PMC

Validation of DEGs. (a) Up‐regulated DEGs. (b) Down‐regulated DEGs. GeneBank ID and version number: Hba‐a1: Gene ID: 287167, Refseq: NC_005109.4 Tnnt2: Gene ID: 24837, Refseq: NC_005112.4 Edn2: Gene ID: 24324, Refseq: NC_005104.4, F9: Gene ID: 24946, Refseq: NC_005120.4, Eqtn: Gene ID: 500502, Refseq: NC_005104.4, Ankar: Gene ID: 501138, Refseq: NC_005108.4, Cntnap5b: Gene ID: 301650, Refseq: NC_005112.4, Lad1: Gene ID: 313325, Refseq: NC_005112.4, Asb15: Gene ID: 500050, Refseq: NC_005103.4, Tsga10ip: Gene ID: 361707, Refseq: NC_005100.4, Ltk: Gene ID: 311337, Refseq: NC_005102.4, Impad1: Gene ID: 312952, Refseq: NC_005116.4, Loxhd1: Gene ID: 291427, Refseq: NC_005117.4, Crygc: Gene ID: 24277, Refseq: NC_005108.4, Crygd: Gene ID: 24278, Refseq: NC_005108.4, Piwil1: Gene ID: 363912, Refseq: NC_005111.4, RT1‐Bb: Gene ID: 309622, Refseq: NC_005119.4, H3f3c: Gene ID: 100360868, Refseq: NC_005106.4, Col3a1: Gene ID: 84032, Refseq: NC_005108.4, Pmel: Gene ID: 362818, Refseq: NC_005106.4, Lgsn: Gene ID: 316304, Refseq: NC_005108.4, RT1‐Ba: Gene ID: 309621, Refseq: NC_005119.4, Crygf, Gene ID: 689947, Refseq: NC_005108.4, Cryga: Gene ID: 684028, Refseq: NC_005108.4, Crygb: Gene ID: 301468, Refseq: NC_005108.4, Fam111a, Gene ID: 499322, Refseq: NC_005100.4

Sequence alignments of Rep (A) and Ant (B). Multialignment of S. Typhimurium Rep (UniProtKB accession no. T1S9Z0) against Rep from Salmonella phage epsilon15 (UniProtKB accession no. Q858D7), Escherichia phage phiV10 (UniProtKB accession no. Q286X7), Escherichia phage TL-2011b (UniProtKB accession no. G9L6A6), Salmonella phage SPN1S (UniProtKB accession no. H2D0H9), Salmonella phage SPN9TCW (UniProtKB accession no. M1F232), E. coli O118:H16 str. 2009C-4446 (UniProtKB accession no. A0A028E2H1), E. coli KTE235 (Ensembl Bacteria accession no. ELD77068), E. coli UMEA 3290-1 (Ensembl Bacteria accession no. ESK17367), E. coli MS 196-1 (UniProtKB accession no. D8BV09), E. coli O7:K1 str. CE10 (RefSeq accession no. YP_006144959), E. coli NA114 (RefSeq accession no. YP_006141898), E. coli MS 185-1 (RefSeq accession no. WP_000836295), E. coli 908519 (UniProtKB accession no. V0VMF3), Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000179 (EMBL-WGS accession no. KDQ92900), S. enterica subsp. enterica serovar Agona str. 632182-2 (Ensembl Bacteria accession no. ESH97837), Citrobacter koseri (UniProtKB accession no. A0A0A5IUU2), Enterobacter sp. MGH 15 (RefSeq accession no. WP_032636571), Enterobacter cloacae (RefSeq accession no. WP_032671854), Escherichia vulneris NBRC 102420 (UniProtKB accession no. A0A090UX00), Pantoea sp. GM01 (UniProtKB accession no. J2L6Z7), Serratia grimesii (UniProtKB accession no. A0A084YWL3), Serratia marcescens BIDMC 80 (Ensembl Bacteria accession no. EZQ69436), Candidatus Sodalis pierantonio str. SOPE (UniProtKB accession no. W0HLH1), Yersinia kristensenii (UniProtKB accession no. A0A088L5A4), S. enterica subsp. enterica serovar Newport str. CVM 19470 (Ensembl Bacteria accession no. EJA85693), S. enterica subsp. enterica serovar Enteritidis str. 3402 (UniProtKB accession no. V7Y6W8), Citrobacter werkmanii NBRC 105721 (UniProtKB accession no. A0A090TWG5), Citrobacter freundii GTC 09629 (Ensembl Bacteria accession no. EOD57340), S. enterica subsp. enterica serovar Newport str. CVM 19443 (Ensembl Bacteria accession no. EJA65811), E. coli O127:H6 (strain E2348/69/EPEC) (UniProtKB accession no. B7UGT4), Klebsiella oxytoca (RefSeq accession no. WP_032745644), Enterobacter aerogenes (RefSeq accession no. WP_032715140), Klebsiella pneumoniae (EMBL CDS accession no. AHM80771), Cronobacter sakazakii CMCC 45402 (UniProtKB accession no. V5TYG0), Cronobacter malonaticus (RefSeq accession no. WP_032982558), Cronobacter turicensis 564 (UniProtKB accession no. K8BK39), and C. malonaticus (RefSeq accession no. WP_032983317). Multialignment of Ant (UniProtKB accession no. T1SA45) against Ant from Salmonella phage epsilon15 (UniProtKB accession no. Q858F6), Escherichia phage phiV10 (UniProtKB accession no. Q286Z4), Escherichia phage TL-2011b (UniProtKB accession no. G9L6E3), Salmonella phage SPN1S (UniProtKB accession no. H2D0F7), Salmonella phage SPN9TCW (UniProtKB accession no. M1EZ64), S. enterica subsp. enterica serovar Enteritidis str. 3402 (UniProtKB accession no. V7Y2G6), S. enterica subsp. enterica serovar Newport str. CVM 19470 (Ensembl Bacteria accession no. EJA85653), S. enterica subsp. enterica serovar Agona str. 632182-2 (Ensembl Bacteria accession no. ESH97805), C. freundii GTC 09479 (EMBL-WGS accession no. EMF20587), E. coli O127:H6 (UniProtKB accession no. B7UGQ3), C. malonaticus (RefSeq accession no. WP_032986301), E. vulneris NBRC 102420 (UniProtKB accession no. A0A090V1M3), K. pneumoniae subsp. pneumoniae KPNIH10 (UniProtKB accession no. A0A0E1DF28), C. sakazakii CMCC 45402 (UniProtKB accession no. V5U0K5), Enterobacter sp. MGH 15 (Ensembl Bacteria accession no. EUM54292), K. oxytoca (RefSeq accession no. WP_032745680), S. enterica subsp. enterica serovar Newport str. CVM 19443 (Ensembl Bacteria accession no. EJA65772), E. cloacae (RefSeq accession no. WP_032671830), C. koseri (UniProtKB accession no. A0A0A5IVX8), S. enterica subsp. enterica serovar Bareilly str. CFSAN000179 (Ensembl Bacteria accession no. KDQ92930), E. coli NA114 (RefSeq accession no. YP_006141911), E. coli 908519 (UniProtKB accession no. V0V944), E. coli UMEA 3290-1 (EMBL-WGS accession no. ESK17333), E. coli KTE235 (EMBL-WGS accession no. ELD77031), Y. kristensenii (UniProtKB accession no. A0A088L842), E. coli O7:K1 str. CE10 (RefSeq accession no. YP_006144928), E. aerogenes UCI 15 (RefSeq accession no. WP_032723151), C. malonaticus (RefSeq accession no. WP_032983289), C. turicensis 564 (UniProtKB accession no. K8BRJ5), E. coli O7:K1 (strain IAI39/ExPEC) (RefSeq accession no. YP_002408599), E. coli O1:K1/APEC (RefSeq accession no. YP_853609), C. werkmanii NBRC 105721 (UniProtKB accession no. A0A090TUF1), Pantoea sp. GM01 (UniProtKB accession no. J2LY07), S. marcescens BIDMC 80 (Ensembl Bacteria accession no. EZQ69401), and E. coli FCP1 (RefSeq accession no. WP_025651152). Secondary structure elements were assigned by PyMOL (The PyMOL Molecular Graphics System, www.pymol.org). Every tenth residue is marked by a black dot. Strictly 100% conserved residues are highlighted in red. Cylinders above the sequences denote α-helices. A dotted line denotes disordered regions.

Partial multiple alignment of P102 sequence (residues 72-349) with homologs from insect orders except Lepidoptera. The name of the organism and the number of the first amino acid of the aligned region are indicated. The accession numbers for sequences retrieved from NCBI are the following: Aedes aegypti (RefSeq ID: XP_001660282.1), Anopheles darlingi (GenBank ID: EFR21399.1), A. gambiae (RefSeq ID: XP_311978.5), Apis mellifera (RefSeq ID: XP_003251941.1), Camponotus floridanus (GenBank ID: EFN64513.1), Culex quinquefasciatus (RefSeq ID: XP_001864562.1), C. tarsalis (GenBank ID: ACJ64345.1), Drosophila ananassae (RefSeq ID: XP_001963598.1), D. erecta (RefSeq ID: XP_001977186.1), D. melanogaster (RefSeq ID: NP_572668.1), D. mojavensis (RefSeq ID: XP_002010982.1), D. persimilis (RefSeq ID: XP_002025808.1), D. pseudoobscura pseudoobscura (RefSeq ID: XP_001354551.2), D. simulans (RefSeq ID: XP_002106640.1), D. virilis (RefSeq ID: XP_002056809.1), Glossina morsitans morsitans (GenBank ID: ADD19839.1), Harpegnathos saltator (GenBank ID: EFN80024.1), Nasonia vitripennis (RefSeq ID: XP_001603664.1), Solenopsis invicta (GenBank ID: EFZ16938.1), Tribolium castaneum (RefSeq ID: XP_968069.1). Three sequences of Coleoptera (Brassicogethes aeneus, Nicrophorus vespilloides and Phaedon cochleariae), were retrieved from in-house transcriptome databases Identical and conserved amino acids are shaded in light gray and very light gray, respectively. Residues involved in the enzymatic activity are indicated by arrows.

(A) The growth of the RefSeq microbial genomic databases and the database of bacterial genomes excluded from RefSeq for the reason “derived from surveillance project.” Dotted lines represent number of “complete genomes.” The data for 2020 includes genomes submitted before April 17. (B) Relative proportions between the different assembly levels in the bacterial RefSeq genome database. (C) The most frequently used sequencing techniques in the bacterial RefSeq database. (D) Relative proportions between the different Illumina platforms in the bacterial RefSeq genome database. (E) Relative proportions between sequencing techniques used in bacterial RefSeq divided by years. (F) Frequencies of pseudogenes in bacterial RefSeq genomes reported to be produced by one technique alone. (G) Relative proportions between genomes produced by a single sequencing technique and combinations of techniques. (H) Relative proportions between the most frequently used combinations of sequencing techniques in the bacterial RefSeq genome database. (I) Histogram of the reported sequence depth (coverage) used in the bacterial RefSeq genome database and in the bacterial surveillance project genome database.