Ukulandelanisa Kwezitshalo/Isilwane Se-De Novo Genome
Izinzuzo Zesevisi
Ukuthuthukiswa kwamapulatifomu okulandelana kanye ne-bioinformatics kude novoukuhlanganiswa kwe-genome
(Amarasinghe SL et al.,I-Genome Biology, 2020)
● Ukwakha ama-genome amasha kanye nokwenza ngcono ama-genome ayinkomba akhona ngezinhlobo ezithakaselwayo.
● Ukunemba okuphezulu, ukuqhubeka nokuphelela ekuhlanganiseni
● Ukwakha insiza eyisisekelo yocwaningo ngokulandelana kwe-polymorphism, ama-QTL, ukuhlela izakhi zofuzo, ukuzalanisa, njll.
● Ifakwe i-spectrum egcwele yezinkundla zesizukulwane sesithathu zokulandelana: isixazululo sokuhlanganisa igenome eyodwa-stop
● Ukulandelana okuguquguqukayo nokuhlanganisa amasu agcwalisa ama-genome ahlukahlukene anezici ezihlukile
● Ithimba le-bioinformatician elinekhono eliphezulu elinolwazi oluhle kuma-genome assemblies ayinkimbinkimbi, okuhlanganisa ama-polyploid, ama-genome amakhulu, njll.
● Izigameko eziyimpumelelo ezingaphezu kwe-100 ezinesici esikhulayo esishicilelwe esingaphezu kuka-900
● Isikhathi sokushintsha ngokushesha njengezinyanga ezi-3 zokuhlanganisa igenome yeleveli ye-chromosome.
● Usekelo oluqinile lwezobuchwepheshe olunochungechunge lwamalungelo obunikazi namalungelo okushicilela esofthiwe kukho kokubili uhlangothi lokuhlola kanye ne-bioinformatics.
Imininingwane Yesevisi
|
Okuqukethwe
|
Inkundla
|
Funda Ubude
|
Ukuhlanganisa
|
| I-Genome Survey
| Illumina NovaSeq
| I-PE150
| ≥ 50X
|
| Ukulandelana kweGenome
| I-PacBio Revio
| 15 kb Ukufundwa kwe-HiFi
| ≥ 30X
|
| Hi-C
| Illumina NovaSeq
| I-PE150
| ≥100X
|
Ukugeleza komsebenzi
Izidingo Zesampula Nokulethwa
Izimfuneko zesampula:
| Izinhlobo | Izicubu | Okwe-PacBio | OkwaNanopore |
| Izilwane | Izitho ze-Visceral (isibindi, i-spleen, njll.) | ≥ 1.0 g | ≥ 3.5 g |
| Imisipha | ≥ 1.5 g | ≥ 5.0 g | |
| Igazi lezilwane ezincelisayo | ≥ 1.5 mL | ≥ 5.0 mL | |
| Igazi lezinhlanzi noma lezinyoni | ≥ 0.2 mL | ≥ 0.5 mL | |
| Izitshalo | Amaqabunga amasha | ≥ 1.5 g | ≥ 5.0 g |
| I-Petal noma isiqu | ≥ 3.5 g | ≥ 10.0 g | |
| Izimpande noma imbewu | ≥ 7.0 g | ≥ 20.0 g | |
| Amaseli | Isiko lamaseli | ≥ 3×107 | ≥ 1×108 |
Ukulethwa Kwesampula Okunconyiwe
Isitsha: 2 ml centrifuge tube (Tin foil ayinconywa)
Kumasampuli amaningi, sincoma ukuthi ungagcini ku-ethanol.
Isampula yokulebula: Amasampuli adinga ukulebula ngokucacile futhi afane nefomu lesampula lolwazi elithunyelwe.
Ukuthunyelwa: Iqhwa elomile: Amasampula adinga ukupakishwa ezikhwameni kuqala futhi agqitshwe eqhweni elomile.
Ukugeleza Komsebenzi Wesevisi
Idizayini yokuhlola
Ukulethwa kwesampula
Ukukhishwa kwe-DNA
Ukwakhiwa komtapo wolwazi
Ukulandelanisa
Ukuhlaziywa kwedatha
Amasevisi angemuva kokuthengisa
*Imiphumela yedemo eboniswe lapha yonke ivela kuzakhi zofuzo ezishicilelwe nge-Biomarker Technologies
1.Ama-Circos ekuhlanganiseni kwegenome yeleveli yechromosome yeG. rotundifoliumngeplatifomu yokulandelana kweNanopore
Wang M et al.,I-Molecular Biology kanye ne-Evolution, 2021
2.Izibalo zokuhlanganisa i-Weining rye genome nesichasiselo
U-Li G et al.,I-Nature Genetics, 2021
3.Ukubikezela kofuzo lweSechium edulei-genome, etholakala ezindleleni ezintathu zokubikezela:De novoukubikezela, ukubikezela okusekelwe ku-Homology kanye nokubikezela okusekelwe kudatha ye-RNA-Seq
Fu A et al.,Ucwaningo Lwezolimo, 2021
4.Ukuhlonzwa kwetheminali ende engashintshile kumagenome kakotini amathathu
Wang M et al.,I-Molecular Biology kanye ne-Evolution, 2021
5.Hi-C ukushisa map of theC. acuminatai-genome ebonisa ukusebenzisana okubanzi kwe-genome konke konke.Amandla okusebenzelana kwe-Hi-C alingana nebanga lomugqa phakathi kwama-contig.Umugqa oqondile ohlanzekile kule mephu yokushisa ubonisa ukubambelela okunembe kakhulu kwama-contig kuma-chromosome.(Isilinganiso se-Contig anchoring: 96.03%)
Kang M et al.,Ukuxhumana Kwemvelo,2021
Icala le-BMK
Ukuhlanganiswa kofuzo lwekhwalithi ephezulu kugqamisa izici ze-rye genomic kanye nofuzo olubalulekile ngokwezolimo
Kushicilelwe: I-Nature Genetics, 2021
Isu lokulandelanisa:
Ukuhlanganiswa kwegenome: Imodi ye-PacBio CLR enomtapo wolwazi ongu-20 kb (497 Gb, cishe 63×)
Ukulungiswa kochungechunge: I-NGS enelabhulali ye-DNA engu-270 bp (430 Gb, cishe 54×) kuplathifomu ye-Illumina
I-Contigs iqinisa: Ilabhulali ye-Hi-C(560 Gb, cishe 71×) kuplathifomu ye-Illumina
Imephu yokubona: (779.55 Gb, cishe 99×) ku-Bionano Irys
Imiphumela esemqoka
1.Inhlanganisela ye-Weining rye genome yashicilelwa enosayizi ophelele we-genome ongu-7.74 Gb(98.74% wosayizi wofuzo olulinganiselwe ngokugeleza kwe-cytometry).I-scaffold N50 yalo mhlangano izuze i-1.04 Gb.Ama-93.67% ama-contig afakwe ngempumelelo kuma-pseudo-chromosomes angu-7.Lo mhlangano uhlolwe ngemephu yokuxhumanisa, i-LAI kanye ne-BUSCO, okuholele ekutholeni amaphuzu aphezulu kukho konke ukuhlaziya.
2.Ucwaningo olwengeziwe mayelana nokuqhathanisa i-genomics, imephu yokuxhumanisa izakhi zofuzo, izifundo ze-transcriptomics zenziwa kusisekelo sale genome.Uchungechunge lwezici ezihlobene nezici ze-genomic zembulwa okuhlanganisa ukuphindaphinda kwezakhi zofuzo ezibanzi kanye nomthelela wazo kuzakhi zofuzo ze-starch biosynthesis;ukuhlelwa ngokomzimba kwe-prolamin loci eyinkimbinkimbi, isisho sofuzo sinezici eziyisisekelo zesici sesihloko sangaphambi kwesikhathi kanye nezifunda ze-chromosomal ezihlotshaniswa nokusetshenziswa kwasekhaya kanye ne-loci ku-rye.
 Umdwebo we-Circos ezicini ze-genomic ze-Weining rye genome |  Ukuhlaziywa kwe-evolutionary kanye ne-chromosome synteny ye-rye genome |
Li, G., Wang, L., Yang, J.et al.Ukuhlanganiswa kofuzo lwekhwalithi ephezulu kugqamisa izici ze-rye genomic kanye nofuzo olubalulekile ngokwezolimo.Nathi Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
