{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T13:19:36Z","timestamp":1777555176963,"version":"3.51.4"},"reference-count":113,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,4,6]],"date-time":"2020-04-06T00:00:00Z","timestamp":1586131200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,4,6]],"date-time":"2020-04-06T00:00:00Z","timestamp":1586131200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007067","name":"Kempestiftelserna","doi-asserted-by":"publisher","award":["JCK-1528"],"award-info":[{"award-number":["JCK-1528"]}],"id":[{"id":"10.13039\/501100007067","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","award":["KAW 2015.0225"],"award-info":[{"award-number":["KAW 2015.0225"]}],"id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007676","name":"Ume\u00e5 Centre for Microbial Research","doi-asserted-by":"publisher","award":["-"],"award-info":[{"award-number":["-"]}],"id":[{"id":"10.13039\/501100007676","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010794","name":"Medicinska fakulteten, Ume\u00e5 Universitet","doi-asserted-by":"publisher","award":["-"],"award-info":[{"award-number":["-"]}],"id":[{"id":"10.13039\/501100010794","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Laboratory for Molecular Medicine Sweden","award":["-"],"award-info":[{"award-number":["-"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Shigella<\/jats:italic>\n                      is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans.\n                      <jats:italic>Shigella<\/jats:italic>\n                      invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We have sequenced, assembled, annotated and manually curated the full genome of\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new hybrid strategy to prepare gapless, highly accurate genome sequences, which also cover AT-rich tracks or repetitive sequences that are transcribed. Furthermore, we have performed genome-wide analysis of transcriptional start sites (TSS) and determined the length of 5\u2032 untranslated regions (5\u2032-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6723 primary TSS (pTSS) and 7328 secondary TSS (sTSS). The\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/regulondb.ccg.unam.mx\/\">http:\/\/regulondb.ccg.unam.mx<\/jats:ext-link>\n                      ) and RSAT (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/embnet.ccg.unam.mx\/rsat\/\">http:\/\/embnet.ccg.unam.mx\/rsat\/<\/jats:ext-link>\n                      ) databases to use their analysis tools in the\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      5a M90T genome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      We provide the first complete genome for\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      5a M90T. Further, we present a new hybrid strategy to prepare gapless, highly accurate genome sequences. Unlike currently used hybrid strategies combining long- and short-read DNA sequencing technologies to maximize accuracy, our workflow using long-read DNA sequencing and short-read RNA sequencing provides the added value of using non-redundant technologies, which yield distinct, exploitable datasets.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-020-6565-5","type":"journal-article","created":{"date-parts":[[2020,4,6]],"date-time":"2020-04-06T06:02:48Z","timestamp":1586152968000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0984-6286","authenticated-orcid":false,"given":"Ram\u00f3n","family":"Cervantes-Rivera","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4643-9831","authenticated-orcid":false,"given":"Sophie","family":"Tronnet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9915-002X","authenticated-orcid":false,"given":"Andrea","family":"Puhar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,4,6]]},"reference":[{"issue":"9888","key":"6565_CR1","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/S0140-6736(13)60844-2","volume":"382","author":"KL Kotloff","year":"2013","unstructured":"Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH, Panchalingam S, Wu Y, Sow SO, Sur D, Breiman RF, et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet. 2013;382(9888):209\u201322.","journal-title":"Lancet"},{"issue":"7","key":"6565_CR2","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1093\/cid\/ciu468","volume":"59","author":"S Livio","year":"2014","unstructured":"Livio S, Strockbine NA, Panchalingam S, Tennant SM, Barry EM, Marohn ME, Antonio M, Hossain A, Mandomando I, Ochieng JB, et al. Shigella isolates from the global enteric multicenter study inform vaccine development. Clin Infect Dis. 2014;59(7):933\u201341.","journal-title":"Clin Infect Dis"},{"key":"6565_CR3","doi-asserted-by":"crossref","unstructured":"Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, Abraham J, Adair T, Aggarwal R, Ahn SY, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the global burden of disease study 2010. Lancet. 2012;380(9859):2095\u2013128.","DOI":"10.1016\/S0140-6736(12)61728-0"},{"issue":"8","key":"6565_CR4","first-page":"651","volume":"77","author":"KL Kotloff","year":"1999","unstructured":"Kotloff KL, Winickoff JP, Ivanoff B, Clemens JD, Swerdlow DL, Sansonetti PJ, Adak GK, Levine MM. Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ. 1999;77(8):651\u201366.","journal-title":"Bull World Health Organ"},{"issue":"10122","key":"6565_CR5","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1016\/S0140-6736(17)33296-8","volume":"391","author":"KL Kotloff","year":"2018","unstructured":"Kotloff KL, Riddle MS, Platts-Mills JA, Pavlinac P, Zaidi AKM. Shigellosis. Lancet. 2018;391(10122):801\u201312.","journal-title":"Lancet"},{"issue":"6","key":"6565_CR6","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1093\/infdis\/159.6.1126","volume":"159","author":"HL DuPont","year":"1989","unstructured":"DuPont HL, Levine MM, Hornick RB, Formal SB. Inoculum size in shigellosis and implications for expected mode of transmission. J Infect Dis. 1989;159(6):1126\u20138.","journal-title":"J Infect Dis"},{"issue":"4","key":"6565_CR7","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/nrmicro.2016.10","volume":"14","author":"DP Thanh","year":"2016","unstructured":"The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol. 2016;14(4):235\u201350.","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"6565_CR8","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1016\/j.chom.2018.04.008","volume":"23","author":"MT Sorbara","year":"2018","unstructured":"Sorbara MT, Foerster EG, Tsalikis J, Abdel-Nour M, Mangiapane J, Sirluck-Schroeder I, Tattoli I, van Dalen R, Isenman DE, Rohde JR, et al. Complement C3 Drives Autophagy-Dependent Restriction of Cyto-invasive Bacteria. Cell Host Microbe. 2018;23(5):644\u201352 e645.","journal-title":"Cell Host Microbe"},{"key":"6565_CR9","doi-asserted-by":"publisher","unstructured":"Abdel-Nour M, Carneiro LAM, Downey J, Tsalikis J, Outlioua A, Prescott D, Da Costa LS, Hovingh ES, Farahvash A, Gaudet RG, et al. The heme-regulated inhibitor is a cytosolic sensor of protein misfolding that controls innate immune signaling. Science. 2019;365:eaaw4144. https:\/\/doi.org\/10.1126\/science.aaw4144.","DOI":"10.1126\/science.aaw4144"},{"key":"6565_CR10","first-page":"168","volume":"8","author":"D Scribano","year":"2016","unstructured":"Scribano D, Damico R, Ambrosi C, Superti F, Marazzato M, Conte MP, Longhi C, Palamara AT, Zagaglia C, Nicoletti M. The Shigella flexneri OmpA amino acid residues 188EVQ190 are essential for the interaction with the virulence factor PhoN2. Biochem Biophys Rep. 2016;8:168\u201373.","journal-title":"Biochem Biophys Rep"},{"issue":"4","key":"6565_CR11","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1016\/j.chom.2014.03.001","volume":"15","author":"A Brotcke Zumsteg","year":"2014","unstructured":"Brotcke Zumsteg A, Goosmann C, Brinkmann V, Morona R, Zychlinsky A. IcsA is a Shigella flexneri adhesin regulated by the type III secretion system and required for pathogenesis. Cell Host Microbe. 2014;15(4):435\u201345.","journal-title":"Cell Host Microbe"},{"issue":"7751","key":"6565_CR12","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1038\/s41586-019-1041-6","volume":"568","author":"Z Liu","year":"2019","unstructured":"Liu Z, Mar KB, Hanners NW, Perelman SS, Kanchwala M, Xing C, Schoggins JW, Alto NM. A NIK-SIX signalling axis controls inflammation by targeted silencing of non-canonical NF-kappaB. Nature. 2019;568(7751):249\u201353.","journal-title":"Nature"},{"issue":"9","key":"6565_CR13","doi-asserted-by":"publisher","first-page":"e1007014","DOI":"10.1371\/journal.pgen.1007014","volume":"13","author":"G Pilla","year":"2017","unstructured":"Pilla G, McVicker G, Tang CM. Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences. PLoS Genet. 2017;13(9):e1007014.","journal-title":"PLoS Genet"},{"issue":"6","key":"6565_CR14","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1016\/j.chom.2018.11.005","volume":"24","author":"S Krokowski","year":"2018","unstructured":"Krokowski S, Lobato-Marquez D, Chastanet A, Pereira PM, Angelis D, Galea D, Larrouy-Maumus G, Henriques R, Spiliotis ET, Carballido-Lopez R, et al. Septins Recognize and Entrap Dividing Bacterial Cells for Delivery to Lysosomes. Cell Host Microbe. 2018;24(6):866\u201374 e864.","journal-title":"Cell Host Microbe"},{"issue":"1","key":"6565_CR15","doi-asserted-by":"publisher","first-page":"2906","DOI":"10.1038\/s41598-019-39749-3","volume":"9","author":"M Pasqua","year":"2019","unstructured":"Pasqua M, Grossi M, Scinicariello S, Aussel L, Barras F, Colonna B, Prosseda G. The MFS efflux pump EmrKY contributes to the survival of Shigella within macrophages. Sci Rep. 2019;9(1):2906.","journal-title":"Sci Rep"},{"issue":"5","key":"6565_CR16","doi-asserted-by":"publisher","first-page":"e1005602","DOI":"10.1371\/journal.ppat.1005602","volume":"12","author":"A Weiner","year":"2016","unstructured":"Weiner A, Mellouk N, Lopez-Montero N, Chang YY, Souque C, Schmitt C, Enninga J. Macropinosomes are key players in early Shigella invasion and vacuolar escape in epithelial cells. PLoS Pathog. 2016;12(5):e1005602.","journal-title":"PLoS Pathog"},{"issue":"4","key":"6565_CR17","doi-asserted-by":"publisher","first-page":"e0122585","DOI":"10.1371\/journal.pone.0122585","volume":"10","author":"SM Sidik","year":"2015","unstructured":"Sidik SM, Salsman J, Dellaire G, Rohde JR. Shigella infection interferes with SUMOylation and increases PML-NB number. PLoS One. 2015;10(4):e0122585.","journal-title":"PLoS One"},{"issue":"4","key":"6565_CR18","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/j.chom.2017.09.007","volume":"22","author":"MP Wandel","year":"2017","unstructured":"Wandel MP, Pathe C, Werner EI, Ellison CJ, Boyle KB, von der Malsburg A, Rohde J, Randow F. GBPs Inhibit Motility of Shigella flexneri but Are Targeted for Degradation by the Bacterial Ubiquitin Ligase IpaH9.8. Cell Host Microbe. 2017;22(4):507\u201318 e505.","journal-title":"Cell Host Microbe"},{"issue":"12","key":"6565_CR19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007469","volume":"14","author":"V Ciancarella","year":"2018","unstructured":"Ciancarella V, Lembo-Fazio L, Paciello I, Bruno AK, Jaillon S, Berardi S, Barbagallo M, Meron-Sudai S, Cohen D, Molinaro A, et al. Role of a fluid-phase PRR in fighting an intracellular pathogen: PTX3 in Shigella infection. PLoS Pathog. 2018;14(12):e1007469.","journal-title":"PLoS Pathog"},{"issue":"7","key":"6565_CR20","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1016\/j.micinf.2014.03.010","volume":"16","author":"A Meghraoui","year":"2014","unstructured":"Meghraoui A, Schiavolin L, Allaoui A. Single amino acid substitutions on the needle tip protein IpaD increased Shigella virulence. Microbes Infect. 2014;16(7):532\u20139.","journal-title":"Microbes Infect"},{"issue":"21","key":"6565_CR21","doi-asserted-by":"publisher","first-page":"3692","DOI":"10.1002\/1873-3468.12873","volume":"591","author":"HN Kim","year":"2017","unstructured":"Kim HN, Seok SH, Lee YS, Won HS, Seo MD. Crystal structure and functional characterization of SF216 from Shigella flexneri. FEBS Lett. 2017;591(21):3692\u2013703.","journal-title":"FEBS Lett"},{"issue":"5","key":"6565_CR22","doi-asserted-by":"publisher","first-page":"1705","DOI":"10.1074\/jbc.M116.746826","volume":"292","author":"AD Roehrich","year":"2017","unstructured":"Roehrich AD, Bordignon E, Mode S, Shen DK, Liu X, Pain M, Murillo I, Martinez-Argudo I, Sessions RB, Blocker AJ. Steps for Shigella gatekeeper protein MxiC function in hierarchical type III secretion regulation. J Biol Chem. 2017;292(5):1705\u201323.","journal-title":"J Biol Chem"},{"key":"6565_CR23","doi-asserted-by":"publisher","unstructured":"Silue N, Marcantonio E, Campbell-Valois FX. RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state. Methods. 2019. https:\/\/doi.org\/10.1016\/j.ymeth.2019.03.017.","DOI":"10.1016\/j.ymeth.2019.03.017"},{"issue":"4","key":"6565_CR24","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1016\/j.celrep.2018.12.091","volume":"26","author":"C Valencia-Gallardo","year":"2019","unstructured":"Valencia-Gallardo C, Bou-Nader C, Aguilar-Salvador DI, Carayol N, Quenech'Du N, Pecqueur L, Park H, Fontecave M, Izard T, Tran Van Nhieu G. Shigella IpaA Binding to Talin Stimulates Filopodial Capture and Cell Adhesion. Cell Rep. 2019;26(4):921\u201332 e926.","journal-title":"Cell Rep"},{"issue":"3","key":"6565_CR25","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1128\/IAI.35.3.852-860.1982","volume":"35","author":"PJ Sansonetti","year":"1982","unstructured":"Sansonetti PJ, Kopecko DJ, Formal SB. Involvement of a plasmid in the invasive ability of Shigella flexneri. Infect Immun. 1982;35(3):852\u201360.","journal-title":"Infect Immun"},{"issue":"27","key":"6565_CR26","doi-asserted-by":"publisher","first-page":"13582","DOI":"10.1073\/pnas.1902922116","volume":"116","author":"ML Ferrari","year":"2019","unstructured":"Ferrari ML, Malarde V, Grassart A, Salavessa L, Nigro G, Descorps-Declere S, Rohde JR, Schnupf P, Masson V, Arras G, et al. Shigella promotes major alteration of gut epithelial physiology and tissue invasion by shutting off host intracellular transport. Proc Natl Acad Sci U S A. 2019;116(27):13582\u201391.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6565_CR27","doi-asserted-by":"crossref","unstructured":"Mirza N, Sowa AS, Lautz K, Kufer TA. NLRP10 Affects the Stability of Abin-1 To Control Inflammatory Responses. J Immunol. 2019;202(1):218\u201327.","DOI":"10.4049\/jimmunol.1800334"},{"issue":"4","key":"6565_CR28","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1046\/j.1365-2958.2000.02179.x","volume":"38","author":"C Buchrieser","year":"2000","unstructured":"Buchrieser C, Glaser P, Rusniok C, Nedjari H, D'Hauteville H, Kunst F, Sansonetti P, Parsot C. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol Microbiol. 2000;38(4):760\u201371.","journal-title":"Mol Microbiol"},{"key":"6565_CR29","doi-asserted-by":"crossref","unstructured":"Sansonetti PJ, Hale TL, Dammin GJ, Kapfer C, Collins HH Jr, Formal SB. Alterations in the pathogenicity of Escherichia coli K-12 after transfer of plasmid and chromosomal genes from Shigella flexneri. Infect Immun. 1983;39(3):1392\u2013402.","DOI":"10.1128\/IAI.39.3.1392-1402.1983"},{"key":"6565_CR30","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1128\/JB.86.6.1251-1258.1963","volume":"86","author":"S Falkow","year":"1963","unstructured":"Falkow S, Schneider H, Baron LS, Formal SB. Virulence of Escherichia-Shigella genetic hybrids for the Guinea pig. J Bacteriol. 1963;86:1251\u20138.","journal-title":"J Bacteriol"},{"issue":"11","key":"6565_CR31","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1046\/j.1462-5822.2003.00320.x","volume":"5","author":"MA Ingersoll","year":"2003","unstructured":"Ingersoll MA, Moss JE, Weinrauch Y, Fisher PE, Groisman EA, Zychlinsky A. The ShiA protein encoded by the Shigella flexneri SHI-2 pathogenicity island attenuates inflammation. Cell Microbiol. 2003;5(11):797\u2013807.","journal-title":"Cell Microbiol"},{"issue":"1","key":"6565_CR32","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1046\/j.1365-2958.1999.01449.x","volume":"33","author":"JE Moss","year":"1999","unstructured":"Moss JE, Cardozo TJ, Zychlinsky A, Groisman EA. The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol Microbiol. 1999;33(1):74\u201383.","journal-title":"Mol Microbiol"},{"issue":"9","key":"6565_CR33","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1046\/j.1462-5822.2002.00216.x","volume":"4","author":"C Bartoleschi","year":"2002","unstructured":"Bartoleschi C, Pardini MC, Scaringi C, Martino MC, Pazzani C, Bernardini ML. Selection of Shigella flexneri candidate virulence genes specifically induced in bacteria resident in host cell cytoplasm. Cell Microbiol. 2002;4(9):613\u201326.","journal-title":"Cell Microbiol"},{"issue":"7296","key":"6565_CR34","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/nature08970","volume":"465","author":"B Marteyn","year":"2010","unstructured":"Marteyn B, West NP, Browning DF, Cole JA, Shaw JG, Palm F, Mounier J, Prevost MC, Sansonetti P, Tang CM. Modulation of Shigella virulence in response to available oxygen in vivo. Nature. 2010;465(7296):355\u20138.","journal-title":"Nature"},{"key":"6565_CR35","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1186\/1471-2164-15-438","volume":"15","author":"M Vergara-Irigaray","year":"2014","unstructured":"Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM. RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics. 2014;15:438.","journal-title":"BMC Genomics"},{"issue":"8","key":"6565_CR36","doi-asserted-by":"publisher","first-page":"4379","DOI":"10.1128\/IAI.70.8.4379-4388.2002","volume":"70","author":"LJ Runyen-Janecky","year":"2002","unstructured":"Runyen-Janecky LJ, Payne SM. Identification of chromosomal Shigella flexneri genes induced by the eukaryotic intracellular environment. Infect Immun. 2002;70(8):4379\u201388.","journal-title":"Infect Immun"},{"issue":"9","key":"6565_CR37","doi-asserted-by":"publisher","first-page":"3068","DOI":"10.1128\/IAI.00537-13","volume":"81","author":"CR Morris","year":"2013","unstructured":"Morris CR, Grassel CL, Redman JC, Sahl JW, Barry EM, Rasko DA. Characterization of intracellular growth regulator icgR by utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri. Infect Immun. 2013;81(9):3068\u201376.","journal-title":"Infect Immun"},{"issue":"11","key":"6565_CR38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0049980","volume":"7","author":"CS Faherty","year":"2012","unstructured":"Faherty CS, Harper JM, Shea-Donohue T, Barry EM, Kaper JB, Fasano A, Nataro JP. Chromosomal and plasmid-encoded factors of Shigella flexneri induce secretogenic activity ex vivo. PLoS One. 2012;7(11):e49980.","journal-title":"PLoS One"},{"issue":"5","key":"6565_CR39","doi-asserted-by":"publisher","first-page":"3271","DOI":"10.1128\/IAI.69.5.3271-3285.2001","volume":"69","author":"MM Venkatesan","year":"2001","unstructured":"Venkatesan MM, Goldberg MB, Rose DJ, Grotbeck EJ, Burland V, Blattner FR. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun. 2001;69(5):3271\u201385.","journal-title":"Infect Immun"},{"issue":"11","key":"6565_CR40","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1128\/JB.00393-12","volume":"194","author":"NT Onodera","year":"2012","unstructured":"Onodera NT, Ryu J, Durbic T, Nislow C, Archibald JM, Rohde JR. Genome sequence of Shigella flexneri serotype 5a strain M90T Sm. J Bacteriol. 2012;194(11):3022.","journal-title":"J Bacteriol"},{"key":"6565_CR41","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1186\/1471-2164-7-173","volume":"7","author":"H Nie","year":"2006","unstructured":"Nie H, Yang F, Zhang X, Yang J, Chen L, Wang J, Xiong Z, Peng J, Sun L, Dong J, et al. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics. 2006;7:173.","journal-title":"BMC Genomics"},{"issue":"7286","key":"6565_CR42","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nature08756","volume":"464","author":"CM Sharma","year":"2010","unstructured":"Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464(7286):250\u20135.","journal-title":"Nature"},{"issue":"10","key":"6565_CR43","doi-asserted-by":"publisher","first-page":"e1003668","DOI":"10.1371\/journal.ppat.1003668","volume":"9","author":"S Hannemann","year":"2013","unstructured":"Hannemann S, Gao B, Galan JE. Salmonella modulation of host cell gene expression promotes its intracellular growth. PLoS Pathog. 2013;9(10):e1003668.","journal-title":"PLoS Pathog"},{"issue":"7","key":"6565_CR44","doi-asserted-by":"publisher","first-page":"e1006532","DOI":"10.1371\/journal.ppat.1006532","volume":"13","author":"S Hannemann","year":"2017","unstructured":"Hannemann S, Galan JE. Salmonella enterica serovar-specific transcriptional reprogramming of infected cells. PLoS Pathog. 2017;13(7):e1006532.","journal-title":"PLoS Pathog"},{"issue":"3","key":"6565_CR45","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1093\/nar\/gkp1032","volume":"38","author":"M Albrecht","year":"2010","unstructured":"Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res. 2010;38(3):868\u201377.","journal-title":"Nucleic Acids Res"},{"key":"6565_CR46","doi-asserted-by":"publisher","unstructured":"Nickerson KP, Chanin RB, Sistrunk JR, Rasko DA, Fink PJ, Barry EM, Nataro JP, Faherty CS. Analysis of Shigella flexneri Resistance, Biofilm Formation, and Transcriptional Profile in Response to Bile Salts. Infect Immun. 2017;85(6):e01067\u201316. https:\/\/doi.org\/10.1128\/IAI.01067-16.","DOI":"10.1128\/IAI.01067-16"},{"issue":"10","key":"6565_CR47","doi-asserted-by":"publisher","first-page":"e7526","DOI":"10.1371\/journal.pone.0007526","volume":"4","author":"A Mendoza-Vargas","year":"2009","unstructured":"Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, et al. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One. 2009;4(10):e7526.","journal-title":"PLoS One"},{"issue":"6","key":"6565_CR48","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.chom.2013.11.010","volume":"14","author":"C Kroger","year":"2013","unstructured":"Kroger C, Colgan A, Srikumar S, Handler K, Sivasankaran SK, Hammarlof DL, Canals R, Grissom JE, Conway T, Hokamp K, et al. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe. 2013;14(6):683\u201395.","journal-title":"Cell Host Microbe"},{"issue":"9","key":"6565_CR49","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/nchembio0907-535","volume":"3","author":"DR Schoenberg","year":"2007","unstructured":"Schoenberg DR. The end defines the means in bacterial mRNA decay. Nat Chem Biol. 2007;3(9):535\u20136.","journal-title":"Nat Chem Biol"},{"issue":"5","key":"6565_CR50","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","volume":"13","author":"A Rhoads","year":"2015","unstructured":"Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics. 2015;13(5):278\u201389.","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"5","key":"6565_CR51","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722\u201336.","journal-title":"Genome Res"},{"issue":"4","key":"6565_CR52","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","volume":"28","author":"T Carver","year":"2012","unstructured":"Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics. 2012;28(4):464\u20139.","journal-title":"Bioinformatics"},{"issue":"16","key":"6565_CR53","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment\/Map format and SAMtools. Bioinformatics. 2009;25(16):2078\u20139.","journal-title":"Bioinformatics"},{"issue":"14","key":"6565_CR54","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"11","key":"6565_CR55","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963.","journal-title":"PLoS One"},{"issue":"7","key":"6565_CR56","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"AC Darling","year":"2004","unstructured":"Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394\u2013403.","journal-title":"Genome Res"},{"key":"6565_CR57","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","volume":"9","author":"RK Aziz","year":"2008","unstructured":"Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.","journal-title":"BMC Genomics"},{"issue":"14","key":"6565_CR58","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139.","journal-title":"Bioinformatics"},{"issue":"14","key":"6565_CR59","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","volume":"44","author":"T Tatusova","year":"2016","unstructured":"Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614\u201324.","journal-title":"Nucleic Acids Res"},{"key":"6565_CR60","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.mib.2014.11.012","volume":"23","author":"I Goodhead","year":"2015","unstructured":"Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Curr Opin Microbiol. 2015;23:102\u20139.","journal-title":"Curr Opin Microbiol"},{"issue":"D1","key":"6565_CR61","doi-asserted-by":"publisher","first-page":"D212","DOI":"10.1093\/nar\/gky1077","volume":"47","author":"A Santos-Zavaleta","year":"2019","unstructured":"Santos-Zavaleta A, Salgado H, Gama-Castro S, Sanchez-Perez M, Gomez-Romero L, Ledezma-Tejeida D, Garcia-Sotelo JS, Alquicira-Hernandez K, Muniz-Rascado LJ, Pena-Loredo P, et al. RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Res. 2019;47(D1):D212\u2013d220.","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"6565_CR62","doi-asserted-by":"publisher","first-page":"W209","DOI":"10.1093\/nar\/gky317","volume":"46","author":"NTT Nguyen","year":"2018","unstructured":"Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, et al. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 2018;46(W1):W209\u2013w214.","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"6565_CR63","doi-asserted-by":"publisher","first-page":"2247","DOI":"10.1093\/bioinformatics\/btu205","volume":"30","author":"R Hilker","year":"2014","unstructured":"Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A. ReadXplorer--visualization and analysis of mapped sequences. Bioinformatics. 2014;30(16):2247\u201354.","journal-title":"Bioinformatics"},{"key":"6565_CR64","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","volume":"17","author":"R Buels","year":"2016","unstructured":"Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66.","journal-title":"Genome Biol"},{"issue":"12","key":"6565_CR65","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1111\/j.1365-2958.1992.tb00885.x","volume":"6","author":"A Allaoui","year":"1992","unstructured":"Allaoui A, Mounier J, Prevost MC, Sansonetti PJ, Parsot C. icsB: a Shigella flexneri virulence gene necessary for the lysis of protrusions during intercellular spread. Mol Microbiol. 1992;6(12):1605\u201316.","journal-title":"Mol Microbiol"},{"issue":"9","key":"6565_CR66","doi-asserted-by":"publisher","first-page":"R64","DOI":"10.1186\/gb-2004-5-9-r64","volume":"5","author":"Y Liu","year":"2004","unstructured":"Liu Y, Harrison PM, Kunin V, Gerstein M. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 2004;5(9):R64.","journal-title":"Genome Biol"},{"issue":"8","key":"6565_CR67","doi-asserted-by":"publisher","first-page":"e1001050","DOI":"10.1371\/journal.pgen.1001050","volume":"6","author":"CH Kuo","year":"2010","unstructured":"Kuo CH, Ochman H. The extinction dynamics of bacterial pseudogenes. PLoS Genet. 2010;6(8):e1001050.","journal-title":"PLoS Genet"},{"key":"6565_CR68","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1471-2164-10-36","volume":"10","author":"KE Holt","year":"2009","unstructured":"Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Simmonds M, et al. Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi a and Typhi. BMC Genomics. 2009;10:36.","journal-title":"BMC Genomics"},{"key":"6565_CR69","doi-asserted-by":"crossref","unstructured":"Feavers IM, Maiden MC. A gonococcal porA pseudogene: implications for understanding the evolution and pathogenicity of Neisseria gonorrhoeae. Mol Microbiol. 1998;30(3):647\u201356.","DOI":"10.1046\/j.1365-2958.1998.01101.x"},{"issue":"11","key":"6565_CR70","doi-asserted-by":"publisher","first-page":"e27754","DOI":"10.1371\/journal.pone.0027754","volume":"6","author":"Y Feng","year":"2011","unstructured":"Feng Y, Chen Z, Liu SL. Gene decay in Shigella as an incipient stage of host-adaptation. PLoS One. 2011;6(11):e27754.","journal-title":"PLoS One"},{"issue":"2","key":"6565_CR71","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1111\/j.1574-6968.2006.00276.x","volume":"259","author":"K Suzuki","year":"2006","unstructured":"Suzuki K, Nakata N, Bang PD, Ishii N, Makino M. High-level expression of pseudogenes in Mycobacterium leprae. FEMS Microbiol Lett. 2006;259(2):208\u201314.","journal-title":"FEMS Microbiol Lett"},{"issue":"2","key":"6565_CR72","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1101\/gr.4106106","volume":"16","author":"H Toh","year":"2006","unstructured":"Toh H, Weiss BL, Perkin SA, Yamashita A, Oshima K, Hattori M, Aksoy S. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res. 2006;16(2):149\u201356.","journal-title":"Genome Res"},{"key":"6565_CR73","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1186\/1471-2164-11-449","volume":"11","author":"E Belda","year":"2010","unstructured":"Belda E, Moya A, Bentley S, Silva FJ. Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. BMC Genomics. 2010;11:449.","journal-title":"BMC Genomics"},{"issue":"6823","key":"6565_CR74","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/35059006","volume":"409","author":"ST Cole","year":"2001","unstructured":"Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, et al. Massive gene decay in the leprosy bacillus. Nature. 2001;409(6823):1007\u201311.","journal-title":"Nature"},{"key":"6565_CR75","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1186\/1471-2164-10-397","volume":"10","author":"DL Williams","year":"2009","unstructured":"Williams DL, Slayden RA, Amin A, Martinez AN, Pittman TL, Mira A, Mitra A, Nagaraja V, Morrison NE, Moraes M, et al. Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics. 2009;10:397.","journal-title":"BMC Genomics"},{"issue":"5","key":"6565_CR76","doi-asserted-by":"publisher","first-page":"2775","DOI":"10.1128\/IAI.71.5.2775-2786.2003","volume":"71","author":"J Wei","year":"2003","unstructured":"Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G 3rd, Rose DJ, Darling A, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun. 2003;71(5):2775\u201386.","journal-title":"Infect Immun"},{"issue":"19","key":"6565_CR77","doi-asserted-by":"publisher","first-page":"6445","DOI":"10.1093\/nar\/gki954","volume":"33","author":"F Yang","year":"2005","unstructured":"Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J, et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 2005;33(19):6445\u201358.","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"6565_CR78","doi-asserted-by":"publisher","first-page":"4432","DOI":"10.1093\/nar\/gkf566","volume":"30","author":"Q Jin","year":"2002","unstructured":"Jin Q, Yuan Z, Xu J, Wang Y, Shen Y, Lu W, Wang J, Liu H, Yang J, Yang F, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002;30(20):4432\u201341.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"6565_CR79","doi-asserted-by":"publisher","first-page":"468","DOI":"10.4161\/rna.8.3.14421","volume":"8","author":"MP Vockenhuber","year":"2011","unstructured":"Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol. 2011;8(3):468\u201377.","journal-title":"RNA Biol"},{"issue":"8","key":"6565_CR80","doi-asserted-by":"publisher","first-page":"R164","DOI":"10.1186\/gb-2007-8-8-r164","volume":"8","author":"R Hershberg","year":"2007","unstructured":"Hershberg R, Tang H, Petrov DA. Reduced selection leads to accelerated gene loss in Shigella. Genome Biol. 2007;8(8):R164.","journal-title":"Genome Biol"},{"issue":"1","key":"6565_CR81","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.meegid.2008.10.003","volume":"9","author":"J Peng","year":"2009","unstructured":"Peng J, Yang J, Jin Q. The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli. Infect Genet Evol. 2009;9(1):147\u201352.","journal-title":"Infect Genet Evol"},{"issue":"19","key":"6565_CR82","doi-asserted-by":"publisher","first-page":"10567","DOI":"10.1073\/pnas.180094797","volume":"97","author":"GM Pupo","year":"2000","unstructured":"Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A. 2000;97(19):10567\u201372.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"6565_CR83","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1007\/s00239-006-0052-8","volume":"64","author":"J Yang","year":"2007","unstructured":"Yang J, Nie H, Chen L, Zhang X, Yang F, Xu X, Zhu Y, Yu J, Jin Q. Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol. 2007;64(1):71\u20139.","journal-title":"J Mol Evol"},{"issue":"6","key":"6565_CR84","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1086\/323035","volume":"184","author":"IM Fernandez","year":"2001","unstructured":"Fernandez IM, Silva M, Schuch R, Walker WA, Siber AM, Maurelli AT, McCormick BA. Cadaverine prevents the escape of Shigella flexneri from the phagolysosome: a connection between bacterial dissemination and neutrophil transepithelial signaling. J Infect Dis. 2001;184(6):743\u201353.","journal-title":"J Infect Dis"},{"issue":"17","key":"6565_CR85","doi-asserted-by":"publisher","first-page":"6482","DOI":"10.1128\/JB.00525-07","volume":"189","author":"AL Prunier","year":"2007","unstructured":"Prunier AL, Schuch R, Fernandez RE, Maurelli AT. Genetic structure of the nadA and nadB antivirulence loci in Shigella spp. J Bacteriol. 2007;189(17):6482\u20136.","journal-title":"J Bacteriol"},{"issue":"3","key":"6565_CR86","doi-asserted-by":"publisher","first-page":"e0121785","DOI":"10.1371\/journal.pone.0121785","volume":"10","author":"V Bravo","year":"2015","unstructured":"Bravo V, Puhar A, Sansonetti P, Parsot C, Toro CS. Distinct mutations led to inactivation of type 1 fimbriae expression in Shigella spp. PLoS One. 2015;10(3):e0121785.","journal-title":"PLoS One"},{"issue":"5","key":"6565_CR87","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1111\/1574-6976.12067","volume":"38","author":"P Siguier","year":"2014","unstructured":"Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev. 2014;38(5):865\u201391.","journal-title":"FEMS Microbiol Rev"},{"issue":"6","key":"6565_CR88","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1080\/1040841X.2017.1303661","volume":"43","author":"J Vandecraen","year":"2017","unstructured":"Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol. 2017;43(6):709\u201330.","journal-title":"Crit Rev Microbiol"},{"key":"6565_CR89","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/s12859-015-0805-8","volume":"16","author":"X Mao","year":"2015","unstructured":"Mao X, Ma Q, Liu B, Chen X, Zhang H, Xu Y. Revisiting operons: an analysis of the landscape of transcriptional units in E coli. BMC Bioinformatics. 2015;16:356.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"6565_CR90","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1128\/JB.137.1.584-594.1979","volume":"137","author":"M Yamamoto","year":"1979","unstructured":"Yamamoto M, Nomura M. Organization of genes for transcription and translation in the rif region of the Escherichia coli chromosome. J Bacteriol. 1979;137(1):584\u201394.","journal-title":"J Bacteriol"},{"issue":"1","key":"6565_CR91","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1073\/pnas.77.1.313","volume":"77","author":"T Horii","year":"1980","unstructured":"Horii T, Ogawa T, Ogawa H. Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1980;77(1):313\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6565_CR92","first-page":"1727","volume":"250","author":"F Jacob","year":"1960","unstructured":"Jacob F, Perrin D, Sanchez C, Monod J. Operon: a group of genes with the expression coordinated by an operator. C R Hebd Seances Acad Sci. 1960;250:1727\u20139.","journal-title":"C R Hebd Seances Acad Sci"},{"issue":"1","key":"6565_CR93","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1111\/j.1365-2958.2008.06256.x","volume":"69","author":"L Krasny","year":"2008","unstructured":"Krasny L, Tiserova H, Jonak J, Rejman D, Sanderova H. The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol Microbiol. 2008;69(1):42\u201354.","journal-title":"Mol Microbiol"},{"issue":"12","key":"6565_CR94","doi-asserted-by":"publisher","first-page":"e1007461","DOI":"10.1371\/journal.ppat.1007461","volume":"14","author":"I Warrier","year":"2018","unstructured":"Warrier I, Ram-Mohan N, Zhu Z, Hazery A, Echlin H, Rosch J, Meyer MM, van Opijnen T. The transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. PLoS Pathog. 2018;14(12):e1007461.","journal-title":"PLoS Pathog"},{"issue":"10","key":"6565_CR95","doi-asserted-by":"publisher","first-page":"R98","DOI":"10.1186\/gb-2011-12-10-r98","volume":"12","author":"M Albrecht","year":"2011","unstructured":"Albrecht M, Sharma CM, Dittrich MT, Muller T, Reinhardt R, Vogel J, Rudel T. The transcriptional landscape of Chlamydia pneumoniae. Genome Biol. 2011;12(10):R98.","journal-title":"Genome Biol"},{"key":"6565_CR96","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/1471-2164-11-245","volume":"11","author":"JP Schluter","year":"2010","unstructured":"Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 2010;11:245.","journal-title":"BMC Genomics"},{"issue":"5","key":"6565_CR97","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1073\/pnas.1812746116","volume":"116","author":"S Saenz-Lahoya","year":"2019","unstructured":"Saenz-Lahoya S, Bitarte N, Garcia B, Burgui S, Vergara-Irigaray M, Valle J, Solano C, Toledo-Arana A, Lasa I. Noncontiguous operon is a genetic organization for coordinating bacterial gene expression. Proc Natl Acad Sci U S A. 2019;116(5):1733\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"6565_CR98","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1128\/JB.02096-14","volume":"197","author":"MK Thomason","year":"2015","unstructured":"Thomason MK, Bischler T, Eisenbart SK, Forstner KU, Zhang A, Herbig A, Nieselt K, Sharma CM, Storz G. Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. J Bacteriol. 2015;197(1):18\u201328.","journal-title":"J Bacteriol"},{"issue":"4","key":"6565_CR99","doi-asserted-by":"publisher","first-page":"e01442","DOI":"10.1128\/mBio.01442-14","volume":"5","author":"T Conway","year":"2014","unstructured":"Conway T, Creecy JP, Maddox SM, Grissom JE, Conkle TL, Shadid TM, Teramoto J, San Miguel P, Shimada T, Ishihama A, et al. Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. mBio. 2014;5(4):e01442\u201314.","journal-title":"mBio"},{"key":"6565_CR100","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.mib.2017.10.022","volume":"39","author":"S Miravet-Verde","year":"2017","unstructured":"Miravet-Verde S, Llorens-Rico V, Serrano L. Alternative transcriptional regulation in genome-reduced bacteria. Curr Opin Microbiol. 2017;39:89\u201395.","journal-title":"Curr Opin Microbiol"},{"issue":"7","key":"6565_CR101","doi-asserted-by":"publisher","first-page":"4006","DOI":"10.1093\/nar\/gkw1172","volume":"45","author":"J Wen","year":"2017","unstructured":"Wen J, Harp JR, Fozo EM. The 5 UTR of the type I toxin ZorO can both inhibit and enhance translation. Nucleic Acids Res. 2017;45(7):4006\u201320.","journal-title":"Nucleic Acids Res"},{"key":"6565_CR102","doi-asserted-by":"crossref","unstructured":"Dong F, Xia L, Lu R, Zhao X, Zhang Y, Zhang Y, Huang X. The malS-5'UTR weakens the ability of Salmonella enterica serovar Typhi to survive in macrophages by increasing intracellular ATP levels. Microb Pathog. 2018;115:321\u201331.","DOI":"10.1016\/j.micpath.2017.12.072"},{"key":"6565_CR103","doi-asserted-by":"publisher","unstructured":"Heroven AK, Nuss AM, Dersch P. RNA-based mechanisms of virulence control in Enterobacteriaceae. RNA Biol. 2017;14(5):471\u201387. https:\/\/doi.org\/10.1080\/15476286.2016.1201617.","DOI":"10.1080\/15476286.2016.1201617"},{"key":"6565_CR104","doi-asserted-by":"publisher","unstructured":"Di Martino ML, Romilly C, Wagner EG, Colonna B, Prosseda G. One Gene and Two Proteins: a Leaderless mRNA Supports the Translation of a Shorter Form of the Shigella VirF Regulator. mBio. 2016;7(6):e01860\u201316. https:\/\/doi.org\/10.1128\/mBio.01860-16.","DOI":"10.1128\/mBio.01860-16"},{"issue":"7","key":"6565_CR105","doi-asserted-by":"publisher","first-page":"2331","DOI":"10.1002\/j.1460-2075.1990.tb07405.x","volume":"9","author":"P Blomberg","year":"1990","unstructured":"Blomberg P, Wagner EG, Nordstrom K. Control of replication of plasmid R1: the duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J. 1990;9(7):2331\u201340.","journal-title":"EMBO J"},{"key":"6565_CR106","doi-asserted-by":"publisher","first-page":"1338","DOI":"10.12688\/f1000research.15931.2","volume":"7","author":"SW Wingett","year":"2018","unstructured":"Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Research. 2018;7:1338.","journal-title":"F1000Research"},{"issue":"19","key":"6565_CR107","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels P, Magnusson M, Lundin S, Kaller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047\u20138.","journal-title":"Bioinformatics"},{"issue":"6","key":"6565_CR108","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16(6):276\u20137.","journal-title":"Trends Genet"},{"issue":"7176","key":"6565_CR109","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/nature06475","volume":"451","author":"A Deana","year":"2008","unstructured":"Deana A, Celesnik H, Belasco JG. The bacterial enzyme RppH triggers messenger RNA degradation by 5\u2032 pyrophosphate removal. Nature. 2008;451(7176):355\u20138.","journal-title":"Nature"},{"issue":"15","key":"6565_CR110","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114\u201320.","journal-title":"Bioinformatics"},{"issue":"4","key":"6565_CR111","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357\u20139.","journal-title":"Nat Methods"},{"issue":"24","key":"6565_CR112","doi-asserted-by":"publisher","first-page":"3702","DOI":"10.1093\/bioinformatics\/btw541","volume":"32","author":"R Hilker","year":"2016","unstructured":"Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A. ReadXplorer 2-detailed read mapping analysis and visualization from one single source. Bioinformatics. 2016;32(24):3702\u20138.","journal-title":"Bioinformatics"},{"issue":"2","key":"6565_CR113","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166\u20139.","journal-title":"Bioinformatics"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-020-6565-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12864-020-6565-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-020-6565-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,5]],"date-time":"2021-04-05T19:07:53Z","timestamp":1617649673000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-020-6565-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,6]]},"references-count":113,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["6565"],"URL":"https:\/\/doi.org\/10.1186\/s12864-020-6565-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/595066","asserted-by":"object"}]},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,6]]},"assertion":[{"value":"24 June 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 April 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"285"}}