INdibano yeGenome esekwe kwi-Hi-C
Iinkonzo eziluncedo
Isishwankathelo se-Hi-C
(uLieberman-Aiden Et al.,Inzululwazi, 2009)
● Akukho mfuneko yokuba kwakhiwe inani lemfuzo ukuze kufakwe i-ankile;
● Uxinaniso lwamanqaku oluphezulu olukhokelela kumlinganiselo ophezulu we-ankile we-contigs ngaphezulu kwe-90%;
● Yenza uvavanyo kunye nezilungiso kwiiassemblies ezikhoyo zegenome;
● Ixesha elifutshane lokujika-jika ngokuchaneka okuphezulu kwindibano ye-genome;
● Amava amaninzi anamathala eencwadi e-Hi-C angaphezu kwe-1000 akhelwe iintlobo ezingaphezu kwama-500;
● Ngaphezulu kwe-100 leemeko eziyimpumelelo ezinempembelelo eyongezelelweyo epapashiweyo engaphezu kwama-760;
● I-Hi-C based genome assembly ye-polyploid genome, i-100% yezinga le-anchoring yaphunyezwa kwiprojekthi yangaphambili;
● Ilungelo elilodwa lomenzi wechiza angaphakathi kunye namalungelo esoftware yeemfuniselo ze-Hi-C kunye nohlalutyo lwedatha;
● Isoftware ephuhliswe ngokwayo yokulungisa idatha, yenza ukuba ibhloko ishukunyiswe ngesandla, ijikwe, irhoxiswe kwaye iphinde yenziwe.
IiNgcaciso zeNkonzo
|
Uhlobo lweThala leencwadi
|
Iqonga | Funda Ubude | Cebisa iQhinga |
| Hi-C | Illumina NovaSeq | PE150 | ≥ 100X |
Uhlalutyo lwe-Bioinformatics
● Ulawulo lomgangatho wedatha ekrwada
● Ulawulo lomgangatho wethala leencwadi le-Hi-C
● Hi-C based genome assembly
● Uvandlakanyo lwasemva kwendibano
IiMfuno zeSampulu kunye nokuhanjiswa
IiMfuno zeSampulu:
| Isilwanyana | Umngundo | Izityalo
|
| Ithishu ekhenkcezisiweyo: 1-2g kwithala leencwadi ngalinye Iiseli: 1x 10^7 iiseli kwithala leencwadi ngalinye | Ithishu ekhenkcezisiweyo: 1g kwithala leencwadi ngalinye | Ithishu ekhenkcezisiweyo: 1-2g kwithala leencwadi ngalinye
|
| *Sicebisa ngamandla ukuba sithumele ubuncinane ii-aliquots ezi-2 (1 g nganye) kumfuniselo we-Hi-C. | ||
Unikezelo lweSampuli eCetyisiweyo
Isikhongozeli: 2 ml centrifuge ityhubhu (Ifoyile yeTin ayikhuthazwa)
Kwiisampulu ezininzi, sincoma ukuba ungayigcini kwi-ethanol.
Iisampulu zokufakwa ileyibhile: Iisampulu kufuneka zibhalwe ngokucacileyo kwaye zifane nefom yesampulu yolwazi engenisiweyo.
Ukuthumela: Umkhenkce owomileyo: Iisampulu kufuneka zipakishwe kwiingxowa kuqala kwaye zingcwatywe kwindawo eyomileyo.
Ukuhamba komsebenzi weNkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampuli
Ukutsalwa kwe-DNA
Ukwakhiwa kwethala leencwadi
Ukulandelelanisa
Uhlalutyo lwedatha
Iinkonzo emva kokuthengisa
*Iziphumo zedemo eziboniswe apha zonke zivela kwiigenomes ezipapashwe ngeBiomarker Technologies
1.Hi-C imephu yobudlelwane bobushushu beCamptotheca acuminataigenome.Njengoko kubonisiwe kwimephu, ubunzulu bonxibelelwano bunxulunyaniswa kakubi nomgama womgca, obonisa indibano yomgangatho wechromosome echaneke kakhulu.(Umlinganiselo we-Anchoring: 96.03%)
Kang M et al.,Unxibelelwano lweNdalo, 2021
I-2.Hi-C iququzelele ukuqinisekiswa kokuguqulwa phakathiGossypium hirsutumL. TM-1 A06 kunyeG. arboreumChr06
Yang Z et al.,Unxibelelwano ngeNdalo, ngo-2019
3.I-Assembly kunye ne-biallelic umahluko we-cassava genome SC205.Imephu yobushushu ye-Hi-C ibonisiwe ukwahlulwa okucacileyo kwiichromosomes ezilinganayo.
Hu W et al.,Isityalo seemolekyuli, 2021
Imephu yokufudumala ye-4.Hi-C kwiintlobo ezimbini ze-Ficus genome assembly:F.microcarpa(i-anchoring ratio: 99.3%) kunyeF.hispida (umlinganiselo we-anchoring: 99.7%)
UZhang X et al.,Iseli, 2020
Ityala le-BMK
IiGenomes zoMthi weBanyan kunye nePollinator Wasp zibonelela ngokuqonda kwiFig-wasp Coevolution
Ipapashiwe: Iseli, 2020
Iqhinga lokulandelelanisa:
F. microcarpa igenome: malunga.I-84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)
F. hispidaigenome: malunga.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)
Ehlotyeni verticillataigenome: malunga.170 X PacBio RSII (65 Gb)
Iziphumo eziphambili
1.Ijenomes ezimbini ze-banyan tree kunye ne-pollinator wasp genome zakhiwa kusetyenziswa ulandelelwano lwe-PacBio, i-Hi-C kunye nemephu yonxibelelano.
(1)F. microcarpaI-genome: Indibano ye-426 Mb (i-97.7% yobungakanani obuqikelelweyo be-genome) yasekwa kunye ne-contig N50 ye-908 Kb, i-BUSCO inqaku le-95.6%.Iyonke yolandelelwano lwe-423 Mb lufakwe kwiichromosomes ze-13 ngu-Hi-C.Inkcazo ye-Genome ivelise i-29,416 ye-protein-coding genes.
(2)F. Hispidai-genome: Indibano ye-360 Mb (i-97.3% yobungakanani obuqikelelweyo be-genome) ivelise i-contig N50 ye-492 Kb kunye ne-BUSCO amanqaku e-97.4%.Iyonke yolandelelwano lwe-359 Mb lugxininiswe kwiichromosomes ezili-14 ngu-Hi-C kwaye zifana kakhulu nemephu yoqhagamshelwano oluphezulu.
(3)Ehlotyeni verticillataI-genome: Indibano ye-387 Mb (Ubungakanani obuqikelelweyo be-genome: 382 Mb) yasekwa nge-contig N50 ye-3.1 Mb kunye ne-BUSCO amanqaku angama-97.7%.
2.Uhlalutyo lwe-genomics oluthelekisayo luveze inani elikhulu lokwahluka kwesakhiwo phakathi kwesibiniFicusiigenomes, ezibonelele ngezibonelelo zemfuzo ezixabiseke kakhulu kwizifundo zendaleko eziguqukayo.Olu phononongo, okokuqala, lubonelele ngengqiqo kwiFig-wasp coevolution kwinqanaba le-genomic.
 Umzobo weCircos kwiimpawu zegenomic ezimbiniFicusiigenomes, kubandakanywa iichromosomes, ukuphindaphindwa kwecandelo (SDs), transposons(LTR, TEs, DNA TEs), ukubonakaliswa kofuzo kunye nesynteny |  Ukuchongwa kwe-chromosome ye-Y kunye nejini yomviwa wokuzimisela ngokwesondo |
UZhang, X., kunye nabanye.“IiGenomes zoMthi weBanyan kunye nePollinator Wasp zibonelela ngeembono ngeFig-Wasp Coevolution.”Iseli 183.4(2020).
