Hi-C raws li Genome Assembly
Kev Pabcuam Zoo
Txheej txheem cej luam ntawm Hi-C
(Lieberman-Aiden E thiab al.,Kev tshawb fawb, 2009)
● Tsis xav tau kev tsim cov noob caj noob ces rau contig anchoring;
● Cov cim cim ntau dua ua rau ntau dua contigs anchoring piv ntawm siab dua 90%;
● Ua kom muaj kev ntsuam xyuas thiab kho ntawm cov genome uas twb muaj lawm;
● Lub sijhawm tig rov qab luv dua nrog qhov tseeb dua hauv kev sib dhos genome;
● Muaj kev paub dhau los nrog ntau dua 1000 Hi-C tsev qiv ntawv tsim rau ntau dua 500 hom;
● Ntau tshaj 100 qhov teeb meem ua tiav nrog cov ntawv luam tawm cuam tshuam ntau dua 760;
● Hi-C raws li genome sib dhos rau polyploid genome, 100% anchoring tus nqi tau ua tiav hauv qhov project dhau los;
● In-house patents thiab software copyrights rau Hi-C thwmsim thiab cov ntaub ntawv tsom xam;
● Tus kheej-tsim visualized cov ntaub ntawv tuning software, enables phau ntawv thaiv txav, thim rov qab, tshem tawm thiab rov ua dua.
Service Specifications
|
Hom tsev qiv ntawv
|
Platform | Nyeem Length | Qhia tswv yim |
| Nyob zoo-C | Illumina NovaSeq | PEB 150 | ≥ 100 X |
Bioinformatics tsom xam
● Raw cov ntaub ntawv zoo tswj
● Hi-C lub tsev qiv ntawv zoo tswj
● Hi-C raws genome los ua ke
● Kev ntsuam xyuas tom qab sib dhos
Sample Requirements thiab Delivery
Cov Qauv Xav Tau:
| Tsiaj | Kab mob | Nroj tsuag
|
| Cov ntaub qhwv khov: 1-2g rau ib lub tsev qiv ntawv Cells: 1x 10^7 cells ib lub tsev qiv ntawv | Cov ntaub qhwv khov: 1g rau ib lub tsev qiv ntawv | Cov ntaub qhwv khov: 1-2g rau ib lub tsev qiv ntawv
|
| * Peb xav kom xa tsawg kawg 2 aliquots (1 g txhua) rau qhov kev sim Hi-C. | ||
Pom zoo coj mus kuaj
Ntim: 2 ml centrifuge tube (Tin foil tsis pom zoo)
Rau feem ntau ntawm cov qauv, peb pom zoo kom tsis txhob khaws cia hauv ethanol.
Sample labeling: Cov qauv yuav tsum tau sau kom meej meej thiab zoo ib yam rau xa cov qauv ntaub ntawv.
Kev Thauj Khoom: Dry-ice: Cov qauv yuav tsum tau ntim rau hauv hnab ua ntej thiab muab faus rau hauv cov dej khov qhuav.
Kev Pabcuam Ua Haujlwm Flow
Kev sim tsim
Qauv xa tuaj
DNA rho tawm
Kev tsim kho tsev qiv ntawv
Sequencing
Cov ntaub ntawv tsom xam
Kev pab cuam tom qab muag
*Cov txiaj ntsig tau pom ntawm no yog tag nrho los ntawm genomes luam tawm nrog Biomarker Technologies
1.Hi-C sib cuam tshuam tshav kub daim ntawv qhia ntawmCamptotheca acuminatagenome.Raws li pom nyob rau hauv daim ntawv qhia, qhov kev siv ntawm kev sib cuam tshuam yog tsis zoo correlated nrog linear nrug, uas qhia tau hais tias ib tug high-qib chromosome-theem sib dhos.(Anchoring ratio: 96.03%)
Kang M et al.,Nature Communications, 2021 ib
2.Hi-C pab txhawb kev siv tau ntawm kev hloov pauv ntawmGossypium pajL. TM-1 A06 thiabG. arboreumkev 06
Yang Z et al.,Nature Communications, 2019
3.Assembly thiab biallelic sib txawv ntawm cov cassava genome SC205.Hi-C heatmap qhia meej cais hauv homologous chromosomes.
Hu W et al.,Molecular Cog, 2021 ib
4.Hi-C heatmap ntawm ob hom Ficus genome los ua ke:F.microcarpa ua(anchoring ratio: 99.3%) thiabF.hispida (anchoring ratio: 99.7%)
Zhang X et al.,Cell, xyoo 2020
BMK Cas
Genomes ntawm tsob ntoo Banyan thiab pollinator Wasp muab kev nkag siab rau hauv Fig-wasp Coevolution
Luam tawm: Cell, xyoo 2020
Sequence Strategy:
F. microcarpa genome: kwv.84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)
F. hispidagenome: kwv.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)
Eupristina verticillatagenome: kwv.170 X PacBio RSII (65 Gb)
Cov txiaj ntsig tseem ceeb
1.Ob tug banyan ntoo genomes thiab ib tug pollinator wasp genome tau tsim siv PacBio sequencing, Hi-C thiab linkage map.
(1)F. microcarpagenome: Ib qho kev sib dhos ntawm 426 Mb (97.7% ntawm kwv yees genome loj) tau tsim nrog contig N50 ntawm 908 Kb, BUSCO qhab nia ntawm 95.6%.Nyob rau hauv tag nrho ntawm 423 Mb sequences tau anchored rau 13 chromosomes los ntawm Hi-C.Genome annotation yielded 29,416 protein-coding noob.
(2)F. Hispidagenome: Ib qho kev sib dhos ntawm 360 Mb (97.3% ntawm kwv yees genome loj) tau tawm los nrog contig N50 ntawm 492 Kb thiab BUSCO qhab nia ntawm 97.4%.Tag nrho ntawm 359 Mb ib ntus tau muab tso rau ntawm 14 chromosomes los ntawm Hi-C thiab zoo ib yam rau daim ntawv qhia kev sib txuas siab.
(3)Eupristina verticillatagenome: Ib qho kev sib dhos ntawm 387 Mb (Kev kwv yees genome loj: 382 Mb) tau tsim nrog contig N50 ntawm 3.1 Mb thiab BUSCO qhab nia ntawm 97.7%.
2.Comparative genomics tsom xam pom ntau tus qauv variations ntawm obFicusgenomes, uas muab cov peev txheej tseem ceeb ntawm cov caj ces rau kev hloov pauv hloov pauv hloov pauv.Txoj kev tshawb no, thawj zaug, muab kev nkag siab txog Fig-wasp coevolution ntawm genomic-theem.
 Circos daim duab ntawm genomic nta ntawm obFicusgenomes, suav nrog chromosomes, segmental duplications (SDs), transposons (LTR, TEs, DNA TEs), gene qhia thiab synteny |  Kev txheeb xyuas ntawm Y chromosome thiab kev txiav txim siab poj niam txiv neej tus neeg sib tw |
Zhang, X., et al."Genomes ntawm tsob ntoo Banyan thiab pollinator Wasp muab kev nkag siab rau hauv Fig-Wasp Coevolution."Cell 183.4 (2020).
