Dhirta/Xayawaanka De Novo Genome Sequencing
Faa'iidooyinka Adeegga
Horumarinta aaladaha isku xigxiga iyo bioinformatics inde novoururinta genome
(Amarasinghe SL iyo al.,Biology-ga Genome, 2020)
● Dhisidda genome-ga cusub iyo hagaajinta genome tixraaceedka jira ee noocyada xiisaha.
● Saxnaanta sare, sii wadida iyo dhamaystirka kulanka
● Dhisidda ilaha aasaasiga ah ee cilmi-baarista ee taxanaha polymorphism, QTLs, tafatirka hidda-socodka, taranta, iwm.
● Ku qalabaysan qaab-dhismeedka jiilka saddexaad ee isku xigxiga oo buuxa: xalka isu-ururinta genome-ka-hal-joog
Xeelado isku xigxig dabacsan iyo isku-dubarid oo buuxinaya genome-ga kala duwan oo leh astaamo kala duwan
● Kooxda bioinformatician xirfad sare leh oo khibrad weyn u leh isu imaatinka genome-ga adag, oo ay ku jiraan polyploids, genomes giant, iwm.
● In ka badan 100 kiis oo lagu guulaystay oo leh isugeyn la daabacay oo saameyn ah oo ka badan 900
● Wakhtiga-wareega sida ugu dhakhsaha badan 3 bilood isu imaatinka heerka koromosoomyada.
● Taageero farsamo oo adag oo leh shatiyo taxane ah iyo xuquuqda daabacaadda software ee dhinaca tijaabada iyo bioinformatics labadaba.
Tilmaamaha Adeegga
|
Nuxurka
|
Platform
|
Akhri Dhererka
|
Daboolista
|
| Sahanka Genome
| Illumina NovaSeq
| PE150
| ≥ 50X
|
| Taxanaha Genome
| PacBio Revio
| 15 kb HiFi ayaa akhriya
| ≥ 30X
|
| Hi-C
| Illumina NovaSeq
| PE150
| ≥100X
|
Socodka shaqada
Tusaalaha Shuruudaha iyo Bixinta
Tusaalaha Shuruudaha:
| Noocyada | Nudaha | Loogu talagalay PacBio | ee Nanopore |
| Xoolaha | Xubnaha aragga (beerka, beeryarada, iwm.) | ≥ 1.0 g | ≥ 3.5 g |
| Muruq | ≥ 1.5 g | ≥ 5.0 g | |
| Dhiiga naasleyda | ≥ 1.5 ml | ≥ 5.0 ml | |
| Dhiiga kalluunka ama shimbiraha | ≥ 0.2 ml | ≥ 0.5 ml | |
| Dhirta | Caleemo cusub | ≥ 1.5 g | ≥ 5.0 g |
| Petal ama jirid | ≥ 3.5 g | ≥ 10.0 g | |
| Xididdada ama iniinaha | ≥ 7.0 g | ≥ 20.0 g | |
| Unugyada | Dhaqanka unugga | ≥ 3×107 | ≥ 1×108 |
Tusaalaha keenista lagu taliyay
Weel: 2 ml oo tuubo sentrifuge ah (Faylada qasacadaysan laguma talinayo)
Inta badan shaybaarada, waxaan kugula talineynaa inaan lagu keydin ethanol.
Calaamadaynta Tusaalaha: Muunaduhu waxay u baahan yihiin in si cad loo calaamadiyo oo la mid ah foomka macluumaadka muunada ee la gudbiyay.
Shixnadda: Barafka qallalan: Muunadodu waxay u baahan yihiin in marka hore bac lagu shubo oo lagu aaso baraf qallalan.
Socodka Shaqada Adeegga
Naqshadaynta tijaabada
Tusaalaha keenista
Soo saarista DNA
Dhismaha maktabadda
Isku xigxiga
Falanqaynta xogta
Adeegyada iibka kadib
*Natiijooyinka bandhiga halkan lagu muujiyey waxay dhamaantood ka yimaaddeen genome-yada lagu daabacay Tignoolajiyada Biomarker
1.Circos on chromosome-level genome kulanka eeG. rotundifoliumby Nanopore madal isku xigxiga
Wang M iyo al.,Biology-ga Molecular iyo Evolution, 2021
2.Statistics of Weining galley genome kulanka iyo sharraxaad
Li G iyo al.,Hiddaha Dabeecada, 2021
3.Gene saadaashaSechium edulegenome, oo laga soo qaatay saddex hab oo saadaalin ah:De novosaadaasha, saadaasha Homology-ku salaysan iyo RNA-Seq xogta ku salaysan saadaasha
Fu A iyo al.,Cilmi-baarista Dhirta, 2021
4.Aqoonsiga soo noqnoqda terminalka dheer ee saxda ah ee saddexda genome suufka ah
Wang M iyo al.,Biology-ga Molecular iyo Evolution, 2021
5.Hi-C khariidada kulaylka eeC. acuminatagenome oo muujinaya is dhexgalka genome-ballaaran oo dhan.Xoojinta isdhexgalka Hi-C waxay u dhigantaa fogaanta toosan ee u dhaxaysa contigs.Xariiq toosan oo nadiif ah oo ku taal khariidadda kulaylka ayaa tilmaamaysa ku xidhidh aad u sax ah oo ku xidhan koromosoomyada.(saamiga ku xidhidhiyaha joogtada ah: 96.03%)
kang M et al.,Isgaarsiinta Dabeecadda,2021
Kiiska BMK
Isugeynta genome-ga oo tayo sare leh ayaa muujisa sifooyinka genomic galley iyo hidde-sidayaasha muhiimka ah ee beeraha
La daabacay: Hiddaha Dabeecada, 2021
Istaraatiijiyada isku xigxiga:
Isugeynta Genome: Habka PacBio CLR oo leh maktabad 20 kb ah (497 Gb, qiyaastii 63×)
Sixitaan isku xigxiga: NGS oo leh 270 bp DNA maktabadda (430 Gb, qiyaastii. 54×) ee ku yaala madal Illumina
Xirmooyinka xiritaanka: Maktabadda Hi-C(560 Gb, qiyaastii 71×) ee ku taal madal Illumina
Khariidadda indhaha: (779.55 Gb, qiyaastii. 99×) ee Bionano Irys
Natiijooyinka muhiimka ah
1.An shir of Weining galley genome ah ayaa la daabacay oo leh wadarta guud ee genome cabbirka 7.74 Gb(98.74% qiyaasta genome cabbirka cytometry socodka).Scaffold N50 ee golahan ayaa gaadhay 1.04 Gb.93.67% contigs ayaa si guul leh loogu dhejiyay 7 koromosoomyada been abuurka ah.Golahan waxa lagu qiimeeyay khariidad isku xidhan, LAI iyo BUSCO, taas oo keentay in natiijooyin sare laga helo dhamaan qiimayntii.
2. Daraasado dheeraad ah oo ku saabsan genomics isbarbardhigga, khariidadda xiriirka hidaha, daraasadaha transcriptomics ayaa lagu sameeyay saldhigga genome-kan.Sifooyin taxane ah oo la xidhiidha sifooyin genomic ah ayaa shaaca laga qaaday oo ay ku jiraan nuqul ka mid ah hiddo-wadaha genome-ballaaran iyo saamaynta ay ku leeyihiin hiddo-sidaha biosynthesis istaarijka;abaabulka jireed ee prolamin loci kakan, muujinta hidda-sidaha sifooyin ka hooseeya sifada ciwaanka hore iyo gobalada koromosoomyada ee la xidhiidha gurigaaga iyo loci ee galley.
 Jaantuska Circos ee astaamaha genomic ee genome-ka Weining rye |  Falanqaynta korriinka iyo koromosoomyada synteny ee genome-ga galley |
Li, G., Wang, L., Yang, J.iyo al.Isugeynta genome-ga oo tayo sare leh ayaa muujisa sifooyinka genomic galley iyo hidde-sidayaasha muhiimka ah ee beeraha.Nat Genet 53,574-584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
