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Genome sequencing yakamutsiridza ndima yekutsvagisa chirwere chinotapukira, kuburitsa chirwere chechirwere, pathogenesis, kupindirana kwepathogen, uye maitiro ekushanduka akaiswa pahutachiona. Iyo Mycobacterium tuberculosis complex (MTBC) inotora Mycobacterium bovis seimwe yenhengo dzayo dzinochinja mhuka dzinokonzera tuberculosis (TB) mumhuka dzepasi, uye muenzaniso wakajairwa wekushanduka kwebhakitiriya. Kufanana nedzimwe nhengo dzeMTBC, Mycobacterium bovis inofungidzirwa kuti yakanyatsogadzirwa, inoshanduka zvishoma nezvishoma, uye zviri pachena kuti hapana chiratidzo chekubatanidzazve kana kuchinjika gene kutamiswa. Mubasa iri, tinoshandisa comparative genomics kune yese genome sequence (WGS) dataset inoumbwa ne70 mombe M. kubva kumarudzi akasiyana (Europe neAfrica) kuti tiwane ruzivo rwekusiyana kwemajini emombe M. Evolutionary simba. Nzira nhatu dzakasiyana dzinoshandiswa kufungidzira zviratidzo zvekuronga patsva. Pasi rose, nhamba shomanana yezviitiko zvekugadzirisa zvakare yakaonekwa uye yakasimbiswa nenzira mbiri dzakazvimiririra nerutsigiro rwakasimba. Zvakadaro, kana zvichienzaniswa nekuchinja, kubatanidzwazve kune mhedzisiro isina simba pakusiyana kweM. bovis (yakazara r/m = 0.037). Musiyano r/m avhareji yakawanikwa muiyo clonal complex yeMycobacterium bovis mune yedu data seti inoenderana nepfungwa yakajairika yekuti dhigirii rekubatanidza rinogona kusiyana zvakanyanya pakati pemitsara yakagoverwa kune imwechete taxonomic mhando. Zvichienderana nebasa iri, kubatanidzwazve muMycobacterium bovis hakugone kurambwa, saka inofanirwa kunge iri nyaya yekuwedzera kuedza mune ramangwana rekuenzanisa genomics tsvagiridzo, umo WGS yedata hombe seti kubva kwakasiyana epidemiological mamiriro epasirese yakakosha. Imwezve ongororo yakazoitwa pane diki Mycobacterium bovis data set (n = 42) kubva kune akawanda-host TB kuwanda, uye anopfuura 1,800 loci akaonekwa, iyo kanenge imwe strain yakaratidza imwechete nucleotide polymorphism (SNP) . Zvizhinji (87.1%) zviri munharaunda yekodhi, uye chiyero chepasi rose chekuchinja kusingafananidzi (dN / dS) yekuchinja kwakafanana kunodarika 1.5, zvichiratidza kuti kusarudzwa kwakanaka isimba rinokosha rekushanduka-shanduka rinoitwa paM. bovis. Chikamu chepamusoro cheSNPs chakaonekwa mumajeni akapfuma muzvikamu zvinoshanda zve "lipid metabolism", "cell wall uye cellular process", uye "metabolism yepakati nekufema", zvichiratidza kugona kwavo mubiology uye kushanduka kweMycobacterium bovis kukosha. Kunyatsotarisisa majini ari muMTBC madzitateguru anowanzo kuchinjika kuchinjisa gene uye anosanganisirwa mu3R (DNA kugadzirisa, kudzokorodza, uye recombination) system inoratidza huwandu hwepasi rose husina kunaka kukosha kweTaijima's D neutral bvunzo, iyo inoratidza yapfuura yakasarudzika scanning.
Mycobacterium tuberculosis complex (MTBC) ndeimwe yemitero yakabudirira kwazvo yemabhakitiriya pathogens uye yakajairika nyaya yekushanduka kwebhakitiriya. Nhengo dzayo dzinoratidza zvinoshamisa nucleotide identity pane genomic level (> 99%)1,2. Kusiyana kweMTBC ecotypes kunogona kukonzera tuberculosis (TB), iyo inotapukira chirwere chegranulomatous, mumhando dzakasiyana-siyana dzemarudzi kubva kune micro-mammals kusvika kuvanhu3,4,5. Parizvino, iyo yakaoma inosanganisira vanhu [M. Tuberculosis (Mtb), Mycobacterium africanum] uye utachiona hunoenderana nemhuka (Mycobacterium bovis, Mycobacterium capitum, Mycobacterium pinnipedum, Mycobacterium microtobacter , Mycobacterium mongee, Mycobacterium miysani, Mycobacterium surika, "Bacillus chimpanzee") 5 uye "6". M. canettii (inozivikanwawo se "Nodobacter glabrata") Ivhareji nucleotide identity ine mycobacteria yambotaurwa ndeye 98%, uye kuenzanisa genomics basa rakaratidza kuti M. canettii uye mamwe ose eMTBC achangobva kuparadzaniswa kubva kune tateguru.7 Tichifunga nezvepfungwa iyi, vamwe vanyori vanogona kudana MTBC nhengo yeM.
MTBC inotsanangurwa zvakarongeka seyakaomesesa clonal yakaoma, uye chimiro chayo chehuwandu chinodzorwa zvakajeka nekuderedzwa kwakasiyana, mabhodhoro, kusarudza scanning, uye genetic drift9,10. Tichifunga yakaoma yakaoma clonal shanduko, senge isipo polymorphisms haigone kudzoreredzwa nekubatanidzwazve. Zvichienderana nechikonzero ichi, zviitiko zvakatevedzana zvekudzimwa kwegenomic yedunhu rakasiyana (RD) uye TbD1 (Mtb chaiyo yekudzima 1 dunhu) zvakatsanangurwa semamorekuru emakaki eMTBC evolution2,5,11. Comparative genomics uye yese genome sequencing (WGS) basa rinotsigira kupatsanurwa kwenhengo dzakagadziriswa nevanhu kuita mitsara mipfumbamwe (Mycobacterium tuberculosis L1 kusvika L4, L7, uye L8; uye Mycobacterium africanum L5, L6, uye L9), mutsara L2 kusvika L4 yakagovaniswa bvisa TbD1 region2,1. Pamusoro pezvo, nhengo dzakachinjirwa mhuka dzinonzi dzigovane tateguru mumwe chete, izvo zvinotsanangurwa neclade-chaiyo kubviswa muRD7, RD8, RD9 uye RD102, 5, uye 14.
Horizontal gene transfer (HGT) uye zviitiko zvekugadzirisa zvinoonekwa sezvisingawanzo uye zvinoitika mumadzitateguru eMTBC, pane nhoroondo yakasiyana yenhengo yose yeMTBC15,16,17. Mishumo miviri yepakutanga yakaitwa naHughes nevabatsiri (2002) uye Gutacker nevabatsiri (2006) vakaratidza kuti zviitiko zvekudzokorora zvinogona kubatsira kuumba mapolymorphisms anoratidza loci chaiyo muM. tuberculosis strains18,19. Zvikonzero zvekushayikwa kuri pachena kwekubatanidzazve muMTBC ndezvi: (1) mechanical process uye kurasikirwa kwekugona kweHGT; (2) kuwanda kwezviitiko zveHGT; (3) hapana mukana wekudzokorora zviitiko muMTBC niche14,17. Nguva pfupi yadarika, zvimwe zvidzidzo zvewse-genome sequencing (WGS) zvakashandiswa kuMTBC strain 20 uye Mycobacterium bovis 21 zvakapa humbowo hwekubatanidzwazve, yekutanga kuratidza kuti MTBC strains anowanzo chinjana madiki eDNA zvidimbu, asi nekuda kwekuganhurwa kwekutevedzana kweiyo nucleotide, zviitiko izvi zvakadaro hazvisati zvaonekwa.
Mycobacterium bovis ndiyo inonyanya kudzoserwa nhengo yeMTBC kubva kumombe (kunyanya mombe), kunyangwe ichigonawo kuparadzaniswa nemhuka dzesango dzakasununguka uye dzakakomberedzwa4,22,23,24. M. bovis yakashanduka kuita shanu huru clonal complexes [European 1 (Eu1), European 2 (Eu2), European 3 (Eu3), African 1 (Af1) uye Africa 2 (Af2)], maererano ne spoligotyping profile, chaiyo deletions Uye single nucleotide polymorphisms (SNPs) 25, 7, 292 mu genes chaiyo. Aya ma clonal complexes anoratidza chimiro chakasiyana chehuwandu hweMycobacterium bovis uye kushamwaridzana kwayo nenzvimbo dzenzvimbo. Uye zvakare, iro richangoburwa WGS basa rakaitwa neZimpel nevabatsiri (2020) rakagadzira phylogeny yakavakirwa paSNP yeMycobacterium bovis, ine anopfuura 1,900 genomes, zvichiratidza kuti kune anokwana mana mitsara akasiyana (anonzi Lb1 kusvika Lb1 kusvika Lb4), iwo haana kutsanangurirwa zvizere neiyo geographic yakaoma. Vanyori ava vakaita ongororo yakasiyana yephylogeny uye molecular dating, asi havana kudzidza recombination30.
Basa rakapfuura richishandisa nzira dzakasiyana-siyana dzema molecular, dzakadai se spoligotyping, MIRU-VNTR (mycobacterial interspersed repeat unit-variable tandem repeat number), uye ichangoburwa SNP kutaipa yakaratidza imwe nhanho yekusiyana kwemajini pakati peM. bovis strains 31,32,33, 34,35. Kusiyanisa kwekusiyana kwemajini kwakave chinhu chakakosha mukudzidza kwechirwere chechirwere, iyo inobatsira pakunzwisisa kwakadzama kwepathogenesis, virulence uye kutapurirana kwechirwere. Kubuda kweiyo nzira yeWGS kunopa mukana wekuburitsa evolutionary kutyaira zvinhu zvakaiswa neMycobacterium bovis genome mukugadzirisa uye kushingirira kune akasiyana mauto uye epidemiological scenarios.
Mubasa iri, tinoshandisa kuenzanisa genomic ongororo pane dzakasiyana siyana dzeMycoplasma bovis datasets (n=70), kusanganisira yekuzviparadzanisa kubva kune akasiyana clonal complexes, kuti tiwane ruzivo rwekushanduka kweMycoplasma bovis, kunyanya kugadzirisa hukama hwephylogenetic Uye zviitiko zvekudzokorora. Sekuwedzera kune iyi ongororo, sub-data seti yeM. bovis inotsaura (n = 42) yakawanikwa kubva kune inonyatso zivikanwa nzvimbo yakawanda yetibhii muPortugal 31,36 yakazoongororwa zvakare kuti infer kusazivikanwa Chiyero chiri pakati pechiyero chehukama chepfungwa (dN) kune synonymous (dS) nucleotide inotsiva, zvinyorwa zvinotsiva, zvinyorwa zvinotsiva, pamwe nezvinyorwa zvinotsiva. 37,38 yakawanikwa neMTBC madzitateguru kuburikidza neHGT, uye encode 3R (DNA kugadzirisa, replication, uye recombination) system gene components 39. Sarudza majini akawanikwa kuburikidza neHGT nokuti anogona kumiririra mapolymorphisms ekare, saka zvinotarisirwa kuti angave ane chikamu chepamusoro chekuchinja kwakafanana. Majini akabatanidzwa muhurongwa hwe 3R akasarudzwa nokuti basa rekare pamusoro peM. tuberculosis strains rakaratidza kusarudzwa kwakawanda kusina kunaka / kucheneswa kunoshanda pamajini aya, uye vanogona kuita basa rinokosha mukushanduka-shanduka 39. Chimwe chinangwa chebasa iri ndechekuita kuti kuvepo kwekugadzirisazve zviitiko. Nechikonzero ichi, tichifunga kuti dataset yedu kubva kuPortugal inongori nema genomes eEuropean clone complex 2 uye strains asina kupa clone complex, takasarudza kusanganisa inowanikwa pachena genome data kuti tiwane mumiriri wezvose clone complexes, uye Kuvandudza kusimba uye kufara kwemigumisiro.
42 ichangobva kuteedzerwa Mycoplasma bovis genomes kubva kuPortuguese endemic multi-host tuberculosis scene (details pazasi), yaimbozivikanwa kubva pa epidemiological maonero36, ndiwo musimboti webasa iri. Tichifunga kuti data rakaiswa kubva kuPortugal rinongori nevamiriri veEuropean 2 clone complexes uye strains pasina akatarwa macomplexes, inowanikwa pachena yakazara-genome sequencing data yakawedzerwa kuwedzera iyo data set inosanganisira vese vamiriri veM. bovis clone complexes. Naizvozvo, matatu akazara-genome sequencing data zvinyorwa zvakashandiswa mubasa iri: yakakwana / dhizaini genome musangano, kusvika ku10 scaffolds yakachengetwa muNCBI (National Center yeBiotechnology Information) (n = 15 inotsaura); yakachengetwa muSRA ( The Illumina fastq file of the sequence read archive) inomiririra kusiyana kwakaoma kweM. bovis clones (n = 12 isolates) 30; uye 42 ichangobva kutevedzana genomes kubva kuPortugal. Mycobacterium bovis BCG (Bacille Calmette-Guerin) yakabviswa mukutsvaga kweNCBI. M. bovis AF2122/97 inowanzo shandiswa sereferensi genome inofanira kuiswa mudhatabheti. Nekuda kwekusavapo kweruzhinji kutevedzana kwegenome yese inomiririrwa neAfrican 1 cloning complex, uye nenhamba shoma yema genomes kubva kune anomiririra strains eAf2 neEu1, iyo yekutanga sequencing data yakapihwa neSRA yakashandiswa mune idzi nyaya. Basa raZimpel nevaanoshanda navo (2020) rakabatsira kuona genome kubva kune yambotaurwa cloning complex uye yakabatsira kusarudza Mycobacterium bovis kuti ibatanidzwe mu data set. Kune Eu3, mhando imwe chete yegenome inotsanangurwa (Branger et al., 2020), saka genome yatinosanganisira mumiriri akaparadzana weEu3 yakaoma.
Pasi rose, iyi data seti inosanganisira makumi manomwe emombe M. bovis akaparadzaniswa kubva ku8 hombe marudzi, akagoverwa munyika 12 kubva 1985 kusvika 2016. 36 marudzi anosarudzwa seEu2, 7 marudzi ari Eu1, 1 marudzi ari Eu3, 3 marudzi ari Af1, 4 marudzi ari Af2 uye 19 ari muswe ari pazasi akaomerwa. Ruzivo rwakadzama (kusanganisira nhamba yekutora) yeMycobacterium bovis yakashandiswa muchidzidzo ichi inoratidzwa muTebhura 1 neTafura 1 yekuwedzera.
42 ichangobva kutevedzana yakazara genomes yeMycobacterium bovis kubva kuPortugal's mhuka tuberculosis hotspots uye akagoverwa kwemakore anopfuura 12 ndiwo musimboti wechidzidzo ichi, sezvo zvingangoita mhuka dzesango-zvipfuyo zvirwere zvirongwa zvakagara zvichiongororwa 31,36 (Supplementary Fig. 1). Zvinoenderana nemaitiro akatevera, mhando idzi dzakaparadzaniswa nemombe (n = 14), deer dzvuku (n = 16) uye nguruve yemusango (n = 12) kubva 2003 kusvika 2015: kuunganidza uye kubata mhuka zvinoenderana neyakakurudzirwa protocol nhungamiro Matishu samples ari muOIE Terrestrial Animal Handbook uye akaiswa inoculated yakasimba yemvura yeStonewebrink uye Lruvabrinkstein inoculated paStonewepy yemvura yakasimba. pakati. Tsika dzinoiswa pa37 °C uye kukura kunotariswa kamwe chete pasvondo kweanokwana mavhiki gumi nemaviri. Makoroni anochengeterwa zvakananga mugavi reglycerol pa -80ºC. MuMycobacterium selective medium (Middlebrook 7H9, BD Diagnostics), masampula epakutanga akachengetwa akapfuudzwa nemuchikamu chimwe chete mu vitro mu vitro kuti vawane DNA yechirongwa cheWGS. Nekuda kweizvi, iyo yakaomeswa tsika stock solution yakapfumiswa ne5% sodium pyruvate uye 10% ADS (50 g albumin, 20 g glucose, 8.5 g sodium chloride mu1 L mvura) paMiddlebrook 7H9 pa37°C Retrain. Mushure memavhiki e4 ekukura, svikiro yakagadziridzwa uye tsika yaigara ichiongororwa kusvikira kukura kwaonekwa. Masero acho akakohwewa ne centrifugation, iyo pellet yakamiswazve mu500 µL phosphate buffered saline (PBS), ichipisa pa99 ° C kwemaminetsi makumi matatu, centrifuged, uye supernatant yakachengetwa pa -20 ° C kusvika WGS. Ese maitiro anoitwa muchikamu chechitatu biosafety zvivakwa.
Iyo WGS yakapetwa-yekupedzisira genome raibhurari inogadzirirwa ichishandisa yakasarudzika index yega yega sampuli yeDNA, uye inoshandisa Illumina MiSeq (2 × 250 pb) (40 samples) uye HiSeq (2 × 150 pb) (mbiri isolates) tekinoroji (Eurofins Genomics, Germany) yekutevedzana. Zvinoenderana nemirairo yemugadziri, shandisa Illumina Genome Analyzer ine kaviri-inopera module yekunamatira kuteedzera iyo genomic DNA, uye shandisa Nextera XT DNA Library Prep Kit kubva kuIllumina kuvaka raibhurari.
Tichifunga nezve data yakatorwa kubva kuSRA (n = 12), kuzivikanwa kweiyo clone yakaoma inogona kushandiswa semetadata yeinowirirana chinyorwa 30, 41, 43. Paunenge uchifunga nezve genome yakakwana, kunze kweMycobacterium bovis AF2122/97 uye Mycobacterium bovis 3601, iyo Eunal1 nhengo dzeEunal 5 dzinozivikanwa uye Eunal1 yakaoma. 29, zvichiteerana, yakafanana neiyo genome yakazara yeMycobacterium tuberculosis H37Rv (NCBI yekuwedzerwa nhamba NC_000962.3). Genome alignment inoitwa uchishandisa MAFFT (yakawanda alignment program yeamino acid kana nucleotide sequence, version 7.458) uye parameter -addfragments48. Zvadaro, tsvaga kusavapo kweakasiyana clonal complexes uye / kana kuvapo kweSNP maitiro.
Iyo ichangobva kuteedzerwa Mycobacterium bovis (n = 42) uye yepakutanga kuverenga kweakaunganidzwa genome dhizaini (n = 3) batanidza iyo yakaoma nereferensi genome Mycobacterium tuberculosis H37Rv kuburikidza nepombi yevSNP uye kuvapo kwekudzima uye / kana SNP maficha emhando dzakasiyana Kutsvaga kwakaitwa.
Unganidza ruzivo kubva mukushaikwa kwezvinhu uye / kana kuvapo / kusavapo kweSNP uye spoligotyping profiles kuti upe genomic data kune inoenderana clonal yakaoma. Pamagungano mana ekunyorwa, chimiro che spoligotyping hachigone kutaurwa, saka chinosanganisirwa muboka re "hapana kuoma".
Iyo bioinformatics workflow inoteverwa nebasa iri inotanga kubva ku de novo gungano uye mepu kune referenzi zano, nechinangwa chekuongorora zviitiko zvekubatanidza uye chaiyo genome polymorphisms. Mufananidzo 1 unopa kuyerera kwematanho anoteverwa. Kuongorora kudzokororwa, ese genomes anoshandiswa kuwedzera kusimba kwezviratidziro uye zvine hukama zviratidzo.
Kuti tideredze zvikanganiso mukugadzirwa kwegenome consensus sequences, takatanga tawana de novo assembly, tichibva tawana core multiple alignments. Iyo Unicycler pombi iripo pa https://github.com/rrwick/Unicycler49 uye inoshandiswa kuita de novo gungano re54 sequenced genomes (42 ichangobva kutevedzana uye gumi nemaviri fastq mafaera akadzoserwa kubva kuSRA). Muchidimbu, tisati taungana kubva mukutanga, verenga ongororo yemhando yakaitwa muFastQC vhezheni 0.11.7 (https://github.com/s-andrews/FastQC), uye Trimmomatic vhezheni 0.36 (sarudzo "kucheka Adapter uye kumwe kuteedzana-kwakanangana nemwenje kubva pakuverenga" uye "Cheka mabhesi maviri, kana akadzikira mabhesi kubva kumabhesi maviri kubva kumagumo emhando." kushandiswa) (http://www.usadellab.org/cms/?page= trimmomatic) 50. Zvadaro, SPAdes optimiser49 yakashandiswa kuungana kwegenome, uye Pilon version 1.1851 yakashandiswa kugadzirisa post-assembly. Iyo inochengetedza bhiriji modhi yakasarudzwa kudzivirira kusangana kwakashata, uye saizi ye-k-mer yakatsvaga uye yakasarudzwa pakati pe20% ne95% yehurefu hwekuverenga. Tevera nhungamiro dzeSPAdes uye funga nezvehukuru hwekuverenga, bvisa contigs madiki pane 300 bp, uye gadzira 20 kuverenga zvakadzama coverage cutoff ye52. Muchirongwa chegungano re de novo, matunhu egenomic akadai seanodzokorora zvakanyanya proline-glutamate (PE) uye proline-proline glutamate (PPE) paralogs haana kubviswa.
Hunhu hwegungano re de novo hunoongororwa kuburikidza nepombi yeQUAST (http://quast.sourceforge.net/quast.html), inofambisa kuvandudzwa kweiyo contig uye M. bovis AF2122/97 referensi genome (NCBI yekuwedzera nhamba LT708304.1) Mepu (ona 1 yezvemhando yeTable parameter).
Nerubatsiro rwepombi yevSNP (https://github.com/USDA-VS/vSNP), faira reFASTQ reM. bovis ichangobva kutevedzana kubva kuIllumina sequencing inofananidzwa neM. bovis AF2122/97 reference genome (LT708304.1)). Zvinoenderana neakanakisa maitiro ekurudziro eGenome Analysis Toolkit (GATK) 53, 54, 55 shandisa yakajairwa mafirita paramita kana akasiyana misa zvibodzwa zvekudzokorora. Mhedzisiro yacho inosefa pachishandiswa yakaderera SAMtools mass score ye150 uye AC = 2. Uyezve shandisa Kraken (http://ccb.jhu.edu/software/kraken/) kutarisa kuverenga kuti kusasvibiswa. Iyo vSNP pombi inoshandiswa kumepu kuteedzera mazano mubasa redu inoongorora akatevedzana akatsanangurwa SNPs uye tarisiro, uye zvakare isingabatanidzi mamiriro ehutachiona akasanganiswa. Iyo yekuverenga genome coverage iri nani pane 99% (Supplementary Tafura 1).
Kuti udzivise zvikanganiso zvemepu uye SNPs isiriyo, sefa mutsauko muzviitiko zvinotevera: (1) inotsigirwa neasingasviki makumi maviri kuverenga, (2) inowanikwa ine frequency isingasviki 0.9, (3) iri mune kanenge maStrains, asi pane zvishoma pane mamwe mapeji mune imwe dhizaini. Iyo Integrated genomics viewer (IGV) version 2.4.19 (http://software.broadinstitute.org/software/igv/)56 yakashandiswa kuona SNPs nezvinzvimbo zvine matambudziko ekugadzira mepu kana kurongeka. Sezvo proline-glutamate (PE) uye proline-proline glutamate (PPE) majini akanyanya kudhindwa uye ari chikamu chemhuri yakawanda-gene, zviri nyore kusanzwisiswa neIllumina sequencing uye mismapping, saka vanosarudzwa The mycobacterial bioinformatics workflow yakabviswa nhengo dzechirwere chetachiona chetachiona pakushandisa nzira yekutevedza mapping kuSNP. Naizvozvo, isu takasefa PE/PPE majini uye indels kubva mukuongororwa.
Zvinoenderana neBovilist (http://genolist.pasteur.fr/BoviList/), ese maSNP akakamurwa kuita zvikamu zvinoshanda. Iyo SnpEff pombi (https://pcingola.github.io/SnpEff/) inoshandiswa kuratidza mhedzisiro yeSNP (shanduko dzinofanana kana dzisiri-zita). Yakagadzira dhatabhesi nyowani yeMycobacterium bovis AF2122/97 genome (LT708304.1).
Iyo core genome multiple alignment yakaitwa pachishandiswa Parsnp v1.2, iripo pa https://github.com/marbl/parsnp57, uchishandisa 69 yakakwana genomes/draft assemblies (ine sarudzo -c) uye M. bovis AF2122/97 (LT708304.1) inoshandiswa sereferensi. Mana epakati akawanda magadzirirwo akaitwa: chete nhengo dzeEu2 cloning complex (n = 37), kusanganisira nhengo dzese dzeEuropean cloning complex (n = 44), kusanganisira nzvimbo yekusangana yeEuropean and African cloning complex (n = 51), uye inosanganisira ese Mycobacterium bovis muchidzidzo ichi (n = 70).
Iko kurongeka kwepakati kunogadzirwa neParsnp kunoshandiswa kufungidzira iyo yakanyanya mukana (ML) phylogenetic muti uchishandisa CIPRES Science Gateway v3.3 (http://www.phylo.org/)58 uchishandisa RAxML, uye kuita 1000 inotungamirwa replications.
Zvitatu zvakasiyana-siyana zvealgorithms uye maturusi ebioinformatics anoshandiswa kutarisa kuvepo kwezviitiko zvekudzokorora zvakafanana: SplitsTree4 software, Gubbins (mutsara usina kurerekera kuburikidza nekubatanidzwazve mu nucleotide sequences) pombi, uye RDP4 (recombination yekuongorora chirongwa, shanduro beta 4.101) software.
Nzira yekuparara kwekupatsanura inoshandiswa muSplitsTree4 v4.15.1 (http://www.splitstree.org/)59 inoshandiswa kuverenga rootless phylogenetic network, uchishandisa Phi test yekuongorora nhamba, uye kukosha kwepakati p = 0.05. Iyo yepakati-yakawanda-alignment ongororo yeParsnp inoshandiswa sekuisa, uye kupatsanurwa kwekuparara seyetiweki chiyero kunoitika.
Gubbins pombi v2.3.1 (https://github.com/sanger-pathogens/gubbins60 inomhanya neyakagadzika paramita seimwe nzira yekuongorora maitiro ekubatanidzazve paMycobacterium bovis. Iyo algorithm inoshandiswa mupombi inovaka patsva mutsara wakakodzera weiyo clone Iyo yakazara genome/dhizaini gungano reyedu data seti (AF215 genome 2bovid) LT708304.1) vari pamwe chete; uye tarisa nzvimbo yeSNP pabazi rega rega remuti kuti uone iyo SNP cluster inomiririra chiitiko chekubatanidza zvakare, izvo zvinoreva kuti iyo SNPs inoitika pabazi inofanirwa kugoverwa zvakaenzana mafaera eParRA anoshandiswa zvakanyanya kubva pamuti weParRA.
Chekupedzisira, kuitira kusimbisa chiitiko chekuronga patsva chakakurudzirwa nepombi yeGubbins, iwo matanhatu algorithms akaiswa muRDP467 (RDP61, GENECONV62, Bootscan63, Maxchi64, Chimaera65 uye SiScan66) anoiswa kuParsnp's core multiple alignment pasi pezvirongwa zvakasarudzika. Isu takaona kuti anokwana matatu emaalgorithms akaiswa muRDP4 anofanirwa kugara achiratidza chiratidzo chakakosha chekutarisa chiitiko chega chega chekubatanidza.
Tichifunga kuti ese maGubbins neRDP software anotarisa masaini ekubatanidza nekutarisa epakati akawanda machinjiro pahwindo rinosvika ku500 bp, uye kusimbisa kuti kuisirwa kwePE/PPE genes panguva yemusangano we de novo hakuzokanganisa masaini ekubatanidza akawanikwa, kumwe kuongorora kunoitwa nehomolinearity Tarisa nzvimbo iri padyo neiyo gene yekuzivisa chiitiko. Mepu ye synlinear ichishandisa genome yakazara yakavakwa pachishandiswa MAUVE-multi-genome alignment (http://darlinglab.org/mauve/mauve.html) kusabatanidza kutamiswa kwegenome kana kuchinjika. Pamusoro pezvo, iyo genome yese yakashandiswa kuita ongororo yehomolinearity pane amino acid sequence kuburikidza neSyntTax web server (https://archaea.i2bc.paris-saclay.fr/SyntTax/).
Kuongorora kwakadzama kweiyo genome data set yakawanikwa kubva kuPortugal multi-host tuberculosis system ndeyekutarisa polymorphism yemajini anotaurwa mumabhuku. Majini aya i37,38 uye gene encoding 3R yakawanikwa neMTBC madzitateguru kuburikidza neHGT (DNA repair, replication and recombination) system components 39. Shandisa ClustalX v2.1 (http://www.clustal.org/clustal2/) uye shandisa DnaSP v6.12.03 (http://u/edub divers divers and dub . nucleotide diversity (π) uye Tajima's D isina kwayakarerekera bvunzo parameter kupinza.
Iyo yakanyanya mukana (ML) phylogenetic muti wakavakirwa pa69 Mycoplasma bovis inotsaura uye rengedzo genomes yakawanikwa (Mufananidzo 2A). Kuenzaniswa nemiti imwe chete-yakagadzirwa nemiti kana miti yakawanda-yakavakirwa, iyi sarudzo inobvumira kuberekwa kwemiti ine simba yakawanda isingatore kusiyana kwegenome yose uye naizvozvo inoratidzira kukwanisa kuderera kusarura pakati pemarudzi 68,69. Iyo topological chimiro chemuti weML inowanzoenderana neyakaomesesa kupatsanurwa kwema clones. Iyo genome yeEu2 yakaunganidzwa mubazi, uye iyo genome yeAf1 inobatanidzwawo pamwechete (Mufananidzo 2A). Mhedzisiro yacho zvakare inopindirana nehukama hunozivikanwa hwekushanduka-shanduka kweMycobacterium bovis, ndiko kuti, pane musiyano mukuru pakati penhengo yeEu1 neboka rinosanganisira mamwe ese maclonal complexes uye genomes, asi iyo clonal yakaoma 30 haina kutaurwa. Kusawirirana kuduku pakati peklonal complex uye hukama hunoonekwa pamuti we phylogenetic hunogona kutsanangurwa nechokwadi chokuti clonal complex inotsanangurwa zvichienderana nenharaunda dzakananga dzegenomic, nepo muti we phylogenetic unobva pakugadzirisa kwakawanda kweiyo core genomes inomiririra genome yose.
Iyo yakanyanya mukana we phylogenetic muti (GTR) inovakwa zvichienderana neiyo core genome alignment yeMycobacterium bovis genome pamberi (A) uye mushure (B) kubviswa kwenzvimbo yekubatanidza. Mavara ebazi anomiririra Mycobacterium bovis clone complex: Europe 1 ipepuru, Europe 2 yakatsvuka, Europe 3 iblue, Africa 1 ndeyeorenji, uye Africa 2 yakasvibira. Muti wakadzika midzi uye unokweverwa kuchiyero, uye urefu hwebazi hunoyerwa sechinotsiva nzvimbo yega yega.
Iyo Mycobacterium tuberculosis complex inotsanangurwa seyakashanduka-shanduka, uye humbowo hwakawanda hwakaunganidzwa nekufamba kwemakore hunotsigira pfungwa yekuti inoenderera mberi HGT uye zviitiko zvekusanganazve hazvizoitike padanho rinoonekwa reMTBC15,17,18.
Basa rakapfuura rakaratidza kuti panogona kunge paine kushomeka kudzokororwa pakati peMTBC strain20,21, nepo vamwe vakatadza kuona zviitiko zvinoyerwa zvekudzokorora70,71. Kurukurazve nyaya iyi nekutarisa kuMycobacterium bovis, iyo yakasiyana nebasa rekare raingoona Mycobacterium tuberculosis 70,71; kana kufunga MTBC yose, pasina M. bovis anomiririra makumi maviri; kana kungofunga zvikamu zvemombe zvinorambidzwa. Iyo mycobacteria dhatabheti, mubasa iri, kune huwandu hwemakumi manomwe emhando, inomiririra ese clonal complexes, anoshandiswa kuvharidzira kubatanidzwazve. Iyo data seti inoyerwa zvichienderana nematanho mana akawedzera: (1) nhengo dzeEu2, (2) nhengo dzese dzeEuropean clone dzakaoma (kureva Europe), (3) European and African clone complex (Eu + Af) uye (4) iyo yose data Collections (kusanganisira genomes iyo isingabatanidzwe mune chero cloning complexes yakatsanangurwa kare).
Kuti uenderere mberi nekudzidza iyi pfungwa, kupatsanurwa-kuparara network yakaitwa kuti iongorore kusavapo kwezviitiko zvekugadzirisa zvakare pakati pema genomes, nokuti nzira iyi inogona kuona hukama hwemadzitateguru pakati pevanhu uye kuratidza zviratidzo zvephylogenetic zvinopesana. Ese mana eseti e data mukuongorora akasimbisa kuvepo kwezvishwe mumambure (kureva, nzvimbo dzisingashanduke kuita muti mumwe), asi iyo Phi bvunzo haina tsigiro yenhamba (Eu2, p = 0.0956; Europe, p = 0.1637; Eu + Af p = 0.2774; iyo yese data set pganiza = 0.2), iyo yepasirese data set pganiza = 0.2 inopa humbowo humbowo hwe5. 3A-D).
MuEurope 2 genomes (n = 37) (A), European genomes (n = 44) (B), European uye African genomes (n = 51) (C) uye yose data set (n = 70) (D).
Mushure mekuongorora uku, uye tichifunga nezve cyclic inocherechedzwa mumanetiweki ese, algorithm yekuvaka patsva yakaitwa muGubbins pombi yakashandiswa kuvaka patsva mutsara weclonal uye kuwedzera fungidziro yemhedzisiro yekubatanidzwa patsva paM. bovis genome. Infer iyo yakawedzera nhamba yezviitiko zvekubatanidzazve, mazhinji acho akaitika mumatavi ekupedzisira (kureva, mune imwechete genome) (Tafura 2). Izvi zviratidzo zvinoratidza kuwirirana kweseti yedata uye inoratidza kuti kuwanda kwezviitiko zvekudzokorora ndeye 200 kusvika ku300 nguva yekuchinja. Pane imwe nguva iyo rho / theta parameter inomiririra chiyero chekuenzanisa uye kushanduka kwenheyo pabazi inoratidzika kuva pakati pe0.0037 ne0.0056 (Table 3). Munguva ichangopfuura, basa rakadhindwa re38 M. bovis strain rakaratidza kukosha kwerho/theta yakakwirira (rho/theta = 0.1) kupfuura yakawanikwa mudhatabheti rino, asi basa raPatané nevamwe vaaishanda navo vakashandisa referensi-based assembly kuti vape recombination parameters , Tsanangudzo yemaitiro, nekuda kwemaitiro egungano, yakabatanidzwa nekuwanda kwezviitiko zvebazi.
Zvadaro, r/m parameter inomiririra chiyero chekusiyana-siyana chekubatanidza uye kuchinja kwekutanga, uye kukosha kwayo pakati pe 0.025 ne0.037, zvichiratidza kuti kana zvichienzaniswa nekuchinja, kubatanidza kune kuderera kwehuwandu hwehuwandu hwehuwandu hweM. bovis (Tafura 3) . Pakuenzanisa zvakanyanya, imwe nzira yakafanana yakashandiswa kufungidzira r/m parameter yeMTBC dataset inoumbwa ne23 genomes, ichiratidza avhareji kukosha kwe0.48620, nepo Patané nevamwe vaaishanda navo '38 M. bovis dataset, yakaratidza kukosha kweavhareji Is 0.98. Muchidzidzo chekutanga, maviri chete e23 genomes akabatanidzwa mubasa reM. bovis (M. bovis BCG uye chirevo chekutsvaga), saka kukosha kwakawanikwa kunogona kunge kwakashata nekuda kwekuwedzera kweM. tuberculosis genome. Mumushumo wechipiri, iyo yakaongororwa Mycobacterium bovis huwandu hwakanyanya kuwanikwa kubva kuUnited States uye zvipfuwo. Kusiyana neizvi, mune yedu data seti, nzvimbo dzakawanda dzenzvimbo nemhando dzemhando dzinomiririrwa, uye genomes akaiswa muzvikamu zvakasiyana zveclonal zvine maitiro akasiyana ehuwandu hwemajini anoshandiswawo, nekudaro kuwana kwakadzama uye kwakakura ruzivo rweVanhu. Musiyano r / m avhareji kukosha kwakawanikwa nedata yedu yakatarwa inopindirana nepfungwa yekuti dhigirii recombination inosiyana zvakanyanya pakati pemitsara yakagoverwa kune imwechete taxonomic mhando, saka mhedzisiro idzi dzinoratidza kuti iyo M. bovis clone complex inogona kuratidza recombination misiyano Inowanikwawo sezvakataurwa naDidelot & Maiden72. Zvakadaro, kuwedzera zvakanyanya data iyi yakaiswa nekubatanidza nhamba yakakura yeM. bovis genomes ichabvumira imwe kujekeswa kweiyi pfungwa. Ose ari maviri r/m uye rho/theta paramita anoratidza kusiyana pakati pematavi, uye mhedzisiro iyi inoenderana nemishumo kune mamwe marudzi ebhakitiriya72,73.
Chekupedzisira, kuitira kusimbisa zviitiko zvekuronga patsva zvakaonekwa nepombi yeGubbins, matanhatu akasiyana algorithms akashandiswa muRDP4 software kuyedza yakazvimiririra yakasiyana-siyana maenzaniso akawanda. Pasi rose, isingasviki hafu yezviitiko zvakaonekwa naGubbins zvakasimbiswa neRDP4 (Tables 4 uye 5). Tichifunga nezvese data data, zviitiko zvitatu zvekubatanidza zvakasimbiswa, zviviri zvinosanganisira node dzomukati uye imwe inosanganisira genome imwe chete mubazi rekupedzisira, iyo clonal complexes isingagoni kugoverwa (Tables 4 uye 5). Kuzivikanwa kwezviitiko mumapazi ekupedzisira kunogona kuratidza kuti kubatanidzwazve kuchiri kuenderera mberi mune zvemazuva ano M. bovis strains kana kuti mhedzisiro yakaiswa panzvimbo70. Munharaunda iyi yekufungidzira yekubatanidza, inenge 20% yezvinzvimbo zvine nucleotides isina kutsanangurwa (N), nokudaro inokanganisa chiratidzo chekubatanidza (Supplementary Figure 2). Pamusoro pezvo, iyi dunhu inokanganisa rrs gene, kukodha iyo 16S ribosomal RNA inotarisirwa kuchengetedzwa zvakanyanya, saka iyi putative recombination chiratidzo inogona kunge iri mhedzisiro yekutevedzana kukanganisa kana kusarongeka. Zvadaro genome yose kurongeka pakati Mb0003 uye Mycobacterium bovis AF2122/97 akaitwa, uye kuvapo undefined nucleotides uye SNPs akasimbiswa, saka zvinobvira matambudziko chokuita kurongeka kwakaipa akanga asiri nokuda mashoko zvipenyu kushandiswa mubasa iri Akaonekwa pashure kudzidza chirongwa.
Hapana mapeji kana nucleotide isina kutsanangurwa yakawanikwa munzvimbo dzekubatanidza dzemukati node (Mifananidzo 4 uye 5). Nezvezviitiko izvi, imwe ine chete Eu2 genome uye inokanganisa pks12 gene, iyo inoisa iyo inogoneka polyketide synthase; nepo imwe yacho yakanyoreswa muEu1 genome uye inokanganisa narX gene iyo inokodha inogoneka nitrate reductase (Tafura 4). Kazhinji, kuongororwa kwekugadzirisa kunoratidza kuti kune nhamba shoma yezvimedu zvekubatanidza nerutsigiro rwenhamba, uye zviratidzo zvinotaridzirwa zvinoratidza kuti kusanganiswa kune simba rakaderera pamutsara weM. bovis. Chiratidzo chekubatanidza chinotarisirwa kuve chakaderera, asi zvakakosha kusiyanisa chiratidzo chechokwadi chekushanduka kubva kune ruzha rwekumashure, rinova basa rakaoma. Kuti uderedze chiratidzo cheruzha chinounzwa nereferensi-based kusangana uye kusawirirana matambudziko 70, 71, mamwe ese kunze kweiyo genome yakazara yakaunganidzwa kubva kutanga, uye kunaka kwegungano kwakatariswa uye kuvimbiswa neQUAST pombi yekuongorora (Yekuwedzera Tafura 1). Pamusoro pezvo, nhevedzano yeongororo yekuwedzera yakaitwa kuti ipe kusimba uye kurongeka kweongororo yese. Naizvozvo, kutevedzana kwemhando ye narX uye pks12 majini yakaongororwa nekuverenga mepu ichipesana neMycobacterium bovis AF2122/97. Iyo yakakurudzirwa nzvimbo yeSNP munharaunda yekubatanidza yakasimbiswa nekushandisa maitiro akataurwa muchikamu chenzira (inenge 20 kuverenga uye 0.9 shanduko frequency). Iyo polymorphism yenarX gene yakasimbiswa zvizere mumajenomes maviri (Mb1792361 uye Mb7240415; 2.3%) uye genomes eiyo pks12 genome: Mb0891, Mb1711, Mb1789, Mb1870, Mb17062 uye M17074. Zvisinei, kune genome Mb2043, zvitanhatu zvezvisere zvinzvimbo hazvikwanisi kuverenga kudzika chiyero nokuti SNP inotsigirwa nehuwandu hwehuwandu hwe17, iyo iri pasi peiyo yakasimbiswa cutoff kukosha kwe 20. Nokudaro, kusanganiswa kwemajenome matanhatu (8.6%) panzvimbo ino yejenome inogona kusimbiswa (Figure 4 uye 5).
Iyo yakadzama yekuona kweiyo recombination dunhu kurongeka kweMycobacterium bovis dataset inokanganisa iyo narX gene inokodha inogoneka nitrate reductase. Hapana mapundu kana nucleotides isina kutsanangurwa yakawanikwa munharaunda yekubatanidza ye node dzomukati. Ichi chiitiko chakanyoreswa muEu1 genome. Hunhu hwekutevedzana hwenarX gene hwakaongororwa nekuronga kuverenga kweMycobacterium bovis AF2122/97. Simbisa iyo yakakurudzirwa SNP nzvimbo munzvimbo yekubatanidza nekushandisa iyo nzira yakataurwa muchikamu chenzira (inenge makumi maviri kuverenga uye 0.9 shanduko frequency). Iyo polymorphism yenarX gene yakasimbiswa zvizere mumajenomes eMb1792361 uye Mb7240415 (2.3%).
Yakadzama yekuona kweiyo recombination dunhu kurongeka kweMycoplasma bovis dataset inobata pks12 gene. Hapana mapundu kana nucleotides isina kutsanangurwa yakawanikwa munharaunda yekubatanidza ye node dzomukati. Nezve chiitiko chinokanganisa pks12 gene encoding inogoneka polyketide synthase, inongova neEu2 genome. Hunhu hwekutevedzana kwepks12 hwakaongororwa nekuverenga mepu yeMycobacterium bovis AF2122/97. Simbisa iyo yakakurudzirwa SNP nzvimbo munzvimbo yekubatanidza nekushandisa iyo nzira yakataurwa muchikamu chenzira (inenge makumi maviri kuverenga uye 0.9 shanduko frequency). Mapolymorphisms ejenomes Mb0891, Mb1711, Mb1789, Mb1870, Mb1758, Mb2043, uye Mb1960 akasimbiswa zvizere.
Majini ePE nePPE ane matunhu anodzokororwa ari nyore kuverengerwa zvisirizvo neIllumina kutevedzana uye kukanganisa, saka anowanzo kudzimwa kubva kubioinformatics workflow yeM. tuberculosis nhengo chete kana uchishandisa mepu-ku-kutevedzana zano. Iko kufungidzira kwezviitiko zvekudzokorora zvakashandiswa mubasa iri zvakavakirwa pamusangano we de novo pasina kusefa PE/PPE. Isu tinotenda kuti nekushandisa nzira nhatu dzakasiyana dzekuwedzera uye algorithms kuburikidza neSplitsTree, Gubbins pombi uye RDP4 software, nzira dzakashandiswa dzakasimba mukugadzirisa uye kusefa matunhu akarongwa zvakare akakonzerwa nezviratidzo zvekukanganisa. Zvisinei, kuitira kuti usabvisa kupindira kwepe PE / PPE gene paGubbins uye RDP4 software yekuziva masumbu eSNP, uye naizvozvo kuzivikanwa kwenharaunda dzekubatanidza dzakarongwa kukanganisa narX uye pks12 genes, nharaunda yemajini aya akaongororwa (Supplementary Fig. 3-5). MuM. bovis AF2122/97, narX gene inoparadzaniswa narK2 uye Mb1764c, nepo pks12 yakakomberedzwa neMb2075c e Mb2073c (Supplementary Figure 3-5). Mepu inogadzirwa uchishandisa iyo MAUVE synline mepu yeiyo genome yakazara inopa ruzivo nezve gene kutevedzana kuchengetedza uye kurongazve, kuratidza ina collinear blocks, uye hapana zviratidzo zvegenome translocation kana inversion. Pamusoro pezvo, kuongororwa kwekuwedzera pamwe neamino acid kutevedzana kwakaratidza iyo homology mune ese akazara genomes, uye hapana PE/PPE yakawanikwa munzvimbo dziri pedyo dze narX kana pks12. Kune narX, imwe genome (Mb0030) ine yakaderera synonymy mamakisi nekuti iyo narX gene yakaonekwa sezvimedu zviviri (zvidimbu 1891 uye 1890). Kune pks12, nekuda kwekufanana, Mb0030 uye Mb003 yakaratidza yakaderera synlinearity zvibodzwa, nepo pks12 yakaonekwa muzvikamu zviviri uye zvitatu, zvichiteerana, zvinomiririra nzvimbo dzakasiyana dzeprotein (Supplementary Figure 3-5). Tichifunga nezveruzivo urwu, uye Gubbins neRDP4 software vese vanoita ongororo, tarisa musimboti wakawanda kurongeka kwepamusoro 500 bp pahwindo, takasimbisa kuti PE / PPE gene haizokanganisa chiratidzo chekubatanidza chinokanganisa narX uye pks12.
Kunyange zvazvo zviratidzo zvekubatanidza zvakaonekwa mune iyi data seti zvinganzi zvakasara, ichokwadi kuti kubatanidzwazve muM. bovis hakugoni kubviswa, saka inofanira kuramba iri nyaya yekuenderera mberi kwekuongorora, umo majenomes ose kubva kune zvakasiyana-siyana epidemiological scenarios anoteedzana kune Zvakakosha.
Kuenzanisa miti yeML phylogenetic yakawanikwa isati yasvika uye mushure mekugadzirisa zvakare (Mufananidzo 2A, B) haina kutungamirira kukuchinja kukuru muhukama hwefilogenetic inferred, uye M. bovis strains dzakabatanidzwa muboka rimwechete.
Mushure memepu makumi mana nembiri ichangobva kuteedzerwa M. bovis inoverengwa nereferensi genome yeM. bovis AF2122/97, kurongeka kweSNP kuine 1816 polymorphic positions yakawanikwa. Mazhinji SNPs (87.1%) anowanikwa munharaunda yekodhi, uye majini akabatwa anoratidzirwa maererano nemaitiro anoshanda anoratidzwa muBovilist (Mufananidzo 6A, B). Tichifunga nezvehuwandu hwehuwandu hwemajini muchikamu chega chega chekushanda, majini ari muchikamu che "lipid metabolism" airatidza mamwe maSNP, achiteverwa ne "cell wall uye cell process" uye "metabolism yepakati nekufema", zvichiratidza kuti vari muM. bovis evolution.
Ongororo yeHierarchical yeM. bovis dataset kubva kuPortugal (n = 42). Huwandu hwese hweSNPs dzakanyoreswa uye majini akakanganisika kune yega yega inoshanda chikamu (A). Huwandu hwese hweshanduko dzinofanana uye dzisiri-dzimwechete dzakanyoreswa nechikamu chebasa (B).
Pasi rose, chiyero chedN/dS chiri nani pane 1.5, izvo zvinoratidza kuti dzvinyiriro yepasi rose ndeyekubvisa mamiriro emadzitateguru uye inomiririra yakanaka (yakasiyana-siyana kana kutungamirirwa) uye / kana yakasununguka sarudzo yekuchenesa. Muzvikamu zve "virulence, detoxification, adaptation", "insertion sequences uye phages", uye "regulatory proteins", zvinopfuura zvikamu zviviri kubva muzvitatu zveSNPs hazvifananidzi (Mufananidzo 6B).
Muzvikamu zvose, kune majini ane maSNP akawanda, zvichiita kuti pave neavhareji mutation rate (kureva, muvhareji SNP per gene) yakakura kudarika 1 (Mufananidzo 6A). Pks12 (Mb2074c) ine 15 SNPs uye fas (Mb2553c) ine 8 SNPs ine yakakwirira mutation tsika. Ose maviri majini aya anobatanidzwa mufatty acid metabolism. Iyo pks gene encodes polyketide synthase (PKS), inova yakawanda enzyme inobatanidzwa mu mycobacterial cell wall lipid biosynthesis74,75. Iri jena rinobatanidza polypeptide inoshanda yakawanda inobatanidzwa mukugadzirwa kwe mycoketides74,76. Iyo fas gene inobatanidzwa mukuumbwa kwe mycolic acid. Ose maviri aya majini anoita basa rakakosha mu biosynthesis yesero madziro mukubata neanotambira.
Kuti uenderere mberi nekudzidza kushanduka kweMycobacterium bovis, mapoka maviri emajini chaiwo akaongororwa. Zvakambodhindwa mabasa achishandisa kutevedzana kuumbwa uye phylogenetic nzira dzakaona majini akatorwa neMTBC madzitateguru kuburikidza neHGT isati yasiyana37,38. Aya majini akanyorwa muSupplementary Table 2. Kugoverwa kweSNP kwehuwandu hwe77 genes inogona kunge yakabatana neHGT yakaongororwa, uye nzvimbo dze26 dzepolymorphic dzakaonekwa, iyo kazhinji (78%) yakaguma nekusafanana (NS) kuchinja (Supplementary Table 2). Basa rakapfuura paMTBC genome rakaratidza kuti iyo putative HGT dunhu inoratidza yakakwira NS SNP reshiyo kana ichienzaniswa nemamwe ese genome. Kana munhu achifunga kuti nzvimbo idzi dzekubatanidza dzakatorwa nemadzitateguru eMTBC, uye naizvozvo, dzinonyanya kudarika mapolymorphisms ekare, ipapo chikamu chekuchinja kwakafanana chinotarisirwa kuva chepamusoro, nokuti NS inotsiva inotarisirwa kubviswa nekusarudzwa kusina kunaka nekuda kwekuchinja kweamino acid Inogona kuchinja basa reprotein. Naizvozvo, mhedzisiro yedu inoratidza kuti mhedzisiro yekushanda inogona kubva mukutsiviwa kweHGT-senge majini, ayo anoratidza kukosha kwawo kune yakakosha adaptive genetic kusiyana.
Zvichienderana nekuongorora uku, majini anokodha zvikamu zve3R (DNA kugadzirisa, kudzokorodza, uye recombination) system yakanyatsoongororwa zvichienderana nerondedzero yakamboburitswa na dos Vultos nevabatsiri (2008)39. Kutsinhana kwezvikamu zveDNA zvakafanana hazvigoni kuonekwa zvakananga, kunyange zvazvo zvingava zvinowanzoitika apo mabhakitiriya ane hukama hwepedyo anobatanidzwa, zvakadai sechiitiko che data iyi; uyezve, maitiro aya anogona kunge ari kiyi kune nzira dzekugadzirisa DNA72, saka Tamba basa mukudzokorodza homologous. Zvose zve 26 polymorphic nzvimbo dzakagoverwa ne54 genes dzakaonekwa (Supplementary Table 3). Mune iyi seti yemajini, shanduko yeNS yakaverengera inosvika 65% yemhedzisiro, inowirirana nemishumo yapfuura pamusoro peMycobacterium tuberculosis strains.
Nguva yekutumira: Oct-21-2021