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Ulandelelwano lweMetagenomic -NGS
I-metagenome yingqokelela yemathiriyeli yemfuzo iyonke yoluntu oluxubeneyo lwezinto eziphilayo, ezifana nokusingqongileyo kunye neemetagenomes zabantu. Iqulethe ii-genomes zombini ii-microorganisms ezinokulinywa kunye nezingenakulinywa. I-Shotgun metagenomic sequencing kunye ne-NGS yenza ukuba kuphononongwe le mihlaba intsonkothileyo ye-genomic emiliselwe kwiisampulu zokusingqongileyo ngokubonelela ngokungaphaya kweprofayili ye-taxonomic, inika ulwazi oluphangaleleyo kwiyantlukwano yeentlobo, ukuguquguquka kobuninzi, kunye nezakhiwo ezintsonkothileyo zabemi. Ngaphandle kwezifundo ze-taxonomic, i-shotgun metagenomics ikwabonelela ngembono esebenzayo ye-genomics, eyenza ukuphononongwa kofuzo olufakwe kwikhowudi kunye neendima zabo zokubeka kwiinkqubo zendalo. Okokugqibela, ukusekwa kothungelwano lothungelwano phakathi kwezinto zofuzo kunye nemiba yokusingqongileyo inegalelo ekuqondeni okupheleleyo konxibelelwano oluntsonkothileyo phakathi koluntu lwemicrobial kunye nemvelaphi yazo yendalo. Ukuqukumbela, ulandelelwano lwe-metagenomic limi njengesixhobo esibalulekileyo sokutyhila ubugocigoci be-genomic boluntu olwahlukeneyo lwe-microbial, ikhanyisela ubudlelwane obuninzi phakathi kofuzo kunye ne-ikholoji ngaphakathi kwezi zixokelelwano zendalo ezintsonkothileyo.
Iiplatforms: Illumina NovaSeq kunye ne-DNBSEQ-T7
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Ulandelelwano lweMetagenomic-TGS
I-metagenome yingqokelela yemathiriyeli yemfuzo yoluntu oluxubeneyo lwezinto eziphilayo, ezifana nokusingqongileyo kunye neemetagenomes zabantu. Iqulethe ii-genomes zombini ii-microorganisms ezinokulinywa kunye nezingenakulinywa. Ulandelelwano lwe-Metagenomic lwenza uphononongo lwezi ndawo zintsonkothileyo ze-genomic ezizinziswe kwiisampulu ze-ikholoji ngokubonelela ngokungaphezulu kweprofayili ye-taxonomic. Ikwabonelela ngembono esebenzayo ye-genomics ngokuphonononga ijene ekhowudiweyo kunye neendima zabo zokubeka kwiinkqubo zokusingqongileyo. Ngelixa i-shotgun yendabuko isondela kunye nokulandelelana kwe-Illumina isetyenziswe ngokubanzi kwizifundo ze-metagenomic, ukufika kwe-Nanopore kunye ne-PacBio yokulandelelana kwexesha elide iguqule intsimi. Itekhnoloji yeNanopore kunye nePacBio iphucula uhlalutyo lwe-bioinformatic esezantsi, ngakumbi indibano yemetagenome, iqinisekisa iindibano eziqhubekayo. Iingxelo zibonisa ukuba i-Nanopore-based and PacBio-based metagenomics ivelise ngempumelelo i-genomes yebhakteria epheleleyo kunye nevaliweyo ukusuka kwi-microbiomes eyinkimbinkimbi (Moss, EL, et al., Nature Biotech, 2020). Ukudibanisa i-Nanopore ifundeka kunye nokufundwa kwe-Illumina kunika indlela yobuchule yokulungiswa kweempazamo, ukunciphisa ukuchaneka okuphantsi kweNanopore. Le ndibaniselwano ye-synergistic iphakamisa amandla eqonga ngalinye lokulandelelana, linikezela ngesisombululo esomeleleyo sokunqoba imida enokubakho kunye nokuqhubela phambili ukuchaneka kunye nokuthembeka kohlalutyo lwe-metagenomic.
Iqonga: iNanopore PromethION 48, Illumia kunye nePacBio Revio
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16S/18S/ITS Amplicon Sequencing-PacBio
Iijini ze-rRNA ze-16S kunye ne-18S, kunye nengingqi ye-Internal Transcribed Spacer (ITS), isebenza njengeyona nto ibalulekileyo yokuphawula iminwe yemolekyuli ngenxa yokudityaniswa kwemimandla egcinwe kakhulu kunye ne-hyper-variable, izenza izixhobo ezixabiseke kakhulu zokubonisa iimpawu zeprokaryotic kunye ne-eukaryotic. Ukwandiswa kunye nolandelelwano lwale mimandla lubonelela ngendlela engenakwahlulwa yokuphanda ubume bemicrobial kunye neyantlukwano kuzo zonke ii-ecosystems. Ngelixa ulandelelwano lwe-Illumina ngokuqhelekileyo lujolise kwimimandla emifutshane ye-hypervariable efana ne-V3-V4 ye-16S kunye ne-ITS1, kubonakaliswe ukuba i-taxonomic annotation ephezulu ifikeleleke ngokulandelelana ubude obupheleleyo be-16S, 18S, kunye ne-ITS. Le ndlela ibanzi iphumela kwiipesenti eziphezulu zolandelelwano oluhlelwe ngokuchanekileyo, ukufikelela kwinqanaba lesisombululo esinabela ekuchongweni kweentlobo. I-PacBio ye-Single-Molecule ye-Real-Time (SMRT) iqonga lokulandelelanisa iqonga livelele ngokubonelela ngofundo oluchanekileyo olude (i-HiFi) olugubungela i-amplicon yobude obupheleleyo, ikhuphisana nokuchaneka kokulandelelana kwe-Illumina. Esi sikhundla sivumela abaphandi ukuba bafumane inzuzo engenakulinganiswa - imbono ye-panoramic ye-genetic landscape. Ugutyulo olwandisiweyo lusiphakamisa kakhulu isisombululo kwingcaciso yeentlobo, ngakumbi phakathi kweebhaktiriya okanye kuluntu lomngundo, okwenza ukuba kuqondwe nzulu ukuntsonkotha kobuninzi bentsholongwane.
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16S/18S/ITS Amplicon Sequencing-NGS
Ukulandelelana kwe-Amplicon kunye neteknoloji ye-Illumina, ejolise ngokukodwa kwi-16S, i-18S, kunye neempawu ze-ITS zofuzo, yindlela enamandla yokutyhila i-phylogeny, i-taxonomy, kunye nobuninzi beentlobo ngaphakathi kwe-microbial community. Le ndlela ibandakanya ukulandelelana kwemimandla eguquguqukayo yogcino lweempawu zofuzo. Yaziswa ekuqaleni njengophawu lweminwe yemolekyuli nguWoeses et alngo-1977, obu buchule buguqule iprofayili ye-microbiome ngokwenza uhlalutyo olungakhethiyo. Ngokulandelelana kwe-16S (iibhaktheriya), i-18S (i-fungi), kunye ne-Internal Transcribed Spacer (ITS, i-fungi), abaphandi abakwazi ukuchonga kuphela iintlobo ezininzi kodwa kunye nezinqabileyo nezingaziwa. Yamkelwa ngokubanzi njengesixhobo esibalulekileyo, ulandelelwano lwe-amplicon lube sisixhobo ekuqondeni ukuqanjwa kwe-microbial eyahlukileyo kwiindawo ezahlukeneyo, kubandakanya umlomo womntu, amathumbu, isitulo, nangaphaya.
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IBacterial kunye neFungal Whole Genome Re-Sequencing
Iiprojekthi zebhaktiriya kunye nokungunda kokulandelelana kwakhona kwegenome zibalulekile ekuqhubeleni phambili i-microbial genomics ngokwenza ukuba kugqitywe kwaye kuthelekiswe i-microbial genomes. Oku kuququzelela ubunjineli bokubiliswa, ukulungelelaniswa kweenkqubo zoshishino, kunye nokuphononongwa kweendlela zemetabolism yesibini. Ngaphaya koko, ulandelelwano lokungunda kunye nebhaktiriya lubalulekile ekuqondeni ulungelelwaniso lwendalo esingqongileyo, ukukhulisa ubunzima, kunye nokutyhila ukuguquguquka kofuzo, kunye nefuthe elibanzi kwezamayeza, ezolimo, kunye nesayensi yokusingqongileyo.
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Prokaryotic RNA Ulandelelwano
Ulandelelwano lwe-RNA luxhobisa iprofayili ebanzi yazo zonke iikopi ze-RNA ngaphakathi kweeseli phantsi kweemeko ezithile. Le teknoloji ye-cutting-edge isebenza njengesixhobo esinamandla, ityhila iiprofayili zegenesis ezintsonkothileyo, ulwakhiwo lwemfuza, kunye neendlela zemolekyuli ezinxulumene neenkqubo ezahlukeneyo zebhayoloji. Yamkelwa ngokubanzi kuphando olusisiseko, uxilongo lweklinikhi, kunye nophuhliso lwamachiza, ulandelelwano lwe-RNA lubonelela ngokuqonda kubuntsonkothe bokutshintshatshintsha kweeseli kunye nolawulo lwemfuzo. Inkqubo yethu yesampulu yeprokaryotic ye-RNA ilungiselelwe i-prokaryotic transcriptomes, ebandakanya ukuncipha kwe-rRNA kunye nokulungiswa kwethala leencwadi.
Iqonga: Illumina NovaSeq
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Ulandelelwano lweMetatranscriptome
Itekhnoloji yokulandelelanisa i-Illumina, inkonzo yolandelelwano ye-metaranscriptome ye-BMKGENE ityhila ukubonakaliswa kofuzo oluguquguqukayo lweentlobo ngeentlobo zeentsholongwane, ezithatha ii-eukaryotes ukuya kwiiprokaryotes kunye neentsholongwane, ngaphakathi kwendawo yendalo efana nomhlaba, amanzi, ulwandle, isitulo, kunye namathumbu. Inkonzo yethu ebanzi ixhobisa abaphandi ukuba baphengulule kwiiprofayile ezipheleleyo zegenesis yegenesis yasekuhlaleni. Ngaphandle kohlalutyo lwe-taxonomic, inkonzo yethu yolandelelwano ye-metatranscriptome iququzelela ukuphononongwa ekutyebiseni okusebenzayo, ikhanyisela iigenes ezichazwe ngokwahlukileyo kunye neendima zabo. Fumanisa ubutyebi bengqiqo yebhayoloji njengoko ujonga kumhlaba ontsonkothileyo wokuchazwa kofuzo, iyantlukwano yetaxonomic, kunye nokuguquguquka okusebenzayo ngaphakathi kwezi niches zahlukeneyo zokusingqongileyo.
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De novo Fungal Genome Assembly
I-BMKGENE ibonelela ngezisombululo eziguquguqukayo kwiigenomes zokungunda, ukulungiselela iimfuno zophando ezahlukeneyo kunye nokugqibelela kwegenome enqwenelekayo. Ukusebenzisa ukulandelelana kwe-Illumina okufutshane kuphela kuvumela ukuveliswa kwe-genome eyidrafti. Ukufundwa okufutshane kunye nokulandelelana kwexesha elide usebenzisa i-Nanopore okanye i-Pacbio zidityanisiwe kwi-genome yefungal esulungekileyo kunye ne-contigs emide. Ngaphezu koko, ukudibanisa ulandelelwano lwe-Hi-C kuphucula ngakumbi amandla, okwenza ukuba kufunyanwe igenome yomgangatho wechromosome epheleleyo.
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De novo i-Bacterial Genome Assembly
Sinikezela ngenkonzo epheleleyo yebhaktiriya yendibano yejenome, eqinisekisa izithuba ezi-0. Oku kunokwenzeka ngokudibanisa itekhnoloji yokulandelelanisa ixesha elide lokufunda, njengeNanopore kunye nePacBio yokuhlanganisa kunye nokulandelelanisa okufutshane kunye ne-Illumina yokuqinisekiswa kwendibano kunye nokulungiswa kwempazamo yokufundwa kwe-ONT. Inkonzo yethu ibonelela ngokuqhutywa kwe-bioinformatic epheleleyo ukusuka kwindibano, inkcazo esebenzayo, kunye nohlalutyo oluphambili lwe-bioinformatic, ukuzalisekisa iinjongo ezithile zophando. Le nkonzo yenza ukuba kuphuhliswe iigenome zesalathiso ezichanekileyo kwiintlobo ezahlukeneyo zezifundo zofuzo kunye ne-genomic. Ukongeza, yenza isiseko sezicelo ezinje ngokuphuculwa koxinzelelo, ubunjineli bemfuza, kunye nophuhliso lobuchwephesha bemicrobial, iqinisekisa idatha yegenomic ethembekileyo nengenasikhewu ibalulekile ekuqhubeleni phambili ukuqonda kwezenzululwazi kunye nokuveliswa kwezinto ezintsha zebhayoloji.
