Zogulitsa

Hi-C yochokera ku Genome Assembly

Hi-C based Genome Assembly Featured Image

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 imatha kuwongolera kusanjika, kuyitanitsa ndi kuwongolera katsatidwe kamene kamasonkhanitsidwa mumtundu wa ma genome ndikumangirira iwo pamitundu ina ya ma chromosome.Ukadaulo uwu umathandizira kuphatikiza kwa ma chromosome genome popanda mapu otengera kuchuluka kwa anthu.Genome iliyonse imafunikira Hi-C.

Pulatifomu: Illumina NovaSeq Platform / DNBSEQ

Lumikizanani nafe

Tsatanetsatane wa Utumiki

Zotsatira za Demo

Nkhani Yophunzira

Ubwino wa Utumiki

Zithunzi za Hi-C
(Lieberman-Aiden Et al.,Sayansi, 2009)

● Palibe chifukwa chopanga chibadwa cha anthu kuti akhazikike;
● Kuchulukirachulukira kwa chikhomo kumatsogolera ku chiŵerengero chapamwamba cha contigs choyikira pamwamba pa 90%;
● Imathandizira kuwunika ndi kukonza pamagulu omwe alipo kale;
● Kufupikitsa nthawi yozungulira ndi yolondola kwambiri pakupanga ma genome;
● Kudziwa zambiri ndi malaibulale opitilira 1000 a Hi-C omangidwa amitundu yopitilira 500;
● Milandu yopitilira 100 yopambana ndipo kuchuluka kwake komwe kumasindikizidwa kupitilira 760;
● Hi-C based genome Assembly for polyploid genome, 100% anchoring rate inakwaniritsidwa mu ntchito yapitayi;
● Ma patent a m'nyumba ndi zokopera za mapulogalamu a zoyesera za Hi-C ndi kusanthula deta;
● Pulogalamu yodzipangira yokha yowonera deta, imathandizira chipika chamanja kuyenda, kubweza, kubweza ndikusinthanso.

Mafotokozedwe a Utumiki

Mtundu wa Library

nsanja

Werengani Utali

Ndibwino Njira

Hi-C

Illumina NovaSeq

Mtengo wa PE150

≥ 100X

Bioinformatics kusanthula

● Kuwongolera khalidwe la data yaiwisi

● Kuwongolera khalidwe laibulale ya Hi-C

● Hi-C based genome assembly

● Kupenda pambuyo pa msonkhano

Zitsanzo Zofunika ndi Kutumiza

Zitsanzo Zofunika:

Nyama	Bowa	Zomera
Minofu yachisanu: 1-2g pa laibulale Maselo: 1x 10^maselo 7 pa laibulale iliyonse	Minofu yozizira: 1g pa laibulale iliyonse	Minofu yachisanu: 1-2g pa laibulale
*Timalimbikitsa kwambiri kutumiza ma aliquots osachepera 2 (1 g iliyonse) pakuyesera kwa Hi-C.

Kutumiza Kwachitsanzo Kovomerezeka

Chidebe: 2 ml centrifuge chubu (zojambula za malata ndizosavomerezeka)
Pazitsanzo zambiri, timalimbikitsa kuti musasunge ethanol.
Zitsanzo zolembetsera: Zitsanzo ziyenera kulembedwa momveka bwino komanso zofanana ndi zomwe zatumizidwa.
Kutumiza: Owuma-Izi: Zitsanzo ziyenera kulongedzedwa m'matumba kaye ndikukwiriridwa mu ayezi wouma.

Kuyenda kwa Ntchito Yantchito

Kuyesera kupanga

Kupereka zitsanzo

Kutulutsa kwa DNA

Kumanga laibulale

Kutsata

Kusanthula deta

Pambuyo pogulitsa ntchito

Zam'mbuyo: Zomera / Zinyama za De Novo Genome Sequencing

Ena: Evolutionary Genetics

*Zotsatira zowonetsedwa pano zonse zidachokera ku ma genome omwe amasindikizidwa ndi Biomarker Technologies

1.Hi-C kuyanjana kutentha mapu aCamptotheca acuminatagenome.Monga momwe ziwonetsedwera pamapu, kuchulukira kwa kuyanjana kumalumikizidwa moyipa ndi mtunda wa mzere, zomwe zikuwonetsa kusonkhana kwamlingo wolondola kwambiri wa chromosome.(Chiŵerengero chokhazikika: 96.03%)

3Hi-C-interaction-heatmap-showing-contigs-anchoring-in-genome-assembly

Kang M et al.,Nature Communications, 2021

2.Hi-C idathandizira kutsimikizika kwa ma inversions pakatiGossypium hirsutumL. TM-1 A06 ndiG. arboreumChr06

4Hi-C-heatmap-amathandizira-kuwulula-kwa-inversions-pakati-ma genome

Yang Z et al.,Natural Communications, 2019

3.Assembly and biallelic differentiation of cassava genome SC205.Mapu a kutentha kwa Hi-C akuwonetsedwa momveka bwino mu ma chromosomes ofanana.

5Hi-C-heatmap-showing-homologous-chromosomes

Hu W et al.,Chomera cha Molecular, 2021

4.Hi-C kutentha kwamitundu iwiri ya Ficus genome msonkhano:F.microcarpa(chiŵerengero chokhazikika: 99.3%) ndiF.hispida (chiŵerengero chokhazikika: 99.7%)
6Hi-C-heatmap-kuwonetsa-contig-anchoring-of-Ficus-genomes

Zhang X et al.,Selo, 2020

BMK Case

Ma genomes a Mtengo wa Banyan ndi mavu a Pollinator Amapereka chidziwitso mu Coevolution ya Fig-wasp

Lofalitsidwa: Selo, 2020

Njira yotsatirira:

F. microcarpa genome: Pafupifupi.84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)

F. hispidagenome: Pafupifupi.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)

Chithunzi cha verticillatagenome: Pafupifupi.170 X PacBio RSII (65 Gb)

Zotsatira zazikulu

1. Mitundu iwiri ya mavu a mitengo ya banyan ndi genome imodzi ya mavu adapangidwa pogwiritsa ntchito njira za PacBio, Hi-C ndi mapu olumikizana.
(1)F. microcarpagenome: Msonkhano wa 426 Mb (97.7% ya kukula kwa genome) unakhazikitsidwa ndi contig N50 ya 908 Kb, BUSCO mphambu ya 95.6%.Zotsatizana zonse za 423 Mb zidalumikizidwa ku ma chromosome 13 ndi Hi-C.Mawu ofotokozera a genome adatulutsa ma gene 29,416 a protein-coding.
(2)F. Hispidagenome: Kusonkhana kwa 360 Mb (97.3% ya kukula kwa genome) kunaperekedwa ndi contig N50 ya 492 Kb ndi chiwerengero cha BUSCO cha 97.4%.Zotsatizana zonse za 359 Mb zidakhazikika pa ma chromosome 14 ndi Hi-C ndipo ndizofanana kwambiri ndi mapu olumikizana kwambiri.
(3)Chithunzi cha verticillatagenome: Msonkhano wa 387 Mb (Chiwerengero cha kukula kwa genome: 382 Mb) unakhazikitsidwa ndi contig N50 ya 3.1 Mb ndi mphambu ya BUSCO ya 97.7%.

2.Kusanthula kwa ma genomics kofananira kunavumbulutsa kuchuluka kwamitundu yosiyanasiyana pakati pa awiriFicusma genomes, omwe adapereka zida zamtengo wapatali zama genetic pamaphunziro osinthika a chisinthiko.Kafukufukuyu, kwa nthawi yoyamba, adapereka chidziwitso cha Fig-wasp coevolution pa genomic-level.

PB-full-length-RNA-Sequencing-case-study

Circos chithunzi pa genomic mbali ziwiriFicusma genomes, kuphatikiza ma chromosomes, segmental duplications (SDs), transposons(LTR, TEs, DNA TEs), gene expression ndi synteny