I-Hi-C based Genome Assembly
Izinzuzo Zesevisi
Uhlolojikelele lwe-Hi-C
(Lieberman-Aiden Et al.,Isayensi, 2009)
● Asikho isidingo sokwakha izakhi zofuzo ukuze kuqiniswe i-contig anchoring;
● Ukuminyana komaka okuphezulu okuholela esilinganisweni esiphezulu sokubambelela ama-contigs ngaphezu kuka-90%;
● Inika amandla ukuhlolwa nezilungiso kuma-genome assemblies akhona;
● Isikhathi esifushane sokuguqula ngokunemba okuphezulu ekuhlanganiseni kofuzo;
● Ulwazi oluningi ngemitapo yolwazi ye-Hi-C engaphezu kuka-1000 eyakhelwe izinhlobo ezingaphezu kuka-500;
● Amacala angaphezu kwe-100 aphumelele anesici esikhulayo esishicilelwe esingaphezu kuka-760;
● Ukuhlanganiswa kwegenome okusekelwe ku-Hi-C ye-polyploid genome, isilinganiso esingu-100% sokubambelela sifinyelelwe kuphrojekthi yangaphambilini;
● Amalungelo obunikazi angaphakathi namalungelo esofthiwe okuhlolwa kwe-Hi-C nokuhlaziywa kwedatha;
● Isofthiwe yokushuna idatha ezithuthuke ngokwayo, yenza amabhlogo anyakazayo, ahlehlise, ahoxiswe futhi enze futhi.
Imininingwane Yesevisi
|
Uhlobo Lwelabhulali
|
Inkundla | Funda Ubude | Ncoma Isu |
| Hi-C | Illumina NovaSeq | I-PE150 | ≥ 100X |
I-Bioinformatics ihlaziya
● Ukulawulwa kwekhwalithi yedatha eluhlaza
● Ukulawula ikhwalithi yelabhulali ye-Hi-C
● Ukuhlanganiswa kwegenome okusekelwe ku-Hi-C
● Ukuhlolwa kwangemva komhlangano
Izidingo Zesampula Nokulethwa
Izimfuneko zesampula:
| Isilwane | Isikhunta | Izitshalo
|
| Izicubu eziqandisiwe: 1-2g umtapo ngamunye Amaseli: 1x 10^7 amaseli kulabhulali ngayinye | Izicubu eziqandisiwe: 1g umtapo wolwazi ngamunye | Izicubu eziqandisiwe: 1-2g umtapo ngamunye
|
| *Sincoma ngokuqinile ukuthi uthumele okungenani ama-aliquots angu-2 (1 g ngalinye) ocwaningweni lwe-Hi-C. | ||
Ukulethwa Kwesampula Okunconyiwe
Isitsha: 2 ml centrifuge tube (Tin foil ayinconywa)
Kumasampuli amaningi, sincoma ukuthi ungagcini ku-ethanol.
Isampula yokulebula: Amasampuli adinga ukulebula ngokucacile futhi afane nefomu lesampula lolwazi elithunyelwe.
Ukuthunyelwa: Iqhwa elomile: Amasampula adinga ukupakishwa ezikhwameni kuqala futhi agqitshwe eqhweni elomile.
Ukugeleza Komsebenzi Wesevisi
Idizayini yokuhlola
Ukulethwa kwesampula
Ukukhishwa kwe-DNA
Ukwakhiwa komtapo wolwazi
Ukulandelanisa
Ukuhlaziywa kwedatha
Amasevisi angemuva kokuthengisa
*Imiphumela yedemo eboniswe lapha yonke ivela kuzakhi zofuzo ezishicilelwe nge-Biomarker Technologies
Imephu yokushisa yokusebenzelana ye-1.Hi-C yeI-Camptotheca acuminatai-genome.Njengoba kuboniswe kumephu, ukushuba kokusebenzelana kuhlotshaniswa kabi nebanga lomugqa, okubonisa ukuhlangana kweleveli yekhromosome enembe kakhulu.(Isilinganiso sokumisa: 96.03%)
Kang M et al.,Ukuxhumana Kwemvelo, 2021
I-2.I-Hi-C yenze lula ukuqinisekiswa kokuguquguquka phakathiI-Gossypium hirsutumL. TM-1 A06 kanyeG. arboreumChr06
Yang Z et al.,Ezokuxhumana Ngemvelo, 2019
3.Ukuhlangana nokuhlukaniswa kwe-biallelic ye-cassava genome SC205.Imephu yokushisa ye-Hi-C ibonisiwe ukuhlukana okucacile kuma-chromosome angama-homologous.
Hu W et al.,Isitshalo samangqamuzana, 2021
Imephu yokushisa ye-4.Hi-C ekuhlanganiseni kwezinhlobo ezimbili ze-Ficus genome:F.microcarpa(isilinganiso sokunamathisela: 99.3%) kanyeI-F.hispida (i-anchoring ratio: 99.7%)
UZhang X nabanye,Iseli, 2020
Icala le-BMK
I-Genomes Yesihlahla Se-Banyan Kanye Ne-Pollinator Wasp Ihlinzeka Ngemininingwane Nge-Fig-wasp Coevolution
Kushicilelwe: Iseli, 2020
Isu lokulandelanisa:
F. microcarpa i-genome: Approx.84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)
F. hispidai-genome: Approx.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)
I-verticillata eqoshiwei-genome: Approx.170 X PacBio RSII (65 Gb)
Imiphumela esemqoka
1.Izinhlobo ezimbili ze-banyan tree genome kanye ne-pollinator wasp genome kwakhiwe kusetshenziswa ukulandelana kwe-PacBio, i-Hi-C kanye nemephu yokuxhumanisa.
(1)F. microcarpai-genome: I-assembly ye-426 Mb (97.7% yesilinganiso sosayizi we-genome) yasungulwa nge-contig N50 ye-908 Kb, isikolo se-BUSCO sama-95.6%.Sekukonke ukulandelana okungu-423 Mb kugxilwe kuma-chromosome angu-13 ngu-Hi-C.Isichasiselo se-Genome sikhiqize ama-protein-coding genes angu-29,416.
(2)F. Hispidai-genome: Ukuhlanganiswa kwe-360 Mb (97.3% yosayizi olinganiselwe we-genome) kutholwe nge-contig N50 ye-492 Kb kanye nesikolo se-BUSCO sama-97.4%.Isamba sokulandelana okungu-359 Mb kugxilwe kuma-chromosome angu-14 yi-Hi-C futhi kufana kakhulu nemephu yokuxhumanisa enokuminyana okuphezulu.
(3)I-verticillata eqoshiwei-genome: Umhlangano wama-387 Mb (Usayizi olinganiselwe we-genome: 382 Mb) wasungulwa nge-contig N50 ye-3.1 Mb kanye nesikolo se-BUSCO sama-97.7%.
2. Ukuhlaziywa kwe-genomics yokuqhathanisa kwembula inani elikhulu lokwehluka kwesakhiwo phakathi kokubiliI-Ficusama-genomes, ahlinzeke ngensiza yofuzo eyigugu yezifundo zokuziphendukela kwemvelo.Lolu cwaningo, ngokokuqala ngqá, lunikeze imininingwane mayelana ne-Fig-wasp coevolution ezingeni le-genomic.
 Umdwebo we-Circos ezicini ze-genomic ezimbiliI-Ficusama-genomes, okuhlanganisa ama-chromosome, ukuphindaphindeka kwesigaba (SDs), ama-transposon (LTR, TEs, DNA TEs), ukubonakaliswa kofuzo kanye ne-synteny |  Ukuhlonza i-chromosome engu-Y kanye nofuzo lwekhandidethi lokunquma ubulili |
UZhang, X., et al."Ama-Genomes of the Banyan Tree kanye Ne-Pollinator Wasp Ahlinzeka Ngemininingwane Nge-Fig-Wasp Coevolution."Iseli 183.4(2020).
