Met68_Trpfs*17 | fsaB is now annotated as pseudo |
| Substitution | 2295801 | 2295801 | 1 | 3497393 | 3497393 | 1 | G > A | - | fsaB | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS |
| Substitution | 2334436 | 2334436 | 1 | 3536028 | 3536028 | 1 | C > A | - | Intergenic | - | - | - |
| Deletion | 2334564 | 2334564 | 0 | 3536156 | 3549686 | 13,531 | n/a | rhaT; rhaR; rhaS; rhaB; rhaA; rhaD; yiiL; frvA; frvB; frvX; frvR; yiiG | - | - | - | - |
| Deletion | 2341355 | 2341355 | 0 | 3556478 | 3576238 | 19,761 | n/a | yiiF; yiiE; yiiD; dtd; rbn; yihX; yihW; yihV; yihU; yihT; yihS; yihR; yihQ; yihP; yihO; ompL; yihN; yihM; yihL | - | - | - | - |
| Substitution | 2433549 | 2433549 | 1 | 3668433 | 3668433 | 1 | C > T | - | rfe | Missense | p.Met111Ile | - |
| Substitution | 2449629 | 2449629 | 1 | 3684513 | 3684513 | 1 | G > A | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449740 | 2449740 | 1 | 3684624 | 3684624 | 1 | C > A | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449759 | 2449759 | 1 | 3684643 | 3684643 | 1 | T > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449803 | 2449803 | 1 | 3684687 | 3684687 | 1 | A > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449821 | 2449821 | 1 | 3684705 | 3684705 | 1 | G > A | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449833 | 2449833 | 1 | 3684717 | 3684717 | 1 | A > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449974 | 2449974 | 1 | 3684858 | 3684858 | 1 | A > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2449986 | 2449986 | 1 | 3684870 | 3684870 | 1 | C > T | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450001 | 2450001 | 1 | 3684885 | 3684885 | 1 | T > C | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450037 | 2450037 | 1 | 3684921 | 3684921 | 1 | A > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450043 | 2450043 | 1 | 3684927 | 3684927 | 1 | A > G | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450154 | 2450154 | 1 | 3685038 | 3685038 | 1 | C > T | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450216 | 2450216 | 1 | 3685100 | 3685100 | 1 | A > C | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Substitution | 2450245 | 2450245 | 1 | 3685129 | 3685129 | 1 | T > A | - | ilvG | n/a | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS; restoration of ilvG found in MG1655 |
| Insertion | 2450262 | 2450263 | 2 | 3685145 | 3685145 | 0 | n/a | - | ilvG | Frameshift | p.Glu327_Ilefs*223 | Restoration of complete ilvG found in MG1655 (548 amino acids), fusion of N-ter and C-ter fragments |
| Substitution | 2450385 | 2450385 | 1 | 3685267 | 3685267 | 1 | C > T | - | ilvG | Silent | p.Ala285Ala | - |
| Substitution | 2450430 | 2450430 | 1 | 3685312 | 3685312 | 1 | G > A | - | ilvG | Silent | p.Gly270Gly | - |
| Substitution | 2450447 | 2450447 | 1 | 3685329 | 3685329 | 1 | G > A | - | ilvG | Silent | p.Leu265Leu | - |
| Substitution | 2450451 | 2450451 | 1 | 3685333 | 3685333 | 1 | A > G | - | ilvG | Silent | p.Cys263Cys | - |
| Substitution | 2450472 | 2450472 | 1 | 3685354 | 3685354 | 1 | T > C | - | ilvG | Silent | p.Ala256Ala | - |
| Substitution | 2450487 | 2450487 | 1 | 3685369 | 3685369 | 1 | G > A | - | ilvG | Silent | p.His251His | - |
| Substitution | 2450493 | 2450493 | 1 | 3685375 | 3685375 | 1 | C > T | - | ilvG | Silent | p.Gly249Gly | - |
| Deletion | 2462424 | 2462424 | 0 | 3697305 | 3709526 | 12,222 | n/a | rbsR; rbsK; rbsB; rbsC; rbsA; rbsD; trkD; yieN; yieM; asnA | hsrA | Deletion | p.Val413_Glu475 | hsrA is now annotated as pseudo |
| Deletion | 2483011 | 2483011 | 0 | 3730114 | 3742029 | 11,916 | n/a | bglG; bglF; bglB; bglH; yieL; yieK; cbrC; yieI; yieH; yieG; yieF | - | - | - | - |
| Deletion | 2483916 | 2483916 | 0 | 3742936 | 3744271 | 1,336 | n/a | insD; insC | - | - | - | - |
| Deletion | 2486073 | 2486073 | 0 | 3746428 | 3751980 | 5,553 | n/a | 'tnaB; insH; tnaB'; tnaA; insH; tnaC | - | - | - | - |
| Deletion | 2497001 | 2497001 | 0 | 3762909 | 3772816 | 9,908 | n/a | yidB; yidA; yidX; dgoR; dgoK; dgoA; dgoD; dgoT; cbrA; yidR; yidQ | - | - | - | - |
| Substitution | 2497023 | 2497023 | 1 | 3772839 | 3772839 | 1 | C > A | - | Intergenic | - | - | - |
| Deletion | 2498272 | 2498272 | 0 | 3774088 | 3785257 | 11,170 | n/a | yidE; yidP; glvC; glvB; glvG; ysdC; yidL; yidK; yidJ; yidI; yidH; yidG | yidF | Deletion | p.Met1_Lys152del | yidF is now annotated as pseudo |
| Deletion | 2507702 | 2507702 | 0 | 3794688 | 3803458 | 8,771 | n/a | ade; yicO; yicN; yicM; yicS; nlpA; yicL; setC | - | - | - | - |
| Substitution | 2528521 | 2528521 | 1 | 3824278 | 3824278 | 1 | T > C | - | rph | Missense | p.Val138Ala | - |
| Substitution | 2528567 | 2528567 | 1 | 3824324 | 3824324 | 1 | T > C | - | rph | Silent | p.Asn153Asn | - |
| Substitution | 2528603 | 2528603 | 1 | 3824360 | 3824360 | 1 | A > T | - | rph | Silent | p.Gly165Gly | - |
| Substitution | 2528609 | 2528609 | 1 | 3824366 | 3824366 | 1 | G > A | - | rph | Silent | p.Val167Val | - |
| Substitution | 2528615 | 2528615 | 1 | 3824372 | 3824372 | 1 | C > T | - | rph | Silent | p.Gly169Gly | - |
| Substitution | 2528621 | 2528622 | 2 | 3824378 | 3824379 | 2 | GG > AA | - | rph | Silent; missense | p.Ala171Ala; p.Val172Ile | - |
| Substitution | 2528651 | 2528651 | 1 | 3824408 | 3824408 | 1 | T > A | - | rph | Silent | p.Ser181Ser | - |
| Substitution | 2528755 | 2528755 | 1 | 3824512 | 3824512 | 1 | T > C | - | rph | Missense | p.Ile216Thr | - |
| Substitution | 2528765 | 2528765 | 1 | 3824522 | 3824522 | 1 | T > G | - | rph | Silent | p.Ala219Ala | - |
| Insertion | 2528779 | 2528779 | 1 | 3824535 | 3824535 | 0 | n/a | - | rph | Frameshift | p.Glu224_Glyfs*16 | rph is now annotated as pseudo |
| Substitution | 2529025 | 2529025 | 1 | 3824781 | 3824781 | 1 | T > C | - | pyrE | Silent | p.Asp45Asp | Restoration of pyrE found in MG1655 |
| Substitution | 2529058 | 2529058 | 1 | 3824814 | 3824814 | 1 | G > A | - | pyrE | Silent | p.Ala56Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529070 | 2529070 | 1 | 3824826 | 3824826 | 1 | C > T | - | pyrE | Silent | p.Ser60Ser | Restoration of pyrE found in MG1655 |
| Substitution | 2529124 | 2529124 | 1 | 3824880 | 3824880 | 1 | C > G | - | pyrE | Silent | p.Ala78Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529130 | 2529130 | 1 | 3824886 | 3824886 | 1 | A > T | - | pyrE | Silent | p.Thr80Thr | Restoration of pyrE found in MG1655 |
| Substitution | 2529136 | 2529136 | 1 | 3824892 | 3824892 | 1 | T > C | - | pyrE | Silent | p.Ala82Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529142 | 2529142 | 1 | 3824898 | 3824898 | 1 | A > G | - | pyrE | Silent | p.Ala84Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529157 | 2529157 | 1 | 3824913 | 3824913 | 1 | C > T | - | pyrE | Silent | p.His89His | Restoration of pyrE found in MG1655 |
| Substitution | 2529163 | 2529163 | 1 | 3824919 | 3824919 | 1 | G > T | - | pyrE | Silent | p.Leu91Leu | Restoration of pyrE found in MG1655 |
| Substitution | 2529193 | 2529193 | 1 | 3824949 | 3824949 | 1 | A > G | - | pyrE | Silent | p.Glu101Glu | Restoration of pyrE found in MG1655 |
| Substitution | 2529295 | 2529295 | 1 | 3825051 | 3825051 | 1 | G > A | - | pyrE | Silent | p.Glu135Glu | Restoration of pyrE found in MG1655 |
| Substitution | 2529316 | 2529316 | 1 | 3825072 | 3825072 | 1 | C > T | - | pyrE | Silent | p.Ala142Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529340 | 2529340 | 1 | 3825096 | 3825096 | 1 | G > A | - | pyrE | Silent | p.Val150Val | Restoration of pyrE found in MG1655 |
| Substitution | 2529352 | 2529352 | 1 | 3825108 | 3825108 | 1 | C > T | - | pyrE | Silent | p.Leu154Leu | Restoration of pyrE found in MG1655 |
| Substitution | 2529367 | 2529367 | 1 | 3825123 | 3825123 | 1 | C > G | - | pyrE | Silent | p.Arg159Arg | Restoration of pyrE found in MG1655 |
| Substitution | 2529448 | 2529448 | 1 | 3825204 | 3825204 | 1 | C > T | - | pyrE | Silent | p.Asp186Asp | Restoration of pyrE found in MG1655 |
| Substitution | 2529457 | 2529457 | 1 | 3825213 | 3825213 | 1 | T > C | - | pyrE | Silent | p.Ala189Ala | Restoration of pyrE found in MG1655 |
| Substitution | 2529460 | 2529460 | 1 | 3825216 | 3825216 | 1 | C > T | - | pyrE | Silent | p.Tyr190Tyr | Restoration of pyrE found in MG1655 |
| Substitution | 2575671 | 2575671 | 1 | 3871427 | 3871427 | 1 | G > A | - | Intergenic | - | - | - |
| Deletion | 2576021 | 2576021 | 0 | 3871777 | 3914528 | 42,752 | n/a | yibG; yibJ; yibA; rhsA; yibF; selA; selB; yiaY; aldB; yiaW; yiaV; yiaU; yiaT; sgbE; sgbU; sgbH; lyxK; yiaO; yiaN; yiaM; yiaL; yiaK; yiaJ; yiaI; avtA; malS; bax; xylR; xylH; xylG; xylF; xylA; xylB; yiaB; yiaA; yiaH | - | - | - | - |
| Substitution | 2576125 | 2576125 | 1 | 3914633 | 3914633 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 2576173 | 2576173 | 1 | 3914681 | 3914681 | 1 | C > T | - | Intergenic | - | - | - |
| Deletion | 2579583 | 2579583 | 0 | 3918091 | 3969123 | 51,033 | n/a | insK; insJ; hokA; cspA; yiaG; yiaF; tiaE; yiaD; bisC; yiaC; tag; yhjY; yhjX; eptB; proK; dppA; dppB; dppC; dppD; dppF; yhjV; rdlD; ldrD; bcsG; bcsF; bcsE; yhjR; yhjQ; bcsA; bcsB; bcsZ; bcsC; yhjK; dctA; yhjJ; kdgK; yhjH; yhjG; yhjE; yhjD; yhjC; yhjB | - | - | - | - |
| Deletion | 2597527 | 2597527 | 0 | 3987068 | 3989225 | 2,158 | n/a | insH; yhiS | - | - | - | - |
| Substitution | 2611280 | 2611280 | 1 | 4002979 | 4002979 | 1 | C > T | - | Intergenic | - | - | - |
| Deletion | 2611289 | 2611289 | 0 | 4002989 | 4002989 | 1 | n/a | Intergenic | Intergenic | - | - | - |
| Deletion | 2611305 | 2611305 | 0 | 4003005 | 4021346 | 18,342 | n/a | yhiN; yhiM; yhiL; yhiK; yhiJ; yhiI; rbbA; yhhJ; yhhI; yrhC; yhhH; rhsB | - | - | - | - |
| Deletion | 2645330 | 2645330 | 0 | 4055372 | 4061465 | 6,094 | n/a | yrhB; insB; insA; yrhA; yhhZ; yhhY; ryhB; yhhX; yhhW | - | - | - | - |
| Substitution | 2712097 | 2712097 | 1 | 4128233 | 4128233 | 1 | A > G | - | yhfZ | Silent | p.Glu54Glu | - |
| Deletion | 2712155 | 2712155 | 0 | 4128291 | 4141015 | 12,725 | n/a | yhfY; yhfX; yhfW; php; yhfU; yhfT; yhfS; frlR; frlD; frlC; frlB; frlA; yhfL | yhfZ | Deletion | p.Met74_Tyr301del | yhfZ is now annotated as pseudo |
| Substitution | 2712162 | 2712162 | 1 | 4141023 | 4141023 | 1 | A > C | - | Intergenic | - | - | - |
| Substitution | 2712164 | 2712164 | 1 | 4141025 | 4141025 | 1 | C > A | - | Intergenic | - | - | - |
| Deletion | 2741702 | 2741702 | 0 | 4170563 | 4186908 | 16,346 | n/a | chiA; bfd; bfr; gspO; gspM; gspL; gspK; gspJ; gspI; gspH; gspG; gspF; gspE; gspD; gspC; gspA; pioO | - | - | - | - |
| Substitution | 2794033 | 2794033 | 1 | 4239241 | 4239241 | 1 | T > C | - | Intergenic | - | - | - |
| Insertion | 2794287 | 2794338 | 52 | 4239494 | 4239494 | 0 | n/a | - | Intergenic | - | - | - |
| Deletion | 2794339 | 2794339 | 0 | 4239495 | 4255870 | 16,376 | n/a | yjbE; yjbF; yjbG; yjbH; yjbA; xylE; malG; malF; malE; malK; lamB; malM; yjbI | - | - | - | - |
| Deletion | 2819944 | 2819944 | 0 | 4281477 | 4281477 | 1 | n/a | - | soxR | Frameshift | p.Gly140_Glufs*8 | soxR is now annotated as pseudo |
| Deletion | 2819965 | 2819965 | 0 | 4281498 | 4291254 | 9,757 | n/a | ryjA; yjcD; yjcE; yjcF; actP; yjcH; acs | soxR | Deletion | n/a | Irrelevant mutation, presence of an upstream frameshift in CDS |
| Deletion | 2826782 | 2826782 | 0 | 4298072 | 4366613 | 68,542 | n/a | gltP; yjcO; fdhF; yjcP; yjcQ; yjcR; yjcS; insH; alsK; alsE; alsC; alsA; alsB; rpiR; rpiB; yjdP; phnP; phnO; phnN; phnM; phnL; phnK; phnJ; phnI; phnH; phnG; phnF; phnE; phnD; phnC; phnB; phnA; yjdA; yjcZ; proP; basS; basR; eptA; adiC; adiY; adiA; melR; melA; melB; yjdF; fumB; dcuB; dcuR; dcuS; yjdI; yjdJ; yjdK; yjdO; lysU; yjdL; cadA; cadB; cadC | - | - | - | - |
| Substitution | 2826812 | 2826812 | 1 | 4366644 | 4366644 | 1 | A > G | - | Intergenic | - | - | - |
| Substitution | 2827055 | 2827055 | 1 | 4366887 | 4366887 | 1 | G > A | - | Intergenic | - | - | - |
| Deletion | 2831441 | 2831441 | 0 | 4371274 | 4371275 | 2 | n/a | Intergenic | Intergenic | - | - | - |
| Substitution | 2874927 | 2874927 | 1 | 4414761 | 4414761 | 1 | T > A | - | Intergenic | - | - | - |
| Deletion | 2874934 | 2874934 | 0 | 4414768 | 4428387 | 13,620 | n/a | yjfI; yjfJ; yjfK; yjfL; yjfM; yjfC; aidB; yjfN; yjfO; yjfP; ulaR; ulaG; ulaA; ulaB; ulaC; ulaD; ulaE | ulaF | Deletion | p.Met1_Lys3del | ulaF is now annotated as pseudo |
| Deletion | 2893608 | 2893608 | 0 | 4447062 | 4453719 | 6,658 | n/a | ytfM; ytfN; ytfP; yzfA; chpS; chpB | - | - | - | - |
| Substitution | 2894598 | 2894598 | 1 | 4454710 | 4454710 | 1 | A > C | - | ytfQ | Silent | p.Pro23Pro | - |
| Deletion | 2941326 | 2941326 | 0 | 4501438 | 4514770 | 13,333 | n/a | intB; insC; insD; yjgW; yjgX; yjgZ; insG; yjhB; yjhC; yjhD; yjhE; insN; insI; insM; insO; yjhW | yjhV | Deletion | p.Met1_Glu124del | yjhV is now annotated as pseudo |
| Substitution | 2949591 | 2949591 | 1 | 4523036 | 4523036 | 1 | A > G | - | Intergenic | - | - | - |
| Deletion | 2949669 | 2949669 | 0 | 4523114 | 4604874 | 81,761 | n/a | insA; insB; yjhU; yjhF; yjhG; yjhH; yjhI; sgcR; sgcE; sgcA; sgcQ; sgcC; sgcB; sgcX; yjhP; yjhQ; yjhX; yjhR; yjhS; yjhT; yjhA; fimB; fimE; fimA; fimI; fimC; fimD; fimF; fimG; fimH; gntP; uxuA; uxuB; uxuR; yjiC; yjiD; yjiE; iadA; yjiG; yjiH; kptA; yjiJ; yjiK; yjiL; yjiM; yjiN; yjiO; yjiP; yjiQ; yjiR; yjiS; yjiT; yjiV; mcrC; mcrB; yjiW; hsdS; hsdM; hsdR; mrr; yjiA; yjiX; yjiY; tsr; yjiZ; yjjM; yjjN; mdoB; yjjA | - | - | - | - |
a
Targeted deletions previously performed to generate DGF-298 were annotated as “Deletion_scar” in DGF-298 GenBank annotation file (CP127119.1).
b
GenBank CP127119.1; 08-JUN-2023.
c
GenBank AP009048.1; 07-OCT-2016.
d
Substitution only; n/a, non-applicable.
e
Genes were considered completely deleted below 10 remaining amino acids.
f
Pseudo qualifier (′) was added to GenBank features with the following mutation types: frameshift; mutation in translation start or stop codon; partial gene deletion; new upstream stop codon.
The final DGF-298 genome consists of a single circular chromosome of 2,991,126 bp and 2,831 genes, with an overall genome coverage of ~100× and a G + C content of ~51%.
ACKNOWLEDGMENTS
The authors wish to thank Vincent Baby, Simon Jeanneau, and the Centre de Calcul Scientifique at the Université de Sherbrooke for technical assistance, as well as the National BioResource Project (NBRP) for providing the DGF-298 strain.
This project was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Fonds de recherche du Québec - Nature et technologies (FRQNT). Dominick Matteau and Frédéric Grenier were supported by NSERC doctoral and master's scholarships, respectively. Sébastien Rodrigue holds a Fonds de recherche du Québec - Santé (FRQS) Research Scholars - Senior Award.
Access to computational resources was provided in part by Calcul Québec (http://www.calculquebec.ca) and Compute Canada (http://www.computecanada.ca).
Contributor Information
Sébastien Rodrigue, Email: Sebastien.Rodrigue@USherbrooke.ca.
David Rasko, University of Maryland School of Medicine, Baltimore, Maryland, USA .
DATA AVAILABILITY
This Whole-Genome Shotgun project has been deposited in GenBank under the accession no. CP127119. The version described in this paper is the first version, CP127119.1. Raw ONT and Illumina reads have been deposited in Sequence Read Archive under the accession nos. SRR24843436 and SRR24843435, respectively.
REFERENCES
- 1. Kurokawa M, Ying BW. 2020. Experimental challenges for reduced genomes: the cell model Escherichia coli. Microorganisms 8:3. doi: 10.3390/microorganisms8010003 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Hirokawa Y, Kawano H, Tanaka-Masuda K, Nakamura N, Nakagawa A, Ito M, Mori H, Oshima T, Ogasawara N. 2013. Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli. J Biosci Bioeng 116:52–58. doi: 10.1016/j.jbiosc.2013.01.010 [DOI] [PubMed] [Google Scholar]
- 3. Mizoguchi H, Sawano Y, Kato J, Mori H. 2008. Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Res 15:277–284. doi: 10.1093/dnares/dsn019 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Lachance J-C, Rodrigue S, Palsson BO. 2019. Synthetic biology: Minimal cells, maximal knowledge. Elife 8:1–4. doi: 10.7554/eLife.45379 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Ma S, Su T, Lu X, Qi Q. 2023. Bacterial genome reduction for optimal chassis of synthetic biology: a review. Crit Rev Biotechnol 0:1–14. doi: 10.1080/07388551.2023.2208285 [DOI] [PubMed] [Google Scholar]
- 6. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. doi: 10.1093/bioinformatics/btp324 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Otto TD, Dillon GP, Degrave WS, Berriman M. 2011. RATT: rapid annotation transfer tool. Nucleic Acids Res 39:1–7. doi: 10.1093/nar/gkq1268 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi: 10.1186/gb-2004-5-2-r12 [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This Whole-Genome Shotgun project has been deposited in GenBank under the accession no. CP127119. The version described in this paper is the first version, CP127119.1. Raw ONT and Illumina reads have been deposited in Sequence Read Archive under the accession nos. SRR24843436 and SRR24843435, respectively.