De novo i-Bacterial Genome Assembly
Sinikezela ngenkonzo epheleleyo yokuhlanganisa i-genome yebhaktiriya, siqinisekisa izithuba ezi-0. Oku kunokwenzeka ngokuhlanganisa ubuchwepheshe bokulandelelana obufundwa ixesha elide, obufana neNanopore kunye nePacBio bokuhlanganisa kunye nokulandelelana okufundwayo okufutshane kunye ne-Illumina yokuqinisekisa indibano kunye nokulungiswa kweempazamo ze-ONT reads. Inkonzo yethu ibonelela ngomsebenzi opheleleyo we-bioinformatic ukusuka kwindibano, i-functional analysis, kunye nohlalutyo oluphambili lwe-bioinformatic, oluzalisekisa iinjongo zophando ezithile. Le nkonzo ivumela ukuphuhliswa kwe-genome echanekileyo yezifundo ezahlukeneyo ze-genetic kunye ne-genomic. Ukongeza, yenza isiseko sezicelo ezinje ngokulungiswa koxinzelelo, ubunjineli be-genetic, kunye nophuhliso lwetekhnoloji ye-microbial, ukuqinisekisa idatha ye-genomic ethembekileyo nengenazikhewu ebalulekileyo ekuphuculeni ukuqonda kwesayensi kunye nokuvelisa izinto ezintsha ze-biotechnology.
Iimpawu zeNkonzo
● Kukho iindlela ezimbini onokukhetha kuzo ngokuxhomekeke kwinqanaba elifunekayo lokuphelela kwe-genome.
● Ukhetho lweDrafti yeGenome: Ulandelelwano olufutshane olufundwayo nge-Illumina NovaSeq PE150.
● I-genome epheleleyo ye-gap engu-0.
● Ulandelelwano olude olufundwe kwiNanopore PromethION 48 okanye kwiPacBio Revio ukuze kuhlanganiswe i-genome.
● Ulandelelwano olufutshane kwi-Illumina NovaSeq lokuqinisekisa i-genome kunye nokulungiswa kweempazamo (i-Nanopore) okanye ukuvelisa i-genome eyidrafti.
Iingenelo zeNkonzo
●I-Zero-Gap Genome IqinisekisiweOku kungenxa yokuhlanganiswa kwe-Illumina sequencing kunye ne-long read sequencing (i-Nanopore okanye i-PacBio).
●Uhambo olupheleleyo lomsebenzi we-Bioinformatics:Oku kuquka ukuhlanganiswa kwe-genome kunye nokuqikelela izinto ezininzi ze-genomic, i-functional gene analysis, kunye ne-genome visualisations ezifana ne-Circos plot.
●Ubuchule Obubanzi: Njengoko ii-genome ze-microbial ezingaphezu kwama-20,000 zihlanganisiwe, i-BMKGENE izisa amava angaphezulu kweminyaka elishumi, iqela lohlalutyo elinobuchule obuphezulu, umxholo opheleleyo, kunye nenkxaso ebalaseleyo emva kokuthengisa.
●Inkxaso emva kokuthengisa:Ukuzibophelela kwethu kudlulela ngaphaya kokugqitywa kweprojekthi kunye nexesha leenkonzo emva kokuthengiswa kweenyanga ezi-3. Ngeli xesha, sinikezela ngokulandela iprojekthi, uncedo lokusombulula iingxaki, kunye neeseshoni ze-Q&A ukuphendula nayiphi na imibuzo enxulumene neziphumo.
●Amaqhinga amaninzi okulandelelanisa afumanekayo:Ngeenjongo ezahlukeneyo zophando kunye neemfuno zokuphelela kwe-genome.
Iinkcukacha zeNkonzo
| Inkonzo | Icebo Lokulandelelanisa |
| I-Genome eYilwayo | I-Illumina PE150 100x |
| 0 I-Genome yeGap | I-Nanopore 100x + Illumina PE150 100x Or I-Pacbio HiFi 30x + Illumina PE150 100x (ukhetho) |
Iimfuno zeSampuli:
| Uxinzelelo (ng/µL) | Isixa sisonke (µg) | Umthamo (µL) | OD260/280 | OD260/230 | |
| I-PacBio | ≥20 | ≥1.2 | ≥20 | 1.7-2.2 | ≥1.0 |
| I-Nanopore | ≥40 | ≥2 | ≥20 | 1.7-2.2 | 1.0-3.0 |
| I-Illumina | ≥1 | ≥0.06 | ≥20 | - | - |
· Iintsholongwane: ≥3.5x1010 iiseli
Ukuhamba komsebenzi wenkonzo
Ukuhanjiswa kwesampulu
Ukwakhiwa kweThala leeNcwadi
Ukulandelelana
Uhlalutyo lwedatha
Iinkonzo zasemva kokuthengisa
Kubandakanya uHlahlelo Olulandelayo:
● Ukulandelelanisa Ulawulo Lomgangatho Wedatha
● Ukuhlanganiswa kweGenome
● Uhlalutyo lweenxalenye zeGenome: Ukuqikelela ii-CDS kunye nezinto ezininzi ze-genomic
● Isichazi-magama esisebenzayo esineedathabheyisi ezininzi ngokubanzi (GO, KEGG, njl.njl.) kunye needathabheyisi eziphambili (CARD, VFDB, njl.njl.)
● Ukubona iiGene
Sibonelela nge-genome kwifomathi ekhawulezayo efikelelekayo kunye nefayile ye-genome annotation (gff).
Isichazi-magama se-Gene – GO
Isichazi-magama se-gene – iicarbohydrate ezi-CAZY
Ukuboniswa kwejinomu – iploti yeCircos
Hlola inkqubela phambili eququzelelwe ziinkonzo zokuhlanganisa iibhaktheriya ze-BMKGene ngokusebenzisa ingqokelela yeempapasho ezikhethiweyo.
UDai, W. et al. (2023) 'Ukufunyanwa kweBacteroides uniformis F18-22 njengeProbiotic Bacterium ekhuselekileyo nentsha yoNyango lweUlcerative Colitis evela kwiColon yabantu esempilweni',Ijenali yeHlabathi yeSayensi yeMolekyuli, 24(19), iphe. 14669. doi: 10.3390/IJMS241914669/S1.
UKang, Q. et al. (2021) 'I-Proteus mirabilis engamelaniyo namayeza amaninzi ithwala i-blaOXA-1 kunye ne-blandm-1 evela kwizilwanyana zasendle eTshayina: umngcipheko okhulayo kwimpilo yoluntu',I-Zoology edibeneyo, 16(6), iphepha 798-809. doi: 10.1111/1749-4877.12510.
UWang, TT et al. (2017) 'Ulandelelwano olupheleleyo lwe-genome ye-endophyte Bacillus flexus KLBMP 4941 ityhila indlela yayo yokukhuthaza ukukhula kwezityalo kunye nesiseko se-genetic sokunyamezela ityuwa',Ijenali yeBiotechnology, 260, iphepha 38-41. doi: 10.1016/J.JBIOTEC.2017.09.001.
UWang, X. et al. (2021) 'IiPlasmids zeKlebsiella eziNcinci zokuXhatshazwa kweeMpawu ze-Antimicrobial',Imida kwiMicrobiology, 12, iphe. 754931. doi: 10.3389/FMICB.2021.754931/BIBTEX.
