Urakoze gusura Kamere. Verisiyo ya mushakisha ukoresha ifite ubufasha buke kuri CSS. Kuburambe bwiza, turagusaba ko ukoresha verisiyo nshya ya mushakisha (cyangwa kuzimya uburyo bwo guhuza muri Internet Explorer). Mugihe kimwe, kugirango tumenye neza inkunga, tuzerekana imbuga zidafite imiterere na JavaScript.
Urutonde rwa genome rwasubukuye imbaraga mu bushakashatsi bw’indwara zandura, bugaragaza ibyorezo by’indwara, indwara ziterwa na virusi, hamwe n’imikorere y’ubwihindurize yashyizweho na virusi. Ikigo cyitwa Mycobacterium tuberculose complex (MTBC) gifata Myvisobacterium bovis nk'umwe mu banyamuryango bayo bahuza n'imihindagurikire y'ikirere itera igituntu (igituntu) ku nyamaswa z’inyamabere zo ku isi, kandi ni urugero rusanzwe rw'ihindagurika rya bagiteri. Kimwe nabandi banyamuryango ba MTBC, Mycobacterium bovis ifatwa nkaho ikoronijwe cyane, igenda itera buhoro buhoro, kandi biragaragara ko nta kimenyetso cyerekana ko umuntu yisubiraho cyangwa yimura gene itambitse. Muri iki gikorwa, dukoresha genomics igereranya kuri dataset yose ikurikirana (WGS) igizwe ninka 70 M. ziva mumoko atandukanye (Uburayi na Afrika) kugirango tumenye neza ubwoko butandukanye bwinka M. Imbaraga zubwihindurize. Uburyo butatu butandukanye bukoreshwa mukugereranya ibimenyetso byo kuvugurura. Kwisi yose, umubare muto wibyabaye byongeye kumenyekana kandi byemejwe nuburyo bubiri bwigenga hamwe ninkunga ikomeye. Nubwo bimeze bityo ariko, ugereranije na mutation, recombination igira ingaruka nke muburyo butandukanye bwa M. bovis (muri rusange r / m = 0.037). Itandukaniro r / m impuzandengo yabonetse murwego rwa clon ya Mycobacterium bovis mumibare yacu yashizweho ihuye nigitekerezo rusange kivuga ko urugero rwa recombination rushobora gutandukana cyane hagati yimirongo ihabwa ubwoko bumwe bwamatagisi. Hashingiwe kuri iki gikorwa, kwiyubaka muri Mycobacterium bovis ntibishobora kuvaho, bityo rero bigomba kuba imbaraga zindi mbaraga mubushakashatsi bugereranya genomics igereranya, aho WGS yamakuru manini aturuka mubintu bitandukanye byanduye epidemiologiya ku isi. Isesengura ry'inyongera ryakorewe noneho kuri data ntoya ya Mycobacterium bovis yashyizweho (n = 42) uhereye ku bantu benshi bakwirakwizwa n'igituntu, kandi hamenyekanye loci zirenga 1.800, muri zo byibuze ubwoko bumwe bwerekanaga polymorphism nucleotide imwe (SNP). Byinshi (87.1%) biherereye mukarere ka code, kandi igipimo cyisi yose yimpinduka zidahuye (dN / dS) zimpinduka zisa zirenga 1.5, byerekana ko guhitamo kwiza ari imbaraga zingenzi zubwihindurize zikoreshwa kuri M. bovis. Umubare munini wa SNPs wagaragaye muri gen zikungahaye ku byiciro bikora bya "lipid metabolism", "urukuta rw'utugingo ngengabuzima na selile", na "metabolisme intermediaire na respirasi", byerekana ubushobozi bwabo muri biologiya no mu bwihindurize bw'akamaro ka Mycobacterium bovis. Iyo urebye neza ingirabuzima fatizo ziri mu basekuruza ba MTBC zikunda guhererekanya gene kandi zigashyirwa muri sisitemu ya 3R (gusana ADN, gusana, no kwiyubaka) zigaragaza agaciro kagereranijwe ku isi ku kizamini cya D cya D kidafite aho kibogamiye, ibyo bikaba byerekana ko icyuho giheruka nyuma yo kwaguka kw'abaturage ari cyo kintu nyamukuru gitera ubwihindurize kuri mycobacterium bovis.
Mycobacterium tuberculose complex (MTBC) ni imwe muri tagisi igenda neza ya bagiteri ziterwa na bagiteri kandi ni ibintu bisanzwe byabayeho biturutse ku bwihindurize. Abanyamuryango bayo berekana bitangaje biranga nucleotide kurwego rwa genomic (> 99%) 1,2. Ecotypes zitandukanye za MTBC zirashobora gutera igituntu (TB), nindwara yandura granulomatique, mubwoko butandukanye bwakiriye kuva inyamaswa z’inyamabere kugeza ku bantu 3,4,5. Kugeza ubu, ikigo kirimo abantu [M. Igituntu (Mtb), Mycobacterium africanum] hamwe n’indwara ziterwa n’inyamaswa (Mycobacterium bovis, Mycobacterium capitum, Mycobacterium pinnipedum, Mycobacterium microtobacter, Mycobacterium mongee, Mycobacterium miysani, Mycobacterium " "dassie") 5,6. M. canettii (izwi kandi nka "Nodobacter glabrata") Impuzandengo ya nucleotide hamwe na mycobacteria yavuzwe haruguru ni 98%, kandi imirimo yo kugereranya genomics igereranya yerekanye ko M. canettii hamwe nabandi MTBC baherutse gutandukana nabakurambere basanzwe.7 Urebye iki gitekerezo, abanditsi bamwe bita M. canettii Umunyamuryango wa MTBC 8.
MTBC isobanurwa muburyo bugaragara nkurwego rukomeye rwa clon, kandi imiterere yabaturage bayoborwa neza no kugabanuka kwinshi, kugabanuka, gusikana guhitamo, hamwe na drift 9,10. Dufashe ko ubwihindurize bukomeye bwihindagurika, nko kubura polymorphism ntibishobora kugarurwa na recombination. Hashingiwe kuri iyi ngingo, ibyabaye bikurikiranye byo gusiba genomic yo mukarere kinyuranye (RD) na TbD1 (Mtb yihariye gusiba akarere 1) byasabwe nkibimenyetso bya molekile byerekana ubwihindurize bwa MTBC2,5,11. Kugereranya genomics hamwe na genome yose ikurikirana (WGS) ishyigikira igabanywa ryabanyamuryango bamenyereye abantu mumirongo icyenda (Mycobacterium tuberculose L1 kugeza L4, L7, na L8; na Mycobacterium africanum L5, L6, na L9), imirongo L2 kugeza L4 basangiye gusiba TbD1,13,12,12,11,12 Byongeye kandi, abanyamuryango bahujwe n’inyamanswa basabwe gusangira abakurambere bahuriweho, bisobanurwa no gusiba kwihariye muri RD7, RD8, RD9 na RD102, 5, na 14.
Ihererekanyabubasha rya Gorizontal (HGT) nibikorwa byo kwiyubaka bifatwa nkibidasanzwe kandi bibaho mubisekuruza bya MTBC, aho kuba amateka atandukanye yabanyamuryango ba MTBC bose 15,16,17. Raporo ebyiri za mbere zakozwe na Hughes n'abafatanyabikorwa (2002) na Gutacker n'abafatanyabikorwa (2006) zagaragaje ko ibikorwa byo kongera kwiyubaka bishobora gufasha gukora polymorphism iranga loci yihariye ya M. igituntu 18,19. Impamvu zituma haboneka recombination muri MTBC ni: (1) uburyo bwa mashini no gutakaza ubushobozi bwa HGT; (2) gake kubintu bya HGT; (3) ntamahirwe yo kwiyubaka muri MTBC niche14,17. Vuba aha, ubushakashatsi bwakozwe na genome yose (WGS) bwakoreshejwe kuri MTBC kumurongo wa 20 na Mycobacterium bovis 21 bwatanze gihamya yo kwiyunga, icya mbere cyerekanye ko imirongo ya MTBC ikunze guhana uduce duto twa ADN, ariko kubera itandukaniro rya nucleotide ikurikirana, ibyo bintu biracyagaragara.
Mycobacterium bovis ni umunyamuryango wa MTBC ukunze kugarurwa mu matungo (cyane cyane inka), nubwo ishobora no gutandukanywa n’inyamaswa zo mu gasozi zidafite ubwisanzure kandi zikikijwe 4,22,23,24. M. bovis yahindutse ibice bitanu byingenzi bya clone [Abanyaburayi 1 (Eu1), Abanyaburayi 2 (Eu2), Abanyaburayi 3 (Eu3), Abanyafurika 1 (Af1) na Afurika 2 (Af2)], bakurikije umwirondoro wa spoligotyping, gusiba byihariye Na polymorphism nucleotide imwe (SNPs) 25, 26, 27, 28, 29 muri gen zihariye. Izi ngirabuzimafatizo zerekana imiterere itandukanye yabaturage ba Mycobacterium bovis nisano ifitanye nakarere. Byongeye kandi, imirimo ya WGS iherutse gukorwa na Zimpel hamwe nabafatanyabikorwa (2020) yateguye phylogene ishingiye kuri SNP ya Mycobacterium bovis, ifite genom zirenga 1.900, byerekana ko byibuze hari imirongo ine itandukanye (yitwa Lb1 kugeza Lb1 kugeza Lb4), nubwo bidahuye neza na geologiya 30. Aba banditsi bakoze isesengura ritandukanye rya phylogene na molekuline yo gukundana, ariko ntibize recombination30.
Ibikorwa byabanje gukoresha tekinoroji ya molekuline itandukanye, nka spoligotyping, MIRU-VNTR (mycobacterial interspersed repeat unit-variable tandem repeat number), kandi kwandika SNP biherutse kwerekana urwego runaka rwubwoko butandukanye hagati ya M. bovis 31,32,33, 34,35. Itandukanyirizo rishingiye ku ngirabuzima fatizo ryahindutse igikoresho gikomeye mu bushakashatsi bw’indwara z’indwara, zifasha mu gusobanukirwa byimbitse indwara ziterwa na virusi, virusi no kwanduza indwara. Kugaragara k'uburyo bwa WGS butanga amahirwe yo kwerekana ibintu bitera ubwihindurize byashyizweho na genoside ya Mycobacterium bovis mugihe cyo guhuza n'imihindagurikire y'ikirere bitandukanye ndetse na epidemiologiya.
Muri iki gikorwa, dukoresha isesengura rya genomic igereranya kuri datasets zitandukanye za Mycoplasma bovis (n = 70), harimo no kwitandukanya n’ibice bitandukanye bya clon, kugira ngo tumenye inzira y’ubwihindurize ya Mycoplasma bovis, cyane cyane kugira ngo dukemure umubano wa phylogeneque n’ibintu byo kwiyubaka. Nk’inyongera kuri iri sesengura, amakuru yamakuru ya M. bovis yitaruye (n = 42) yakuwe mu gace karanga abantu benshi b’igituntu cy’igituntu muri Porutugali 31,36 yongeye gushakishwa kugira ngo hamenyekane ko atari indangamuntu Impuzandengo iri hagati y’imyumvire (dS) ihwanye na nucleotide isimburana, hamwe n’umusanzu w’ubwihindurize wa genoside yihariye yavuzwe na HTC 37,38 . Ingirabuzima fatizo zashyizwe muri sisitemu ya 3R zatoranijwe kubera ko imirimo yabanjirije iyerekeye igituntu cya M. yerekanaga uburyo rusange bwatoranijwe bubi / bwoza bukora kuri ubwo bwoko, kandi bushobora kugira uruhare runini mu bwihindurize 39. Indi ntego y’iki gikorwa ni ugusuzuma ko habaho ibintu byongeye kubaho. Kubera iyo mpamvu, urebye ko dataset yacu yo muri Porutugali ikubiyemo gusa genome zo mu bwoko bwa clone zo mu Burayi 2 hamwe n’imiterere itahaye clone complex, twahisemo gushyiramo amakuru ya genome aboneka kumugaragaro kugirango amaherezo tubone uhagarariye ibigo byose bya clone, kandi tunoze imbaraga nubugari bwibisubizo.
Indwara ya Mycoplasma bovis 42 ikurikiranye kuva muri Porutugali icyorezo cyinshi cy’igituntu cyigituntu (ibisobanuro hepfo), mbere cyaranzwe nicyorezo cya epidemiologiya36, nicyo kigo cyakazi. Urebye ko amakuru yaturutse muri Porutugali afite gusa abahagarariye ibigo by’iburayi 2 bya clone hamwe n’imiterere idafite ibigo byagenwe, amakuru aboneka ku mugaragaro ya genome yose yongeweho kugira ngo yongere amakuru yashyizweho arimo abahagarariye ibigo byose bya M. bovis. Kubwibyo, amasoko atatu yuzuye ya genome yakurikiranye yakoreshejwe muriki gikorwa: kuzuza / gutegura inteko ya genome, kugeza kuri 10 scafolds yabitswe muri NCBI (Ikigo cyigihugu gishinzwe amakuru y’ibinyabuzima) (n = 15 yihariye); bibitswe muri SRA (Idosiye ya Illumina yihuta yikurikiranya soma archive) yerekana itandukaniro rinini rya clone ya M. bovis (n = 12 yihariye) 30; na genome 42 zikurikiranye kuva muri Porutugali. Mycobacterium bovis BCG (Bacille Calmette-Guerin) ntiyashyizwe mu bushakashatsi bwa NCBI. M. bovis AF2122 / 97 isanzwe ikoreshwa nka genome yerekanwe kugirango ishyirwe muri dataset. Bitewe nuko rubanda itaboneka kurutonde rwa genome yose ihagarariwe n’urwego nyafurika rwa 1 rukoronije, hamwe n’umubare muto wa genome uva mu bwoko bwa Af2 na Eu1, amakuru y’umwimerere yatanzwe na SRA yakoreshejwe muri ibi bihe. Ibikorwa bya Zimpel nabafatanyabikorwa be (2020) byafashije kumenya genome kuva murwego rwo hejuru rwa cloni kandi byafashije guhitamo Mycobacterium bovis kugirango ishyirwe mumibare yashyizweho. Kuri Eu3, hasobanuwe ubwoko bumwe gusa bwa genome (Branger et al., 2020), bityo genome dushyiramo ni uhagarariye ibice bitandukanye bya Eu3.
Kwisi yose, aya makuru yashyizwemo arimo inka 70 M. bovis zitandukanijwe nubwoko 8 bwakiriye, zikwirakwizwa mu bihugu 12 kuva 1985 kugeza 2016. Amoko 36 yagenwe nka Eu2, amoko 7 ni Eu1, ubwoko 1 ni Eu3, amoko 3 ni Af1, amoko 4 ni Af2 na 19 ntabwo akomoka ku bwoko ubwo aribwo bwose (ibisobanuro bikurikira). Amakuru arambuye (harimo nimero yinjira) ya Mycobacterium bovis yakoreshejwe muri ubu bushakashatsi yerekanwa mu mbonerahamwe ya 1 no ku mbonerahamwe ya 1.
42 genome zose zikurikiranye za Mycobacterium bovis zivuye mu masoko y’igituntu cy’igituntu cy’igituntu cya Porutugali kandi zigakwirakwizwa mu gihe kirenga imyaka 12 nicyo kigo cy’ubu bushakashatsi, kubera ko gahunda z’indwara z’inyamaswa n’amatungo zagiye zikurikiranwa buri gihe 31.36 (Ishusho yinyongera). Ukurikije uburyo bwakurikiyeho, ubwo bwoko bwatandukanijwe n’inka (n = 14), impongo zitukura (n = 16) n’ingurube yo mu gasozi (n = 12) kuva 2003 kugeza 2015: gukusanya no gufata amatungo hakurikijwe amabwiriza ya protocole yasabwe Icyitegererezo cy’inyama ziri mu gitabo cy’amatungo ya OIE ku isi kandi cyandujwe kuri Stonebrink na Löwenstein-Jensen pyruvate ikoresheje uburyo bukomeye kandi bworoshye. Imico iba kuri 37 ° C kandi imikurire igenzurwa rimwe mu cyumweru byibura ibyumweru 12. Ubukoroni bubitswe neza muri glycerol kuri -80ºC. Mu buryo bwo guhitamo Mycobacterium (Middlebrook 7H9, BD Diagnostics), icyitegererezo cyambere cyabitswe cyanyujijwe muri vitro imwe muri vitro kugirango babone ADN ya gahunda ya WGS. Kubwibyo, igisubizo cyumuco wahagaritswe cyakungahaye kuri sodium pyruvate ya 5% na ADS 10% (albumin 50 g, glucose 20 g, sodium chloride 8.5 g mumazi 1 L) kuri Middlebrook 7H9 kuri 37 ° C. Nyuma yibyumweru 4 byo gukura, uburyo bwaravuguruwe kandi umuco uhora ukurikiranwa kugeza igihe iterambere ryagaragaye. Ingirabuzimafatizo zasaruwe na centrifugation, pellet yongeye guhagarikwa muri saline 500 µL ya fosifate ya saline (PBS), yashyutswe kuri 99 ° C muminota 30, centrifuged, kandi ndengakamere yabitswe kuri -20 ° C kugeza WGS. Inzira zose zikorwa murwego rwa 3 rwibinyabuzima.
Isomero rya genome rya WGS ryateguwe hifashishijwe indangagaciro idasanzwe ya buri cyitegererezo cya ADN, kandi ikoresha Illumina MiSeq (2 × 250 pb) (ingero 40) na HiSeq (2 × 150 pb) ikoranabuhanga (Eurofins Genomics, Ubudage) kugirango ikurikirane. Ukurikije amabwiriza yabakozwe, koresha Illumina Genome Analyser hamwe na module-ebyiri zometse kumugereka kugirango ukurikirane ADN genomic, hanyuma ukoreshe Nextera XT DNA Library Library Prep Kit kuva Illumina kugirango wubake isomero.
Urebye amakuru yakuwe muri SRA (n = 12), kumenyekanisha urwego rwa clone birashobora gukoreshwa nka metadata yigitabo gikwiranye na 30, 41, 43. Iyo urebye genome yuzuye, usibye Mycobacterium bovis AF2122 / 97 na Mycobacterium bovis 3601, izwi nkabanyamuryango ba Eu1 na Eu3 clonque ya 25, 29. igituntu H37Rv (NCBI yinjira numero NC_000962.3). Guhuza genome bikorwa hakoreshejwe MAFFT (gahunda nyinshi yo guhuza aside amine cyangwa nucleotide ikurikirana, verisiyo 7.458) hamwe na parameter -addfragments48. Noneho, shakisha kubura kwa clon zitandukanye zitandukanye hamwe na / cyangwa kuba hariho ibimenyetso bya SNP.
Mycobacterium bovis (n = 42) ikurikiranye hamwe nibisomwa byumwimerere byateguwe na genome yateranijwe (n = 3) ihuza urwego hamwe na genome Mycobacterium tuberculose H37Rv ikoresheje umuyoboro wa vSNP kandi hakabaho gusiba na / cyangwa SNP biranga clone zitandukanye Hakozwe ubushakashatsi.
Kusanya amakuru kuva kubura ibiranga na / cyangwa kuba / kutabaho kwa SNP hamwe na spoligotyping imyirondoro kugirango utange amakuru ya genomic kumurongo uhuye. Ku mbanzirizamushinga ine yinteko, umwirondoro wa spoligotyping ntushobora gutangwa, kubwibyo bashyizwe mumatsinda "ntakibazo".
Ibikorwa bya bioinformatics bikurikirwa niki gikorwa bitangirira ku iteraniro rya novo no gushushanya ingamba zifatika, hagamijwe gushakisha ibyabaye hamwe na polymorphism yihariye. Igishushanyo 1 gitanga urupapuro rwintambwe zikurikira. Kubisesengura rya recombination, genome zose zikoreshwa mukongera imbaraga zifatika hamwe nibipimo bifitanye isano.
Kugirango tugabanye amakosa mugisekuru cya genome yumvikanyweho, twabanje kubona inteko ya novo, hanyuma tubona ibyingenzi byinshi. Umuyoboro wa Unicycler kuri ubu uraboneka kuri https://github.com/rrwick/Unicycler49 kandi ukoreshwa mugukora de novo inteko ya genome 54 zikurikiranye (42 zikurikiranye na dosiye 12 yihuta yakuwe muri SRA). Muri make, mbere yo guterana kuva kera, soma isesengura ryiza ryakozwe muri verisiyo ya FastQC 0.11.7 (https://github.com/s-andrews/FastQC), na Trimmomatic verisiyo 0.36 (ihitamo "gukata Adapters hamwe nizindi nteruro zihariye ziva mubisomwa" na "Gabanya ibishingwe uhereye kumpera yisomwa, niba biri munsi yubuziranenge bwa 20"). (http://www.usadellab. Uburyo bwo guhuza ibiraro bwatoranijwe kugirango hirindwe inteko itari yo, kandi ingano ya k-mer yarashakishijwe kandi ihitamo hagati ya 20% na 95% yuburebure bwasomwe. Kurikiza umurongo ngenderwaho wa SPAdes hanyuma urebe ubunini bwasomwe, gusiba ibice bitarenze 300 bp, hanyuma ushyireho ibice 20 byasomwe byimbitse bigera kuri 52. Mu ngamba zo guteranya de novo, uturere twa genomic nka protine-glutamate (PE) hamwe na glutamate ya protine-proline (PPE) ntibyakuweho.
Ubwiza bwinteko ya de novo busuzumwa hifashishijwe umuyoboro wa QUAST (http://quast.sourceforge.net/quast.html), byorohereza kuvugurura kontig hamwe na M. bovis AF2122 / 97 genome yerekana (Ikarita ya NCBI yinjira LT708304.1) Ikarita (reba Imbonerahamwe 1 yinyongera kubipimo byiza).
Hifashishijwe umuyoboro wa vSNP (https://github.com/USDA-VS/vSNP), dosiye ya FASTQ ya M. bovis iherutse gukurikiranwa kuva Illumina ikurikiranwa na M. bovis AF2122 / 97 genome (LT708304.1)). Ukurikije ibyifuzo byiza byimyitozo ya Genome Analyse Toolkit (GATK) 53, 54, 55 koresha ibipimo bisanzwe byungurura cyangwa amanota ya misa kugirango bisubirwemo. Ibisubizo byayunguruwe ukoresheje amanota yo hasi ya SAMtools amanota 150 na AC = 2. Koresha kandi Kraken (http://ccb.jhu.edu/software/kraken/) kugirango urebe ibyasomwe kugirango wirinde kwanduza. Umuyoboro wa vSNP wakoreshejwe gushushanya ingamba zikurikirana mubikorwa byacu usuzuma urukurikirane rwa SNPs hamwe nintego, kandi ukanakuramo ibintu bivanze bivanze. Gusoma genome isomwe iruta 99% (Imbonerahamwe yinyongera).
Kugira ngo wirinde gushushanya amakosa hamwe na SNPs itari yo, shungura ibintu bitandukanye mu bihe bikurikira: (1) ishyigikiwe n’ibisomwa bitarenze 20, (2) iboneka hamwe na frequence iri munsi ya 0.9, (3) iri byibuze muri Strain imwe, ariko byibuze hari icyuho mubindi bice. Indorerezi za genomics zireba (IGV) verisiyo ya 2.4.19 (http://software.broadinstitute.org/software/igv/)56 yakoreshejwe mugusuzuma neza SNPs nimyanya ifite ibibazo byo gushushanya cyangwa guhuza. Kubera ko genine ya protine-glutamate (PE) na protine-proline glutamate (PPE) yigana cyane kandi ikaba igizwe numuryango wa gene nyinshi, ntibasobanuka byoroshye na Illumina ikurikirana no gufata nabi, bityo bakundwa na mycobacterial bioinformatics workflow yakuyeho abanyamuryango b'igituntu mugihe bakoresheje ingamba zo gushushanya amakarita ya SN. Kubwibyo, twashunguye gen / PE / PPE genes na indels duhereye kubisesengura.
Ukurikije Bovilist (http://genolist.pasteur.fr/BoviList/), SNPs zose zigabanyijemo ibyiciro. Umuyoboro wa SnpEff (https://pcingola.github.io/SnpEff/) ukoreshwa muguhitamo ingaruka za SNP (impinduka zisa cyangwa zidahuye). Hakozwe ububiko bushya bwa Mycobacterium bovis AF2122 / 97 genome (LT708304.1).
Intangiriro yibanze ya genome yakozwe hakoreshejwe Parsnp v1.2, kuri ubu iboneka kuri https://github.com/marbl/parsnp57, ukoresheje genome 69 zuzuye / inteko ziteranijwe (hamwe na -c) na M. bovis AF2122 / 97 (LT708304.1) ikoreshwa nkibisobanuro. Hakozwe ibice bine byingenzi byahujwe: gusa abanyamuryango ba Eu2 clonique (n = 37), harimo nabanyamuryango bose bagize uruganda rw’ibihugu by’i Burayi (n = 44), harimo aho ihurira ry’ikigo cy’ibihugu by’i Burayi na Afurika (n = 51), kandi harimo na bovis zose za Mycobacterium muri ubu bushakashatsi (n = 70).
Ihuza ryibanze ryakozwe na Parsnp rikoreshwa muguhitamo bishoboka cyane (ML) igiti cyitwa phylogeneque ukoresheje CIPRES Science Gateway v3.3 (http://www.phylo.org/)58 ukoresheje RAxML, kandi ugakora inshuro 1000 ziyobowe.
Ibikoresho bitatu bitandukanye bya algorithms nibikoresho bya bioinformatics bikoreshwa mukugenzura niba haribintu byongeye kubaho muburyo bubangikanye: software ya SplitsTree4, Gubbins (umurongo utabogamye binyuze muri recombination muburyo bwa nucleotide), hamwe na RDP4 (porogaramu yo kumenya ibyiyumvo, verisiyo ya beta 4.101).
Uburyo bwo gutandukana bwashyizwe mubikorwa muri SplitsTree4 v4.15.1 (http://www.splitstree.org/)59 ikoreshwa mukubara umuyoboro wa phylogeneque udafite imizi, ukoresheje ikizamini cya Phi kugirango ugenzure imibare, kandi umubare wingenzi ni p = 0.05. Isesengura ryibanze-guhuza isesengura rya Parsnp rikoreshwa nkinjiza, kandi gutandukana kubora nkurusobe rusanzwe.
Umuyoboro wa Gubbins v2.3.1 (https://github.com/sanger-pathogens/gubbins60 ikora ifite ibipimo bisanzwe nkubundi buryo bwo gusuzuma ingaruka ziterwa na recombination kuri boc ya Mycobacterium. Algorithm yashyizwe mubikorwa byongera umurongo wa clone bijyanye na genome / umushinga wo guterana amakuru kuri 702) hanyuma usuzume umwanya wa SNP kuri buri shami ryigiti kugirango umenye cluster ya SNP ihagarariye ibyabaye byo kwiyubaka Zeru yishami Dufate ko nta gikorwa cyo kongera kwiyunga, bivuze ko SNPs iboneka kumashami igomba kugabanwa neza kuri parsnp hamwe nigiti cyiza cya ML kuva muri RAxML.
Hanyuma, kugirango twemeze ibyabaye bivugururwa byasabwe numuyoboro wa Gubbins, algorithm esheshatu zashyizwe mubikorwa muri RDP467 (RDP61, GENECONV62, Bootscan63, Maxchi64, Chimaera65 na SiScan66) zikoreshwa muburyo bwa Parsnp guhuza byinshi muburyo budasanzwe. Twahisemo ko byibura bitatu muri algorithms zashyizwe mubikorwa muri RDP4 bigomba guhora byerekana ikimenyetso cyingenzi cyo kugenzura buri kintu cyabaye.
Urebye ko porogaramu ya Gubbins na RDP ishakisha ibimenyetso bya recombination igenzura ibice byinshi bihuza mu idirishya rigera kuri 500 bp, kandi ikemeza ko gushyiramo gen / PE / PPE mu gihe cyo guterana kwa novo bitazabangamira ibimenyetso bya recombination byabonetse, irindi sesengura rikorwa na homolinearity Reba hafi ya gen igaragaza ibyabaye. Ikarita ya synlinear ikoresheje genome yuzuye yubatswe hifashishijwe guhuza MAUVE-byinshi-genome (http://darlinglab.org/mauve/mauve.html) kugirango ukureho ibisobanuro bya genome byaho cyangwa bihindurwe. Mubyongeyeho, genome yose yakoreshejwe mugukora isesengura rya homolinearity kurwego rwa aminide acide binyuze kurubuga rwa SyntTax (https://archaea.i2bc.paris-saclay.fr/SyntTax/).
Isesengura ryimbitse ryamakuru ya genome yashyizweho yakuwe muri sisitemu yo muri Porutugali yakira igituntu kinini ni ugusuzuma polymorphism ya genes zavuzwe mubitabo. Izi genes ni 37,38 kandi gene irimo kodegisi 3R yabonywe nabakurambere ba MTBC ikoresheje ibice bya sisitemu ya HGT (gusana ADN, kwigana no kwiyubaka) 39. Koresha ClustalX v2.1 (http://www.clustal.org/clustal2/) hanyuma ukoreshe DnaSP v6.12.03 (http://www.ub.edu Tajima ya D ibizamini bitagira aho bibogamiye.
Birashoboka cyane (ML) igiti cyitwa phylogeneque gishingiye kuri 69 Mycoplasma bovis yihariye kandi genome yerekanwe (Ishusho 2A). Ugereranije n'ibiti bishingiye kuri gene imwe cyangwa ibiti bishingiye kuri lokusi, iyi ngamba ituma habaho kubyara ibiti bikomeye bidafata imiterere ya genome yose bityo bikagaragaza ubushobozi buke bwo gutandukanya amoko 68,69. Imiterere ya topologiya yibiti bya ML mubisanzwe bihuza nibyiciro bigoye bya clone. Genome ya Eu2 ikusanyirijwe mu ishami, kandi genome ya Af1 nayo ihuriweho hamwe (Ishusho 2A). Ibisubizo kandi bihuye nubusabane buzwi bwubwihindurize bwa Mycobacterium bovis, ni ukuvuga ko hari itandukaniro rinini hagati yumunyamuryango wa Eu1 nitsinda rigizwe nizindi nzego zose za clon na genome, ariko clone complex 30 ntabwo isobanuwe neza. Ukutavuguruzanya gato hagati ya clonque nubusabane bwagaragaye ku giti cya phylogeneque gishobora gusobanurwa n’uko urwego rwa clon rwasobanuwe rushingiye ku turere tumwe na tumwe twa genomique, mu gihe igiti cyitwa phylogeneque gishingiye ku guhuza byinshi kwa genome yibanze byerekana genome yose.
Igiti kinini gishobora kuba cyitwa phylogeneque (GTR) cyubatswe hashingiwe ku guhuza ingirabuzimafatizo ya genoside ya Mycobacterium bovis mbere ya (A) na nyuma yo (B) gukuraho ikibanza cya recombination. Amabara y'ishami agereranya clone ya Mycobacterium bovis: Uburayi 1 ni umutuku, Uburayi 2 ni umutuku, Uburayi 3 ni ubururu, Afurika 1 ni orange, naho Afurika 2 ni icyatsi. Igiti gishinze imizi kandi gishushanyije ku munzani, kandi uburebure bw'ishami bupimwa nk'umusimbura kuri buri rubuga.
Indwara y'igituntu yitwa Mycobacterium isobanurwa ko yabayeho mu buryo bwihuse, kandi ibimenyetso byinshi byakusanyirijwe mu myaka yashize bishyigikira igitekerezo cy'uko ibintu bikomeje HGT na recombination bitazabaho ku rwego rushoboka rwa MTBC15,17,18.
Ibikorwa byabanje byerekanye ko hashobora kubaho kwiyubaka hagati ya MTBC 20,21, mugihe abandi bananiwe kumenya ibyabaye bipima 70,71. Ongera uganire kuri iki kibazo wibanda kuri Mycobacterium bovis, itandukanye nakazi kashize yatekerezaga gusa igituntu cya Mycobacterium 70,71; cyangwa tekereza MTBC muri rusange, hafi ya M. bovis ihagarariye 20; cyangwa tekereza gusa kubice byinka bigabanya. Dataset ya mycobacteria, muriki gikorwa, hari imirongo 70 yose, igereranya ibice byose bya clon, ikoreshwa mugusuzuma kugirango yongere yongere. Ibyatanzwe byapimwe hakurikijwe urwego enye rwo guhuriza hamwe: (1) abanyamuryango ba Eu2, (2) abanyamuryango b’ibihugu by’ibihugu by’i Burayi (ni ukuvuga Uburayi), (3) ikigo cy’ibihugu by’iburayi n’Afurika (Eu + Af) na (4) Ikusanyamakuru ryose (harimo na genome zitashyizwe mu bigo byose byakoronijwe bimaze gusobanurwa).
Kugirango turusheho kwiga iyi hypothesis, hakozwe umuyoboro wacitsemo ibice kugirango harebwe niba hatabayeho kubaho kwongera kubaho hagati ya genome, kubera ko ubu buryo bushobora kwiyumvisha isano ya basekuruza hagati yabantu no kwerekana ibimenyetso bivuguruzanya bya phylogeneque. Ibyiciro byose uko ari bine byasesenguwe byemeje ko hariho imiyoboro mu muyoboro (ni ukuvuga uduce tudahurira mu giti kimwe), ariko ikizamini cya Phi nta nkunga ifatika ifatika (Eu2, p = 0.0956; Uburayi, p = 0.1637; Eu + Af p = 0.2774; amakuru yose yashyizweho p = 0.2451), atanga ibimenyetso bibi byerekana ko habayeho gahunda yo guhindura ibintu (Ishusho 3).
Mu Burayi genome 2 (n = 37) (A), genome zi Burayi (n = 44) (B), genome zi Burayi na Afrika (n = 51) (C) hamwe namakuru yose yashyizweho (n = 70) (D).
Nyuma yiri sesengura, no kuzirikana ibyakurikiranwe ku miyoboro yose, algorithm yo kwiyubaka yashyizwe mu bikorwa mu muyoboro wa Gubbins yakoreshejwe kugira ngo hubakwe umurongo wa clon ndetse no kuzuza igereranyo cy’ingaruka ziterwa na recombination kuri genome ya M. bovis. Shira ku mubare umubare wibintu byongeye kubaho, ibyinshi byabereye mumashami yanyuma (ni ukuvuga muri genome imwe) (Imbonerahamwe 2). Ibi bipimo byerekana guhuza amakuru yose yashyizweho kandi byerekana ko inshuro yibyabaye byikubye inshuro 200 kugeza 300 zingana na mutation. Iyo ibipimo bya rho / theta byerekana igipimo kigereranyo cya recombination hamwe nihinduka ryimiterere kumashami bigaragara ko iri hagati ya 0.0037 na 0.0056 (Imbonerahamwe 3). Vuba aha, imirimo yatangajwe ya 38 M. bovis yerekana agaciro ka rho / theta (rho / theta = 0.1) irenze iyo yabonetse muri iyi dataset, ariko umurimo wa Patané na bagenzi be wakoresheje inteko ishingiye kubisobanuro kugirango ugereranye ibipimo bya recombination, Ibisobanuro birambuye, bitewe nuburyo bwo guterana, bifitanye isano nubwinshi bwibikorwa byo kwisubiramo mu ishami rya terminal.
Ibikurikira, ibipimo bya r / m byerekana igipimo gitandukanye cyo kwinjiza no guhinduranya ihinduka, kandi agaciro kacyo kari hagati ya 0.025 na 0.037, byerekana ko ugereranije na mutation, recombination igira ingaruka nke muri rusange ku moko atandukanye ya M. bovis (Imbonerahamwe 3)). Kugereranya kwinshi, uburyo busa bwakoreshejwe mukugereranya ibipimo bya r / m kuri dataset ya MTBC igizwe na genome 23, byerekana impuzandengo ya 0.48620, mugihe kuri Patané na bagenzi be 38 M. bovis dataset, byagaragaje ko impuzandengo ari 0.98. Mu bushakashatsi bwa mbere, bibiri gusa muri 23 genome zashyizwe mubikorwa bya M. bovis (M. bovis BCG hamwe na reference reference), bityo agaciro kabonetse gashobora kubogama kubera gukabya gukabije kwa gen. M. igituntu. Muri raporo ya kabiri, isesengura rya Mycobacterium bovis ryagaruwe cyane cyane muri Amerika hamwe n’abashinzwe ubworozi. Ibinyuranyo, mumibare yacu yashizweho, hashyizweho ahantu henshi h’ibinyabuzima hamwe n’ibinyabuzima byakiriwe, kandi genome zishyizwe mu bice bitandukanye by’imiterere y’imiterere y’imiterere y’imiterere y’imiterere y’imiterere y’imiterere y’abaturage, bityo bikagera ku bumenyi bwimbitse kandi bwagutse bw’abaturage. Itandukaniro r / m impuzandengo yabonetse hamwe namakuru yacu yashizweho arahuza nigitekerezo kivuga ko urugero rwa recombination rutandukana cyane hagati yumurongo wahawe ubwoko bumwe bwa tagisi, bityo ibisubizo byerekana ko uruganda rwa M. bovis rushobora kwerekana itandukaniro rya recombination Ingaruka nazo nkuko byasabwe na Didelot & Maiden72. Nubwo bimeze bityo ariko, kwagura cyane aya makuru yashyizweho ushizemo umubare munini wa M. bovis genome bizatuma hasobanurwa neza iyi ngingo. Byombi ibipimo bya r / m na rho / theta byerekana itandukaniro riri hagati y amashami, kandi ibisubizo bihuye na raporo ku yandi moko ya bagiteri 72,73.
Hanyuma, kugirango twemeze ibyabaye byongeye kuvugururwa byagaragajwe numuyoboro wa Gubbins, algorithm esheshatu zitandukanye zakoreshejwe muri software ya RDP4 kugirango bigerageze kwigenga kugerageza ibintu bitandukanye bigereranywa. Kwisi yose, munsi ya kimwe cya kabiri cyibyabaye byagaragajwe na Gubbins byemejwe na RDP4 (Imbonerahamwe 4 na 5). Urebye amakuru yose yashyizweho, byemejwe ibyabaye bitatu byo kwiyubaka, bibiri birimo imitwe y'imbere naho ubundi birimo genome imwe mumashami ya terefone, kuberako clon idashobora gutangwa (Imbonerahamwe 4 na 5). Kumenyekanisha ibyabaye mumashami yanyuma birashobora kwerekana ko recombination ikomeje mubikorwa bya M. bovis ya none cyangwa ibisubizo byimuwe 70. Muri kariya karere ka hypothetical recombination, hafi 20% yimyanya ifite nucleotide idasobanutse (N), bityo bigira ingaruka kubimenyetso bya recombination (Ishusho yinyongera 2). Byongeye kandi, kariya karere kagira ingaruka kuri rrs gene, kode ya 16S ribosomal RNA iteganijwe ko izabikwa cyane, bityo iki kimenyetso cyo gushira hamwe gishobora kuba igisubizo cyamakosa akurikirana cyangwa adahuye. Hanyuma genome yose ihuza Mb0003 na Mycobacterium bovis AF2122 / 97 yarakozwe, kandi haremejwe ko habaho nucleotide idasobanutse na SNPs, bityo ibibazo bishoboka bijyanye no guhuza nabi ntabwo byatewe namakuru yibinyabuzima yashyizwe mubikorwa muriki gikorwa Yagaragaye nyuma yo kwiga gahunda.
Nta cyuho cyangwa nucleotide idasobanutse yabonetse mu turere twa recombination ya node y'imbere (Ishusho 4 na 5). Kubyerekeranye nibyabaye, imwe irimo genome ya Eu2 gusa kandi ikagira ingaruka kuri pks12, ikubiyemo synthase ishoboka ya polyketide; mugihe irindi ryanditswe muri genome ya Eu1 kandi rikagira ingaruka kuri gene ya narX ikubiyemo reditase ishoboka (Imbonerahamwe 4). Muri rusange, isesengura rya recombination ryerekana ko hari umubare muto w’ibice bya recombination bifashijwe n’ibarurishamibare, kandi ibipimo bifatika byerekana ko kwiyubaka bigira ingaruka nke ku muryango wa M. bovis. Ikimenyetso cya recombination giteganijwe kuba gito, ariko ni ngombwa gutandukanya ibimenyetso nyabyo byabayeho biturutse ku rusaku rw’imbere, bikaba ari umurimo utoroshye. Mu rwego rwo kugabanya ibimenyetso by’urusaku byatangijwe n’iteraniro rishingiye ku bitabo hamwe n’ibibazo bidahuye 70, 71, ibindi byose usibye genome yuzuye byakusanyirijwe hamwe, kandi ubuziranenge bwiteraniro bwaragenzuwe kandi byemezwa n’isesengura ry’imiyoboro ya QUAST (Imbonerahamwe yinyongera 1). Byongeye kandi, urukurikirane rwisesengura rwinyongera rwakozwe kugirango rutange imbaraga nukuri mubushakashatsi rusange. Kubwibyo, ubuziranenge bwurwego rwa genX na pks12 byasuzumwe no gusoma ikarita yo kurwanya Mycobacterium bovis AF2122 / 97. Umwanya wasabwe na SNP mukarere ka recombination byemejwe no gushyira mu bikorwa ibipimo byavuzwe mu gice cyuburyo (byibuze 20 byasomwe na 0.9 inshuro nyinshi). Polimorphism ya gene ya narX yemejwe byimazeyo muri genome ebyiri (Mb1792361 na Mb7240415; 2,3%) na genome ya gen pks12: Mb0891, Mb1711, Mb1789, Mb1870, Mb17046, Mb1756, na Mb12. Nyamara, kuri genome Mb2043, imyanya itandatu kuri umunani ntabwo yujuje ibyasomwe byimbitse kuko SNP ishyigikiwe nibisomwa ntarengwa 17, biri munsi yagaciro kagabanijwe ka 20. Kubwibyo rero, kongera guhuza genome esheshatu (8,6%) kururu rubuga rwa genome birashobora kwemezwa (Ishusho ya 4 na 5).
Amashusho arambuye yerekana akarere ka recombination guhuza Mycobacterium bovis dataset bigira ingaruka kuri genX ya narX ikubiyemo reditase ishobora kuba. Nta cyuho cyangwa nucleotide idasobanutse yabonetse mukarere ka recombination ya node y'imbere. Iki gikorwa cyihariye cyanditswe muri genome ya Eu1. Ubwiza bukurikirana bwa genX ya genX bwasuzumwe mugutegura ibisomwa bya Mycobacterium bovis AF2122 / 97. Emeza ahantu hasabwa SNP mugace ka recombination ukoresheje ibipimo byavuzwe mubice byuburyo (byibuze 20 wasomye na 0.9 impinduka inshuro). Polimorphism ya gene ya narX yemejwe byimazeyo muri genome ya Mb1792361 na Mb7240415 (2.3%).
Amashusho arambuye yerekana akarere ka recombination guhuza Mycoplasma bovis dataset igira ingaruka kuri gen pks12. Nta cyuho cyangwa nucleotide idasobanutse yabonetse mukarere ka recombination ya node y'imbere. Kubyerekeranye nibyabaye bigira ingaruka kuri pks12 kodegisi ishoboka ya synthase ya polyketide, irimo genome ya Eu2 gusa. Ubwiza bukurikirana bwa pks12 bwasuzumwe no gusoma ikarita ya Mycobacterium bovis AF2122 / 97. Emeza ahantu hasabwa SNP mugace ka recombination ukoresheje ibipimo byavuzwe mubice byuburyo (byibuze 20 wasomye na 0.9 impinduka inshuro). Polimorphism ya genome Mb0891, Mb1711, Mb1789, Mb1870, Mb1758, Mb2043, na Mb1960 byemejwe neza.
Ingirabuzima fatizo za PE na PPE zifite uturere dusubiramo byoroshye gusomwa nabi na Illumina ikurikirana no gufata nabi, bityo rero mubisanzwe bisibwa mubikorwa bya bioinformatics byabakozi ba M. igituntu gusa mugihe bakoresheje ingamba zo gushushanya. Umwanzuro wibikorwa bya recombination ukoreshwa muriki gikorwa ushingiye ku nteko ya novo utayungurura PE / PPE. Twizera ko mugushira mubikorwa uburyo butatu bwuzuzanya hamwe na algorithms binyuze muri SplitsTree, umuyoboro wa Gubbins na software ya RDP4, ingamba zikoreshwa zirakomeye mugutunganya no gushungura uturere twavuguruwe twatewe nibimenyetso byamakosa. Ariko rero, kugira ngo hirengagijwe kwivanga kwa gene PE / PPE kuri software ya Gubbins na RDP4 kugira ngo hamenyekane amatsinda ya SNP, bityo rero kumenya uturere twa recombination twasabye kugira ingaruka kuri genX ya narX na pks12, hasuzumwe abaturanyi b'iyi genes (Ishusho y'inyongera 3-5). Muri M. bovis AF2122 / 97, gene ya narX itandukanijwe na narK2 na Mb1764c, naho pks12 ikikijwe na Mb2075c e Mb2073c (Ishusho yinyongera 3-5). Ikarita yakozwe hakoreshejwe ikarita ya MAUVE ya genome yuzuye itanga amakuru ajyanye no kubungabunga gene ikurikirana no kuyitondekanya, yerekana ibice bine bya collinear, kandi nta kimenyetso cyerekana guhinduranya genome cyangwa guhinduka. Byongeye kandi, isesengura ryuzuzanya hamwe na aside amine ikurikirana ryerekanye homologiya muri genome zose zuzuye, kandi nta PE / PPE wabonetse mukarere kegeranye na narX cyangwa pks12. Kuri narX, genome imwe (Mb0030) ifite amanota make ya synonymy kuko gene ya narX yamenyekanye nkibice bibiri (ibice 1891 na 1890). Kuri pks12, kubera ibisa, Mb0030 na Mb003 bagaragaje amanota yo hasi, mugihe pks12 yamenyekanye mubice bibiri na bitatu, byerekana domaine zitandukanye za poroteyine (Ishusho yinyongera 3-5). Dufatiye kuri aya makuru, hamwe na software ya Gubbins na RDP4 byombi bikora isesengura, reba intangiriro ihuza byinshi bya 500 bp ntarengwa mu idirishya, twemeje ko gene PE / PPE itazabangamira ibimenyetso bya recombination bigira ingaruka kuri narX na pks12.
Nubwo ibimenyetso bya recombination byagaragaye muri aya makuru yashyizweho bishobora gufatwa nkibisigisigi, ni ukuri ko kwiyubaka muri M. bovis bidashobora kuvaho, bityo rero bigomba gukomeza kuba ingingo y’isesengura, aho genome zose ziva mu bihe bitandukanye by’ibyorezo zikurikirana zikenewe.
Ugereranije ibiti bya ML phylogeneque byabonetse mbere na nyuma yo gukosora recombination (Igicapo 2A, B) ntabwo byatumye habaho impinduka zikomeye mumibanire ya phylogeneque, kandi ubwoko bwa M. bovis bwari bukusanyirijwe mumatsinda amwe.
Nyuma yo gushushanya 42 bo M. M. bovis yasomwe hamwe na genome ya M. bovis AF2122 / 97, habonetse guhuza SNP irimo imyanya 1816 ya polymorphique. SNPs nyinshi (87.1%) ziherereye mukarere ka code, kandi genes zanduye zirangwa ukurikije ibyiciro bikora byerekanwe muri Bovilist (Ishusho 6A, B). Urebye umubare rusange wa gen muri buri cyiciro cyibikorwa, ingirabuzimafatizo zo mu cyiciro cya "lipid metabolism" zerekanye SNP nyinshi, zikurikirwa n "urukuta rw'utugingo ngengabuzima hamwe na" metabolisme intermediaire no guhumeka ", byerekana ko ziri mu bwihindurize bwa M. bovis.
Isesengura ryibihe bya dataset ya M. bovis yo muri Porutugali (n = 42). Umubare rusange wa SNPs wanditswemo na gen zigira ingaruka kuri buri cyiciro gikora (A). Umubare rusange wimpinduka zisa kandi zidahuye zanditswe nicyiciro cyimirimo (B).
Ku rwego rwisi, impuzandengo ya dN / dS iruta 1.5, ibyo bikaba byerekana ko igitutu cyubwihindurize kwisi ari ugukuraho leta yabasekuruza kandi kigereranya ibintu byiza (bitandukanye cyangwa byerekanwe) hamwe na / cyangwa guhitamo guhitamo kweza. Mu byiciro bya "virusi, kwangiza, kurwanya imihindagurikire y'ikirere", "gushyiramo ibyiciro n'ibice", na "poroteyine zigenga", ibice bibiri bya gatatu bya SNPs ntabwo ari kimwe (Ishusho 6B).
Mu byiciro byose, hariho genes zifite SNPs nyinshi, bivamo igipimo mpuzandengo cya mutation (ni ukuvuga impuzandengo ya SNP kuri gene) irenze 1 (Ishusho 6A). Pks12 (Mb2074c) hamwe na SNPs 15 na fas (Mb2553c) hamwe na SNPs 8 bifite agaciro gakomeye ka mutation. Izi genes zombi zigira uruhare mu guhinduranya aside aside. Gene ya pks ikubiyemo synthase ya polyketide (PKS), ni enzyme ikora cyane igira uruhare muri mycobacterial selile selile lipid biosynthesis74,75. Iyi gene ikubiyemo polypeptide ikora cyane igira uruhare muri synthesis ya mycoketide74,76. Gene ya fas igira uruhare muri synthesis ya acide mycolike. Izi genes zombi zigira uruhare runini muri biosynthesis y'urukuta rw'akagari ihuye na nyirarureshwa.
Kugirango turusheho kwiga ubwihindurize bwa Mycobacterium bovis, hasesenguwe ibice bibiri bya genes zihariye. Ibikorwa byasohotse mbere ukoresheje ibice bikurikirana hamwe nuburyo bwa phylogeneque bwerekanaga genes zaguzwe nabakurambere ba MTBC binyuze muri HGT mbere yo gutandukana37,38. Izi genes zashyizwe ku mbonerahamwe ya 2. Ikwirakwizwa rya SNP ry’ingirabuzima fatizo zigera kuri 77 zishobora kuba zifitanye isano na HGT zarasesenguwe, hamenyekana ibibanza 26 bya polymorphique, ibyo bikaba akenshi (78%) byatumye habaho impinduka zidahuye (NS) (Imbonerahamwe 2). Ibikorwa byabanje kuri genome ya MTBC byerekanaga ko agace ka HGT gashyira ahagaragara igipimo kinini cya NS SNP ugereranije nizindi genome. Niba umuntu atekereza ko uturere twa recombination twaguzwe nabakurambere ba MTBC, bityo, bakagaragaza polymorphism ya kera, noneho igipimo cyimpinduka zisa nacyo giteganijwe kuba kinini, kuko insimburangingo za NS ziteganijwe kuzakurwaho no guhitamo nabi kubera ihinduka rya aside amine rishobora guhindura imikorere ya proteine. Kubwibyo, ibisubizo byacu byerekana ko ingaruka zimikorere zishobora guturuka ku gusimbuza ingirabuzimafatizo za HGT, zigaragaza akamaro kazo ku miterere y’imiterere y’imiterere y’imiterere.
Mu buryo buhuye n'iri sesengura, gen zigizwe n'ibice bigize sisitemu ya 3R (gusana ADN, kwigana, no kwiyubaka) byasuzumwe neza hakurikijwe urutonde rwatangajwe na dos Vultos n'abafatanyabikorwa (2008) 39. Guhana ibice bya ADN bisa ntibishobora kugaragara neza, nubwo bishobora kuba inzira mugihe bagiteri zifitanye isano rya bugufi, nko mubyerekeranye naya makuru yashyizweho; mubyongeyeho, iyi nzira irashobora kuba urufunguzo rwuburyo bwo gusana ADN72, Gira uruhare rero muburyo bwo guhuza ibitsina. Imyanya 26 ya polymorphique yatanzwe na gen 54 yaramenyekanye (Imbonerahamwe yinyongera 3). Muri ubu bwoko bwa gen, impinduka za NS zagize hafi 65% byingaruka, ibyo bikaba bihuye na raporo zabanjirije iyi kuri Mycobacterium igituntu.
Igihe cyo kohereza: Ukwakira-21-2021