Isityalo/Isilwanyana saseDe Novo Genome Sequencing
Iinkonzo eziluncedo
Ukuphuhliswa kwamaqonga okulandelelanisa kunye ne-bioinformatics kwide novoindibano yegenome
(Amarasinghe SL et al.,Ibhayoloji yeGenome, 2020)
● Ukwakha iigenomes zenoveli kunye nokuphucula iigenome zezalathiso ezikhoyo ukulungiselela iintlobo zomdla.
● Ukuchaneka okuphezulu, ukuqhubeka kunye nokugqibelela kwindibano
● Ukwenza izixhobo ezisisiseko zophando ngokulandelelana kwepolymorphism, ii-QTL, ukuhlelwa kofuzo, ukuzala, njl.
● Ixhotyiswe nge-spectrum epheleleyo yamaqonga okulandelelanisa isizukulwana sesithathu: isisombululo sendibano ye-genome enye-stop
● Ulandelelwano oluguquguqukayo kunye nokudibanisa izicwangciso ezizalisekisa iindidi ezahlukeneyo ze-genome ezineempawu ezahlukeneyo
● Iqela le-bioinformatics elinobuchule obuphezulu elinamava amnandi kwiiassemblies zegenome ezintsonkothileyo, kuquka iipolyploids, iigenome ezinkulu, njl.
● Ngaphezulu kwe-100 leemeko eziyimpumelelo ezinempembelelo eyongezelelweyo epapashiweyo engaphezu kwama-900
● Ukutshintsha-ixesha ngokukhawuleza njengeenyanga ezi-3 zokudibanisa igenome yenqanaba lekhromozomi.
● Inkxaso yobugcisa obuqinileyo ngothotho lwamalungelo awodwa omenzi wechiza kunye namalungelo oshicilelo esoftware kuwo omabini amacala ovavanyo kunye nebhayoinformatics.
IiNgcaciso zeNkonzo
|
Umxholo
|
Iqonga
|
Funda Ubude
|
Ukhuseleko
|
| Uvavanyo lweGenome
| Illumina NovaSeq
| PE150
| ≥ 50X
|
| Ulandelelwano lweGenome
| I-PacBio Revio
| 15 kb Ufundo lweHiFi
| ≥ 30X
|
| Hi-C
| Illumina NovaSeq
| PE150
| ≥100X
|
Ukuhamba komsebenzi
IiMfuno zeSampulu kunye nokuhanjiswa
IiMfuno zeSampulu:
| Iintlobo | Izicubu | YePacBio | KwiNanopore |
| Izilwanyana | Amalungu e-Visceral (isibindi, udaka, njl. | ≥ 1.0 g | ≥ 3.5 g |
| Izihlunu | ≥ 1.5 g | ≥ 5.0 g | |
| Igazi lezilwanyana ezanyisayo | ≥ 1.5 mL | ≥ 5.0 mL | |
| Igazi leentlanzi okanye leentaka | ≥ 0.2 mL | ≥ 0.5 mL | |
| Izityalo | Amagqabi amatsha | ≥ 1.5 g | ≥ 5.0 g |
| Ipetali okanye isiqu | ≥ 3.5 g | ≥ 10.0 g | |
| Iingcambu okanye imbewu | ≥ 7.0 g | ≥ 20.0 g | |
| Iiseli | Inkcubeko yeseli | ≥ 3×107 | ≥ 1×108 |
Unikezelo lweSampuli eCetyisiweyo
Isikhongozeli: 2 ml centrifuge ityhubhu (Ifoyile yeTin ayikhuthazwa)
Kwiisampulu ezininzi, sincoma ukuba ungayigcini kwi-ethanol.
Iisampulu zokufakwa ileyibhile: Iisampulu kufuneka zibhalwe ngokucacileyo kwaye zifane nefom yesampulu yolwazi engenisiweyo.
Ukuthumela: Umkhenkce owomileyo: Iisampulu kufuneka zipakishwe kwiingxowa kuqala kwaye zingcwatywe kwindawo eyomileyo.
Ukuhamba komsebenzi weNkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampuli
Ukutsalwa kwe-DNA
Ukwakhiwa kwethala leencwadi
Ukulandelelanisa
Uhlalutyo lwedatha
Iinkonzo emva kokuthengisa
* Iziphumo zedemo eziboniswe apha zonke zivela kwiigenomes ezipapashwe ngeBiomarker Technologies
1.I-Circos kwi-chromosome-level genome assembly ofG. rotundifoliumnguNanopore iqonga lokulandelelana
Wang M et al.,Ibhayoloji yeMolekyuli kunye ne-Evolution, 2021
2.Statistics of Weining rye genome indibano kunye nenkcazo
Li G et al.,Imfuzo yendalo, 2021
3. Uqikelelo lwemfuza yeSechium eduleigenome, ethatyathwe kwiindlela ezintathu zokuqikelela:De novouqikelelo, uqikelelo olusekwe kwi-Homology kunye ne-RNA-Seq data esekelwe kwingqikelelo
Fu A et al.,Uphando lweHorticulture, 2021
4. Ukuchongwa kwetheminali ende engaguqukiyo ephindaphindwayo kwiigenomes zomqhaphu ezintathu
Wang M et al.,Ibhayoloji yeMolekyuli kunye ne-Evolution, 2021
5.Hi-C imephu yobushushu beC. acuminataigenome ebonisa igenome-wide all-by-all interactions.Ubunzulu bentsebenziswano ye-Hi-C buhambelana nomgama ophakathi phakathi kwee-contigs.Umgca ococekileyo othe ngqo kule mephu yobushushu ibonisa iankile echaneke kakhulu yee-contigs kwiichromosomes.(I-Contig anchoring ratio: 96.03%)
kang M et al.,Unxibelelwano ngeNdalo,2021
Ityala le-BMK
Indibano ye-genome ekumgangatho ophezulu iqaqambisa iimpawu ze-rye genomic kunye nofuzo olubalulekileyo ngokwezolimo
Ipapashiwe: Imfuzo yendalo, 2021
Iqhinga lokulandelelanisa:
Indibano yeGenome: Imo yePacBio CLR enethala leencwadi le-20 kb (497 Gb, malunga ne63×)
Ukulungiswa kolandelelwano: I-NGS enelayibrari ye-270 bp DNA (430 Gb, malunga ne-54×) kwiqonga le-Illumina
Contigs anchoring: Ithala leencwadi le-Hi-C (560 Gb, malunga ne-71×) kwiqonga le-Illumina
Imephu yokubona: (779.55 Gb, malunga ne-99×) kwi-Bionano Irys
Iziphumo eziphambili
1.Indibano ye-Weining rye genome yapapashwa enobungakanani begenome iyonke ye-7.74 Gb (98.74% yobungakanani obuqikelelweyo begenome ngokuqukuqela kwe-cytometry).I-scaffold N50 yale ndibano iphumelele i-1.04 Gb.I-93.67% ye-contigs ifakwe ngempumelelo kwii-chromosomes ezisi-7.Le ndibano yavavanywa yimephu yonxibelelaniso, i-LAI kunye ne-BUSCO, ekhokelele kumanqaku aphezulu kulo lonke uvandlakanyo.
2.Uphononongo olongezelelweyo malunga ne-genomics ethelekisayo, imephu yokunxibelelana kofuzo, izifundo ze-transcriptomics zenziwa kwisiseko sale genome.Uluhlu lweempawu ezinxulumene neempawu ze-genomic ziye zatyhilwa kubandakanywa ukuphindaphindwa kwemfuza ngokubanzi kunye nefuthe labo kwi-starch biosynthesis genes;ulungelelwaniso olubonakalayo lweprolamin loci entsonkothileyo, imbonakalo yemfuza esisiseko sesihloko sakwangoko kunye nemimandla yechromosomal ehambelana nokubekelwa ekhaya kunye neloci kwirye.
 Umzobo weCircos kwiimpawu zegenomic ze-Weining rye genome |  Uhlalutyo lwe-evolutionary kunye ne-chromosome synteny ye-rye genome |
Li, G., Wang, L., Yang, J.okqhubekayo.Indibano ye-genome ekumgangatho ophezulu iqaqambisa iimpawu ze-rye genomic kunye nofuzo olubalulekileyo ngokwezolimo.UNat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
