Semela / Phoofolo De Novo Genome Sequencing
Melemo ea Tšebeletso
Nts'etsopele ea li-platform tsa tatellano le bioinformatics hode novokopano ea genome
(Amarasinghe SL et al.,Genome Biology, 2020)
● Ho etsa liphatsa tsa lefutso tse ncha le ho ntlafatsa liphatsa tsa lefutso tse teng bakeng sa mefuta e meng e khahlang.
● Ho nepahala ho phahameng, ho tsoelapele le ho phethahala ha kopano
● Ho theha lisebelisoa tsa bohlokoa bakeng sa lipatlisiso ka tatellano ea polymorphism, QTLs, ho fetola liphatsa tsa lefutso, ho ikatisa, joalo-joalo.
● E na le li-platform tsa tatellano ea moloko oa boraro: tharollo ea kopano ea genome e le 'ngoe.
● tatellano e feto-fetohang le maano a ho kopanya a phethahatsang liphatsa tsa lefutso tse fapaneng tse nang le likarolo tse fapaneng
● Sehlopha sa litsebi tse nang le litsebo tse phahameng tsa bioinformatician se nang le phihlelo e kholo ea ho kopanya liphatsa tsa lefutso tse rarahaneng, ho akarelletsa le li-polyploid, li-giant genome, joalo-joalo.
● Linyeoe tse fetang 100 tse atlehileng tse nang le tšusumetso e matla e fetang 900
● Nako ea ho fetoha ka potlako e ka bang likhoeli tse 3 bakeng sa kopano ea boemo ba chromosome ea genome.
● Tšehetso e tiileng ea tekheniki e nang le letoto la litokelo tsa molao le li-software mahlakoreng a liteko le bioinformatics.
Litlhaloso tsa Tšebeletso
|
Litaba
|
Sethala
|
Bala Bolelele
|
Kakaretso
|
| Patlisiso ea Genome
| Illumina NovaSeq
| PE150
| ≥ 50X
|
| Genome Sequencing
| PacBio Revio
| 15 khb Ho Bala HiFi
| ≥ 30X
|
| Hi-C
| Illumina NovaSeq
| PE150
| ≥100X
|
Phallo ea mosebetsi
Litlhoko tsa Mohlala le Phano
Litlhoko tsa Mohlala:
| Mefuta | Tishu | Bakeng sa PacBio | Bakeng sa Nanopore |
| Liphoofolo | Litho tsa Visceral (sebete, spleen, joalo-joalo) | ≥ 1.0 g | ≥ 3.5 g |
| Mosifa | ≥ 1.5 g | ≥ 5.0 g | |
| Mali a liphoofolo tse anyesang | ≥ 1.5 mL | ≥ 5.0 mL | |
| Mali a litlhapi kapa linonyana | ≥ 0.2 mL | ≥ 0.5 mL | |
| Limela | Makhasi a macha | ≥ 1.5 g | ≥ 5.0 g |
| Petal kapa kutu | ≥ 3.5 g | ≥ 10.0 g | |
| Metso kapa peo | ≥ 7.0 g | ≥ 20.0 g | |
| Lisele | Setso sa sele | ≥ 3×107 | ≥ 1×108 |
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 hatisitsoeng ka Biomarker Technologies
1.Li-Circos ho kopano ea genome ea boemo ba chromosome eaG. rotundifoliumka Nanopore sequencing sethaleng
Wang M et al.,Biology ea Limolek'hule le Evolution, 2021
2.Lipalopalo tsa kopano ea Weining rye genome le tlhaloso
Li G et al.,Nature Genetics, 2021
3.Polelo ea lefutso eaSechium edulegenome, e nkiloeng mekhoeng e meraro ea ho bolela esale pele:De novoho bolela esale pele, ho bolela esale pele ka Homology le ponelopele e thehiloeng ho data ea RNA-Seq
Fu A et al.,Lipatlisiso tsa Temo ea Lirapa, 2021
4.Identification of the intact long long terminal repeats in three cotton genomes
Wang M et al.,Biology ea Limolek'hule le Evolution, 2021
5.Hi-C mocheso 'mapa oaC. acuminataGenome e bonts'ang litšebelisano tsa genome ka bophara.Matla a litšebelisano tsa Hi-C a lekana le sebaka se pakeng tsa li-contigs.Mohala o hloekileng o otlolohileng 'mapeng ona oa mocheso o bontša tumellano e nepahetseng haholo ea li-contigs ho li-chromosome.(Contig anchoring ratio: 96.03%)
kang M et al.,Tlhaho ea puisano,2021
Taba ea BMK
Kopano ea boleng bo holimo ea genome e totobatsa litšobotsi tsa rye genomic le liphatsa tsa lefutso tsa bohlokoa tsa temo
E hatisitsoe: Nature Genetics, 2021
Leano la tatellano:
Kopano ea Genome: Mokhoa oa PacBio CLR o nang le laeborari ea 20 kb (497 Gb, hoo e ka bang 63×)
Tokiso ea tatelano: NGS e nang le 270 bp DNA library (430 Gb, approx. 54×) sethaleng sa Illumina
Contigs anchoring: Hi-C library (560 Gb, approx. 71×) sethaleng sa Illumina
'Mapa oa pono: (779.55 Gb, hoo e ka bang 99×) ho Bionano Irys
Liphetho tsa bohlokoa
1. Kopano ea Weining rye genome e phatlalalitsoe ka boholo ba genome ea 7.74 Gb (98.74% ea boholo bo hakanyetsoang ba genome ka cytometry ea phallo).Scaffold N50 ea kopano ena e fihletse 1.04 Gb.93.67% ea li-contigs li atlehile ho ts'oaroa ho li-pseudo-chromosome tse 7.Kopano ena e ile ea hlahlojoa ka 'mapa oa khokahano, LAI le BUSCO, e leng se hlahisitseng lintlha tse phahameng litlhahlobong tsohle.
2. Liphuputso tse ling mabapi le genomics e bapisang, 'mapa oa khokahano ea liphatsa tsa lefutso, lithuto tsa transcriptomics li entsoe motheong oa genome ena.Letoto la litšobotsi tse amanang le likarolo tsa genomic li ile tsa senoloa ho kenyelletsa le liphatsa tsa lefutso ka bophara le phello ea tsona ho liphatsa tsa lefutso tsa starch biosynthesis;tlhophiso ea 'mele ea prolamin loci e rarahaneng, polelo ea liphatsa tsa lefutso e na le likarolo tsa mantlha tsa sehlooho le libaka tsa chromosomal tse amanang le ho lula malapeng le loci ho rye.
 Setšoantšo sa Circos mabapi le likarolo tsa genomic tsa Weining rye genome |  Litlhahlobo tsa ho iphetola ha lintho le tsa chromosome synteny ea genome ea rye |
Li, G., Wang, L., Yang, J.le al.Kopano ea boleng bo holimo ea genome e totobatsa litšobotsi tsa rye genomic le liphatsa tsa lefutso tsa bohlokoa tsa temo.Nat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
