I-Hi-C Based Genome Assembly
I-Hi-C iyindlela edizayinelwe ukuthwebula ukucushwa kwe-chromosome ngokuhlanganisa ukusebenzelana okusekelwe ekuhloleni kanye nokulandelana komphumela ophezulu. Ukuqina kwalokhu kusebenzisana kukholakala ukuthi kuhlotshaniswa kabi nebanga elingokomzimba kuma-chromosome. Ngakho-ke, idatha ye-Hi-C isetshenziselwa ukuqondisa ukuhlanganisa, ukuhleleka, nokuqondiswa kokulandelana okuhlanganisiwe ku-genome esalungiswa kanye nokunamathisela lezo ezinombolweni ezithile zama-chromosome. Lobu buchwepheshe bunika amandla ukuhlangana kweleveli ye-chromosome yofuzo lapho ingekho imephu yofuzo esekelwe kubantu. Yonke i-genome eyodwa idinga i-Hi-C.
Izici Zesevisi
● Ukulandelanisa ku-Illumina NovaSeq nge-PE150.
● Isevisi idinga amasampula ezicubu, esikhundleni sama-nucleic acid akhishiwe, ukuze axhumane ne-formaldehyde futhi alondoloze ukusebenzisana kwe-DNA-protein.
● Ukuhlolwa kwe-Hi-C kuhilela ukukhawulela kanye nokuqeda ukulungiswa kweziphetho ezinamathelayo nge-biotin, okulandelwa ukuzungeza kweziphetho ezibuthuntu eziwumphumela kuyilapho kugcinwa ukuxhumana. I-DNA ibe isidonselwa phansi ngobuhlalu be-streptavidin futhi ihlanzwe ukuze kulungiswe umtapo wolwazi.
Izinzuzo Zesevisi
Uhlolojikelele lwe-Hi-C
(Lieberman-Aiden Et al.,Isayensi, 2009)
●Ukuqeda Isidingo Sedatha Yezibalo Zezakhi Zofuzo:I-Hi-C ithatha indawo yolwazi olubalulekile oludingekayo ukuze kufakwe i-contig anchoring.
●Ukuminyana komaka okuphezulu:okuholela esilinganisweni esiphezulu se-contig anchoring esingaphezu kwama-90%.
●Amarekhodi Obungcweti Olubanzi nokushicilela:I-BMKGene inokuhlangenwe nakho okubanzi ngamacala angaphezu kuka-2000 e-Hi-C Genome Assembly evela ezinhlotsheni eziyi-1000 ezihlukene kanye namalungelo obunikazi ahlukahlukene. Amacala ashicilelwe angaphezu kuka-200 anesici esinqwabelene esingaphezu kuka-2000.
●Ithimba le-bioinformatics elinamakhono aphezulu:enamalungelo obunikazi angaphakathi namalungelo e-software okuhlolwa kwe-Hi-C nokuhlaziywa kwedatha, isofthiwe yedatha yokubona ethuthukisiwe yenza ibhulokhi inyakaze, ihlehlise, ihoxise, yenze kabusha.
●Ukusekelwa Kwangemva Kokuthengisa:Ukuzinikela kwethu kudlulela ngalé kokuphothulwa kwephrojekthi ngenkathi yesevisi yezinyanga ezi-3 ngemva kokuthengisa. Ngalesi sikhathi, sinikezela ngokulandelelwa kwephrojekthi, usizo lokuxazulula inkinga, namaseshini e-Q&A ukuze siphendule noma yimiphi imibuzo ehlobene nemiphumela.
●Isichasiselo Esibanzi: sisebenzisa imininingo egciniwe eminingi ukuze sichaze ngokusebenza izakhi zofuzo ngokuhluka okukhonjiwe futhi senze ukuhlaziya okunothisayo okuhambisanayo, sinikeze imininingwane kumaphrojekthi amaningi ocwaningo.
Imininingwane Yesevisi
| Ukulungiswa komtapo wolwazi | Isu lokulandelanisa | Okuphumayo kwedatha okunconyiwe | Ikhwalithi yokulawula |
| Umtapo wezincwadi we-Hi-C | I-Illumina NovaSeq PE150 | 100x | Q30 ≥ 85% |
Izidingo Zesampula
| Izicubu | Inani elidingekayo |
| I-Animal Viscera | ≥ 2 g |
| Imisipha Yezilwane | |
| Igazi Lezilwane Ezincelisayo | ≥ 2 ml |
| Inyama yenkukhu/Inhlanzi Igazi | |
| Isitshalo- Iqabunga Elisha | ≥ 3 g |
| Amaseli Cultured | ≥ 1x107 |
| Isinambuzane | ≥ 2 g |
Ukugeleza Komsebenzi Wesevisi
Idizayini yokuhlola
Ukulethwa kwesampula
Ukwakhiwa komtapo wolwazi
Ukulandelanisa
Ukuhlaziywa kwedatha
Amasevisi angemuva kokuthengisa
1) Idatha eluhlaza ye-QC
2) Ilabhulali ye-Hi-C ye-QC: isilinganiso sokusebenzisana okuvumelekile kwe-Hi-C
3) Umhlangano we-Hi-C: ukuhlanganisa ama-contig ngamaqembu, kulandelwa ukuhleleka kwe-contig ngaphakathi kweqembu ngalinye nokwabela ukuqondiswa kwe-contig
4) Ukuhlolwa kwe-Hi-C
I-Hi-C Library QC – isilinganiso samapheya okusebenzisana avumelekile e-Hi-C
I-Hi-C Assembly - izibalo
Ukuhlolwa kwe-post-assembly - imephu yokushisa yokuqina kwesignali phakathi kwemigqomo
Hlola intuthuko egqugquzelwa amasevisi omhlangano we-BMKGene we-Hi-C ngeqoqo elikhethiwe lokushicilelwe.
Tian, T. et al. (2023) 'Ukuhlanganiswa kwe-Genome kanye nokuhlukaniswa kofuzo kwegciwane lommbila elivelele elimelana nesomiso', Nature Genetics 2023 55:3, 55(3), pp. 496–506. doi: 10.1038/s41588-023-01297-y.
Wang, ZL et al. (2020) 'I-Chromosome-Scale Assembly ye-Asian Honeybee Apis cerana Genome', Frontiers in Genetics, 11, p. 524140. doi: 10.3389/FGENE.2020.00279/BIBTEX.
U-Zhang, F. et al. (2023) 'Ukwembula ukuvela kwe-tropane alkaloid biosynthesis ngokuhlaziya ama-genomes amabili emndenini we-Solanaceae', Nature Communications 2023 14:1, 14(1), pp. 1–18. doi: 10.1038/s41467-023-37133-4.
U-Zhang, X. et al. (2020) 'I-Genomes of the Banyan Tree kanye Ne-Pollinator Wasp Ihlinzeka Ngemininingwane ku-Fig-Wasp Coevolution', Iseli, 183(4), amakhasi 875-889.e17. doi: 10.1016/J.CELL.2020.09.043
