Hi-C Based Genome Assembly
Hi-C ndi njira yomwe idapangidwa kuti ijambule masinthidwe a chromosome pophatikiza kuyesa kuyanjana kochokera kufupi ndi kutsata kwapamwamba. Kukula kwa kuyanjana uku kumakhulupirira kuti kumalumikizidwa moyipa ndi kutalika kwa ma chromosome. Chifukwa chake, data ya Hi-C imagwiritsidwa ntchito kutsogolera kusanja, kuyitanitsa, ndi kalozera wa ma kromozomu omwe asonkhanitsidwa mumtundu wokonzekera ndikumangirira ma chromosome angapo. Ukadaulo uwu umathandizira kuphatikiza kwa ma chromosome genome pakalibe mapu otengera kuchuluka kwa anthu. Genome iliyonse imafunikira Hi-C.
Mawonekedwe a Utumiki
● Kutsata pa Illumina NovaSeq ndi PE150.
● Kutumikira kumafuna zitsanzo za minofu, m'malo mwa nucleic acids, kuti zigwirizane ndi formaldehyde ndi kuteteza kugwirizana kwa DNA ndi mapuloteni.
● Kuyesera kwa Hi-C kumaphatikizapo kuletsa ndi kukonza mapeto a zomata ndi biotin, kutsatiridwa ndi kuzunguliza kwa mapeto osamveka bwino pamene mukusunga kuyanjana. DNA imakokedwa pansi ndi mikanda ya streptavidin ndikuyeretsedwa kuti ikonzekere laibulale.
Ubwino wa Utumiki
Zithunzi za Hi-C
(Lieberman-Aiden Et al.,Sayansi, 2009)
●Kuthetsa Kufunika kwa Ma Genetic Population Data:Hi-C imalowa m'malo mwa chidziwitso chofunikira chofunikira pakuyimitsa contig.
●Kachulukidwe chikhomo chachikulu:zomwe zimatsogolera ku chiŵerengero chapamwamba cha contig anchoring pamwamba pa 90%.
●Mbiri Yambiri Yaukatswiri ndi zofalitsa:BMKGene ili ndi chidziwitso chambiri ndi milandu yopitilira 2000 ya Hi-C Genome Assembly kuchokera ku mitundu 1000 yosiyanasiyana ndi ma patent osiyanasiyana. Milandu yopitilira 200 yosindikizidwa ili ndi kuchuluka kwamphamvu kopitilira 2000.
●Gulu laukadaulo la bioinformatics:yokhala ndi ma patent a m'nyumba ndi ma copyright a mapulogalamu a zoyeserera za Hi-C ndi kusanthula deta, pulogalamu yodzipangira yokha yowonera imathandizira chipika chamanja kuyenda, kubweza, kubweza, ndikukonzanso.
●Thandizo Pambuyo Pakugulitsa:Kudzipereka kwathu kumapitilira kutha kwa projekiti ndi nthawi ya miyezi itatu mutagulitsa. Panthawiyi, timapereka zotsatila za polojekiti, chithandizo chazovuta, ndi magawo a Q&A kuti tiyankhe mafunso aliwonse okhudzana ndi zotsatira.
●Mawu Omveka: Timagwiritsa ntchito nkhokwe zingapo kuti tifotokoze bwino zamitundu yosiyanasiyana ndikuchita kusanthula kofananirako, kupereka zidziwitso pama projekiti angapo ofufuza.
Mafotokozedwe a Utumiki
| Kukonzekera laibulale | Njira yotsatirira | Kutulutsa kovomerezeka kwa data | Kuwongolera khalidwe |
| Hi-C library | Illumina NovaSeq PE150 | 100x pa | Q30 ≥ 85% |
Zitsanzo Zofunika
| Minofu | Ndalama zofunika |
| Animal Viscera | ≥ 2 g |
| Minofu Yanyama | |
| Mammalian Blood | ≥ 2 ml |
| Nkhuku/Nsomba Magazi | |
| Chomera - Tsamba Latsopano | ≥ 3 g |
| Maselo Okhazikika | ≥ 1x107 |
| Tizilombo | ≥ 2 g |
Kuyenda kwa Ntchito Yantchito
Kuyesera kupanga
Kupereka zitsanzo
Kumanga laibulale
Kutsata
Kusanthula deta
Pambuyo pogulitsa ntchito
1) Data yaiwisi QC
2) Hi-C laibulale ya QC: kuyerekezera kovomerezeka kwa Hi-C
3) Msonkhano wa Hi-C: kuphatikiza kwa ma contig m'magulu, kutsatiridwa ndi kuyitanitsa ma contig mkati mwa gulu lililonse ndikugawa mawonekedwe a contig
4) Kuwunika kwa Hi-C
Hi-C Library QC - kuyerekezera kwa mawiri a Hi-C ovomerezeka
Hi-C Assembly - ziwerengero
Kuwunika kwapambuyo-msonkhano - mapu a kutentha kwamphamvu pakati pa nkhokwe
Onani kupita patsogolo komwe kumayendetsedwa ndi misonkhano ya BMKGene ya Hi-C kudzera m'magulu osindikizidwa.
Tian, T. et al. (2023) 'Genome assembly and genetic dissection ya majeremusi odziwika bwino olimbana ndi chilala', Nature Genetics 2023 55:3, 55(3), pp. 496-506. doi: 10.1038/s41588-023-01297-y.
Wang, ZL ndi al. (2020) 'A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome', Frontiers in Genetics, 11, p. 524140. doi: 10.3389/FGENE.2020.00279/BIBTEX.
Zhang, F. et al. (2023) 'Kuwulula kusinthika kwa tropane alkaloid biosynthesis mwa kusanthula ma genomes awiri mubanja la Solanaceae', Nature Communications 2023 14: 1, 14 (1), pp. 1-18. doi: 10.1038/s41467-023-37133-4.
Zhang, X. et al. (2020) 'Genomes of the Banyan Tree and Pollinator Wasp Amapereka Kuzindikira mu Fig-Wasp Coevolution', Cell, 183(4), pp. 875-889.e17. doi: 10.1016/J.CELL.2020.09.043
