Hi-C e thehiloeng ho Genome Assembly
Melemo ea Tšebeletso
Kakaretso ea Hi-C
(Lieberman-Aiden Et al.,Saense, 2009)
● Ha ho na tlhoko ea ho theha palo ea liphatsa tsa lefutso bakeng sa ho ts'ehetsa contig;
● Tšebeliso e phahameng ea matšoao e lebisang ho tekanyo e phahameng ea contigs anchoring ka holimo ho 90%;
● E nolofalletsa tlhahlobo le litokiso ho likopano tse teng tsa genome;
● Nako e khuts'oane ea ho fetola nako e nang le ho nepahala ho phahameng ho kopaneng ea genome;
● Boiphihlelo bo bongata ka lilaebrari tsa Hi-C tse fetang 1000 tse etselitsoeng mefuta e fetang 500;
● Linyeoe tse fetang 100 tse atlehileng tse nang le tšusumetso e ngata ho feta 760;
● Kopano ea genome e thehiloeng ho Hi-C bakeng sa genome ea polyploid, tekanyo ea 100% ea anchoring e ile ea finyelloa morerong o fetileng;
● Litokomane tsa ka tlung le litokelo tsa litokelo tsa software bakeng sa liteko tsa Hi-C le tlhahlobo ea lintlha;
● Mananeo a iketselitseng a iponahatsang a tokiso ea data, a nolofalletsang hore li-blocks li tsamaee, li khutlise morao, li hlakole le ho li etsa hape.
Litlhaloso tsa Tšebeletso
|
Mofuta oa Laebrari
|
Sethala | Bala Bolelele | Khothalletsa Leano |
| Hi-C | Illumina NovaSeq | PE150 | ≥ 100X |
Litlhahlobo tsa Bioinformatics
● Taolo ea boleng ba data e tala
● Taolo ea boleng ba laebrari ea Hi-C
● Kopano ea genome e thehiloeng ho Hi-C
● Tlhahlobo ea ka mor'a kopano
Litlhoko tsa Mohlala le Phano
Litlhoko tsa Mohlala:
| Phoofolo | Li-fungus | Limela
|
| Lithane tse hatselitsoeng: 1-2g ka laeborari e 'ngoe Lisele: 1x 10^7 lisele ho laebrari ka 'ngoe | Lithipa tse hatselitsoeng: 1g laebraring ka 'ngoe | Lithane tse hatselitsoeng: 1-2g ka laeborari e 'ngoe
|
| *Re khothaletsa ka matla ho romella bonyane li-aliquots tse 2 (1 g ka 'ngoe) bakeng sa teko ea Hi-C. | ||
Tlhahiso ea Mehlala e khothalelitsoeng
Setshelo: 2 ml centrifuge tube (Tin foil ha e khothalletsoe)
Bakeng sa lisampole tse ngata, re khothaletsa ho se boloke ethanol.
Mohlala oa ho ngola: Mehlala e hloka ho ngoloa ka ho hlaka le ho tšoana le foromo ea sampole e rometsoeng.
Thomello: Leqhoa le omileng: lisampole li hloka ho kenngoa ka mekotleng pele ebe li patoa ka leqhoa le omileng.
Phallo ea Mosebetsi oa Ts'ebeletso
Moqapi oa liteko
Mohlala oa thomello
Ho ntšoa ha DNA
Kaho ea laebrari
Tatelano
Tlhahlobo ea lintlha
Litšebeletso tsa ka mor'a thekiso
*Liphetho tsa demo tse bontšitsoeng mona kaofela li tsoa ho liphatsa tsa lefutso tse phatlalalitsoeng ka Biomarker Technologies
1.Hi-C tšebelisano 'mapa oa mocheso oaCamptotheca acuminatagenome.Joalo ka ha ho bonts'itsoe 'mapeng, matla a litšebelisano a amana hampe le sebaka sa mola, se bonts'ang kopano e nepahetseng haholo ea boemo ba chromosome.(Anchoring ratio: 96.03%)
Kang M et al.,Tlhaho Puisano, 2021
2.Hi-C e nolofalitse ho netefatsoa ha li-inversions lipakeng tsaGossypium hirsutumL. TM-1 A06 leG. arboreumChr06
Yang Z et al.,Lipuisano tsa Tlhaho, 2019
3.Assembly le biallelic phapang ea cassava genome SC205.'Mapa oa mocheso oa Hi-C o bonts'itsoe karohano e hlakileng ea li-chromosome tsa homologous.
Hu W et al.,Semela sa Molek'hule, 2021
'Mapa oa mocheso oa 4.Hi-C mabapi le kopano ea liphatsa tsa lefutso tse peli tsa Ficus:F.microcarpa(anchoring ratio: 99.3%) leF.hispida (anchoring ratio: 99.7%)
Zhang X et al.,Sele, 2020
Taba ea BMK
Liphatsa tsa lefutso tsa Sefate sa Banyan le Bobi ba Pollinator li fana ka lintlha tse mabapi le Coevolution ea Fig-wasp
E hatisitsoe: Sele, 2020
Leano la tatellano:
F. microcarpa genome: Hoo e ka bang.84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)
F. hispidagenome: Hoo e ka bang.97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)
E rutabana verticillatagenome: Hoo e ka bang.170 X PacBio RSII (65 Gb)
Liphetho tsa bohlokoa
1.Liphatsa tsa lefutso tse peli tsa sefate sa banyan le genome e le 'ngoe ea pollinator wasp li hahiloe ka tatellano ea PacBio, Hi-C le 'mapa oa khokahano.
(1)F. microcarpagenome: Kopano ea 426 Mb (97.7% ea boholo bo hakantsoeng ba genome) e thehiloe ka contig N50 ea 908 Kb, lintlha tsa BUSCO tsa 95.6%.Kakaretso ea tatellano ea 423 Mb e khomaretsoe ho li-chromosome tse 13 ke Hi-C.Tlhaloso ea Genome e hlahisitse liphatsa tsa lefutso tse 29,416 tsa protheine.
(2)F. Hispidagenome: Kopano ea 360 Mb (97.3% ea boholo bo hakantsoeng ba genome) e bile le lihlahisoa tse nang le contig N50 ea 492 Kb le lintlha tsa BUSCO tsa 97.4%.Kakaretso ea tatellano ea 359 Mb e thehiloe ho li-chromosome tse 14 ke Hi-C mme e ts'oana haholo le 'mapa oa khokahano o phahameng haholo.
(3)E rutabana verticillatagenome: Kopano ea 387 Mb (Ho hakanngoa boholo ba genome: 382 Mb) e thehiloe ka contig N50 ea 3.1 Mb le lintlha tsa BUSCO tsa 97.7%.
2.Tlhahlobo ea ho bapisa liphatsa tsa lefutso e senotse palo e kholo ea mefuta e fapaneng ea sebopeho lipakeng tsa tse peliFicusliphatsa tsa lefutso, tse faneng ka mohloli oa bohlokoa oa liphatsa tsa lefutso bakeng sa lithuto tsa ho iphetola ha lintho.Boithuto bona, ka lekhetlo la pele, bo fane ka leseli mabapi le coevolution ea Fig-wasp maemong a genomic.
 Setšoantšo sa Circos mabapi le likarolo tsa genomic tsa tse peliFicusliphatsa tsa lefutso, ho kenyelletsa le li-chromosome, li-segmental duplications (SDs), transposons(LTR, TEs, DNA TEs), polelo ea liphatsa tsa lefutso le synteny. |  Ho tsebahatsa mofuta oa Y chromosome le mofuta oa mokhethoa oa qeto ea thobalano |
Zhang, X., le ba bang.“Liphatsa tsa lefutso tsa Sefate sa Banyan le Bobi ba Sefate sa Pollinator li Fana ka Litlhaloso mabapi le Phetoho ea Fig-Wasp.”Cell 183.4(2020).
