Mgbakọ Genome dabere na Hi-C
Uru ọrụ
Akụkọ ihe mere eme nke Hi-C
(Lieberman-Aiden E et al.,Sayensị, 2009)
● Ọ dịghị mkpa n'ịmepụta ọnụ ọgụgụ mkpụrụ ndụ ihe nketa maka ịgbachi nkịtị;
● Njupụta nrịbama dị elu nke na-eduga n'oke njigide contigs dị elu karịa 90%;
● Na-eme ka nyocha na mgbazi na mgbakọ genome dị ugbu a;
● Oge ntụgharị dị mkpirikpi na nhazi dị elu na mgbakọ genome;
● Ahụmahụ bara ụba na ụlọ akwụkwọ Hi-C karịrị 1000 arụpụtara maka ụdị 500;
● Ihe karịrị ikpe 100 nwere ihe ịga nke ọma nwere ihe mmetụta ebipụtala nke karịrị 760;
● Hi-C dabeere na genome mgbakọ maka polyploid genome, 100% anchoring ọnụego nwetara na mbụ oru ngo;
● Ikike ime ụlọ na ikike nwebisiinka ngwanrọ maka nyocha Hi-C na nyocha data;
● Akụrụngwa nlegharị data nlegharị anya nke emepụtara onwe ya, na-eme ka ngọngọ akwụkwọ ntuziaka na-emegharị, ịtụgharị, kagbuo na imegharị ya.
Nkọwapụta ọrụ
|
Ụdị ọba akwụkwọ
|
Platform | Gụọ Ogologo | Atụmatụ atụmatụ |
| Hi-C | Illumina NovaSeq | PE150 | ≥ 100X |
Nyocha bioinformatics
● Njikwa ogo data raw
● Hi-C njikwa mma ọbá akwụkwọ
● Mgbakọ genome dabeere na Hi-C
● Nlebanya mgbe mgbakọ gachara
Ihe nlele chọrọ na nnyefe
Ihe atụ chọrọ:
| Anụmanụ | Ero | Osisi
|
| Anụ oyi kpọnwụrụ: 1-2g kwa ọbá akwụkwọ Selụ: 1 x 10^7 sel kwa ọba akwụkwọ | Anụ oyi kpọnwụrụ: 1g kwa ọbá akwụkwọ | Anụ oyi kpọnwụrụ: 1-2g kwa ọbá akwụkwọ
|
| * Anyị na-akwado ike izipu opekata mpe 2 aliquots (1 g nke ọ bụla) maka nnwale Hi-C. | ||
Nnyefe nlele akwadoro
Akpa: 2 ml centrifuge tube (Tin foil adịghị akwadoro)
Maka ọtụtụ ihe atụ, anyị na-akwado ka ị ghara ichekwa na ethanol.
Ịkpọ aha nlele: Ọ dị mkpa ka e depụta ihe nlere anya nke ọma yana otu n'ụdị ozi nlele etinyere.
Mbupu: ice-akọrọ: A ga-ebu ụzọ tinye ihe nlele n'ime akpa wee lie ya na ice-akọrọ.
Usoro ọrụ ọrụ
Nnwale imewe
Nbufe ihe atụ
Mwepụta DNA
Ịrụ ụlọ akwụkwọ
Usoro
Nyocha data
Mgbe-ire ọrụ
*Nsonaazụ ngosi egosiri ebe a sitere na genome bipụtara na Teknụzụ Biomarker
1.Hi-C mmekọrịta okpomọkụ map nkeCamptotheca acuminatagenome.Dị ka egosiri na eserese ngosi, ike nke mmekọrịta na-emekọ ihe na-adịghị mma na anya nke ahịrị, nke na-egosi mgbakọ ọkwa chromosome zuru oke.(Nha mgbanaka: 96.03%)
Kang M et al.,Nkwukọrịta okike, 2021
2.Hi-C mere ka nkwenye nke ntụgharị n'etitiGossypium hirsutumL. TM-1 A06 naG. arboreumChr06
Yang Z et al.,Nkwukọrịta okike, 2019
3.Mgbakọ na ihe dị iche iche bialelic nke genome akpu SC205.Hi-C heatmap gosiri nkewa doro anya na chromosomes homologous.
Hu W et al.,Osisi Molecular, 2021
4.Hi-C heatmap na mgbakọ genome nke Ficus abụọ:F.microcarpa(nha nhata: 99.3%) naF.hispida (oke njigide: 99.7%)
Zhang X et al.,Cell, 2020
Okwu BMK
Genomes nke Osisi Banyan na Pollinator Wasp na-enye nghọta na Fig-wasp Coevolution
Ebipụtara: Cell, 2020
Atụmatụ usoro:
F. microcarpa genome: Ihe ruru.84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)
F. hispidagenome: Ihe ruru.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)
Eupristina verticillatagenome: Ihe ruru.170 X PacBio RSII (65 Gb)
Nsonaazụ igodo
1. Abụọ banyan osisi genomes na otu pollinator wasp genome ka e ji PacBio sequencing, Hi-C na linkage map rụrụ.
(1)F. microcarpagenome: Ewubere mgbakọ nke 426 Mb (97.7% nke nha genome e mere atụmatụ) na contig N50 nke 908 Kb, akara BUSCO nke 95.6%.Na mkpokọta usoro 423 Mb ka etinyere na chromosomes 13 site na Hi-C.Nkọwa genome wepụtara mkpụrụ ndụ ihe nketa protein 29,416.
(2)F. Hispidagenome: Mgbakọ nke 360 Mb (97.3% nke nha genome e mere atụmatụ) bụ nke nwere contig N50 nke 492 Kb na akara BUSCO nke 97.4%.Ngụkọta usoro 359 Mb ka edobere na chromosomes 14 site na Hi-C yana nke ukwuu na maapụ njikọ njupụta dị elu.
(3)Eupristina verticillatagenome: Mgbakọ nke 387 Mb (Egompụtara genome size: 382 Mb) ka edoro na contig N50 nke 3.1 Mb na akara BUSCO nke 97.7%.
2.Comparative genomics analysis kpughere ọnụ ọgụgụ dị ukwuu nke nhazi ọdịiche n'etiti abụọFicusgenomes, nke nyere mkpụrụ ndụ ihe nketa bara uru maka ọmụmụ evolushọn na-agbanwe agbanwe.Ọmụmụ ihe a, maka oge mbụ, nyere nghọta na Fig-wasp coevolution na ọkwa genomic.
 Ihe osise Circos na njirimara genomic nke abụọFicusgenomes, gụnyere chromosomes, mbiputegharị akụkụ (SDs), transposons (LTR, TEs, DNA TEs), okwu mkpụrụ ndụ ihe nketa na synteny. |  Nchọpụta nke chromosome Y na mkpụrụ ndụ ihe nketa maka mmekọ nwoke na nwanyị |
Zhang, X., et al."Genomes nke Osisi Banyan na Pollinator Wasp na-enye nghọta n'ime Fig-Wasp Coevolution."Cell 183.4 (2020).
