Ulandelelwano lweGenome yezityalo/yezilwanyana
Iimpawu zeNkonzo
De novo
Le ndlela iluncedo kakhulu kwii-genomes ezinzima ezifana nezo zinezinga eliphezulu le-heterozygosity, iindawo eziphindaphindayo, ii-genomes ze-polypoloid, umxholo ongaqhelekanga we-CG njl.njl.
Isisombululo sethu esipheleleyo sinikezela ngeenkonzo zokulandelelanisa ezidibeneyo kunye nohlalutyo lwe-bioinformatic olunikezela nge-genome ehlanganisiweyo esemgangathweni ophezulu. Uphando lokuqala lwe-genome kunye ne-Illumina lubonelela ngoqikelelo lobungakanani be-genome kunye nobunzima, kwaye olu lwazi lusetyenziselwa ukukhokela inyathelo elilandelayo lokulandelelanisa okude nge-PacBio HiFi, kulandelede novoukuhlanganiswa kwee-contigs. Ukusetyenziswa okulandelayo kwe-HiC assembly kwenza ukuba ii-contigs zinamathele kwi-genome, zifumane i-chromosome-level assembly. Okokugqibela, i-genome ichazwa ngokuqikelela i-gene kunye nokulandelelanisa ii-genes eziveziweyo, kusetyenziswe ii-transcriptomes ezinee-reads ezimfutshane nezinde.
-- Ukuhlanganiswa kweenkonzo ezininzi zokulandelelana kunye neenkonzo ze-bioinformatic kwisisombululo esinyeInkonzo efanelekileyo kwinoveli yokwakha
-- ii-genome okanye ukuphuculwa kwee-genome ezikhoyo zeentlobo ezinomdla.
Ukulandelelana
-- Ukulungiswa kwethala leencwadi kunokuba yinto eqhelekileyo okanye ingabikho kwi-PCR
-- Ifumaneka kwiiplatfomu ezine zokulandelelana: Illumina NovaSeq, MGI T7, Nanopore Promethion P48 okanye iPacBio Revio.
-- Uhlalutyo lwe-Bioinformatic lugxile kwiindlela ezahlukeneyo zokubiza: i-SNP, i-InDel, i-SV kunye ne-CNV
Iingenelo zeNkonzo
●Irekhodi yoBugcisa oBubanzi kunye nokuPapasha: Ngokubade novoiinkonzo zethu, siqokelele amava amaninzi ekuhlanganiseni i-genome esemgangathweni ophezulu yeentlobo ezahlukeneyo, kuquka i-diploid genomes kunye ne-genomes ezintsonkothileyo kakhulu ze-polyploid kunye ne-allopolyploid species. Ukusukela ngo-2018, sibe negalelo kwiimpapasho ezingaphezu kwama-300 ezinefuthe eliphezulu, kwaye ezingama-20+ zazo zipapashwe kwi-Nature Genetics. Ngokulandelanisa kwakhona i-genome, siqokelele iintlobo ezingaphezu kwe-1000, nto leyo ekhokelele kwiimeko ezingaphezu kwe-1000 ezipapashweyo ezine-cumulative impact factor engaphezulu kwe-5000.
●Isisombululo sokuma kunye: Ivuliwede novoUkulandelelanisa, indlela yethu edibeneyo idibanisa iitekhnoloji ezininzi zokulandelelanisa kunye nohlalutyo lwe-bioinformatic kwi-workflow edibeneyo, nto leyo enika i-genome ehlanganisiweyo esemgangathweni ophezulu.
●Yenzelwe Iimfuno Zakho: Indlela esisebenza ngayo inkonzo yethu iyakwazi ukwenziwa ngokwezifiso, ivumela ukulungelelaniswa kwee-genomes ezineempawu ezahlukeneyo kunye neemfuno ezithile zophando.
●Iqela leBioinformatics kunye neLebhu elinobuGcisa obuPhezulu: Nokuba kungenxade novoUkulandelelanisa okanye ukulandelelanisa kwakhona, iqela lethu linezixhobo ezinobuchule kunye nolwazi lokuqinisekisa impumelelo yeprojekthi. Oku kunokuqinisekiswa ngothotho lweepatenti kunye namalungelo okushicilela esoftware abayiphuhlisileyo.
● Inkxaso Emva kokuthengisa:Ukuzibophelela kwethu kudlulela ngaphaya kokugqitywa kweprojekthi kunye nexesha leenkonzo emva kokuthengiswa kweenyanga ezi-3. Ngeli xesha, sinikezela ngokulandela iprojekthi, uncedo lokusombulula iingxaki, kunye neeseshoni ze-Q&A ukuphendula nayiphi na imibuzo enxulumene neziphumo.
●Uhlalutyo olupheleleyo lweBioinformatics: Kubandakanya ukubiza okwahlukileyo kunye nesichazi somsebenzi.
●Ingcaciso epheleleyo yokulandelelanisa: Sisebenzisa iidathabheyisi ezininzi ukuze sichaze iijini ngendlela esebenzayo ngeenguqu ezichongiweyo kwaye senze uhlalutyo lokuphucula oluhambelanayo, sinike ulwazi malunga neeprojekthi zakho zophando.
Iinkcukacha zeNkonzo
| Iindidi eziza kuchongwa | Icebo lokulandelelanisa izinto | Ubunzulu obucetyiswayo |
| I-SNP kunye ne-InDel | I-Illumina NovaSeq PE150 okanye i-MGI T7 | 10x |
| I-SV kunye ne-CNV (engachanekanga kangako) | 30x | |
| I-SV kunye ne-CNV (ichaneke ngakumbi) | I-Nanopore Prom P48 | 20x |
| Ii-SNP, ii-Indels, ii-SV kunye ne-CNV | Uhlaziyo lwePacBio | 10x |
Iimfuno zeSampuli
| Ii-tissue okanye ii-nucleic acids ezikhutshiweyo | I-Illumina/MGI | I-Nanopore | I-PacBio
| ||
| I-Viscera yezilwanyana | 0.5-1 g | ≥ 3.5 g
| ≥ 3.5 g
| ||
| Izihlunu zezilwanyana | ≥ 5 g
| ≥ 5 g
| |||
| Igazi lezilwanyana ezincelisayo | 1.5 mL | ≥ 0.5 mL
| ≥ 5 mL
| ||
| Igazi leNkukhu/Intlanzi | ≥ 0.1 mL
| ≥ 0.5 mL
| |||
| Isityalo- Igqabi Elitsha | 1-2 g | ≥ 2 g
| ≥ 5 g
| ||
| Iiseli ezikhuliswe kakuhle |
| ≥ 1x107
| ≥ 1x108
| ||
| Izicubu ezithambileyo zezinambuzane/Umntu ngamnye | 0.5-1 g | ≥ 1 g
| ≥ 3 g
| ||
| I-DNA ekhutshiweyo
| Uxinzelelo: ≥ 1 ng/ µL Isixa: ≥ 30 ng Ukonakala okanye ukungcola okulinganiselweyo okanye okungekhoyo
| Ukugxila Isixa
OD260/280
OD260/230
Ukonakala okanye ukungcola okulinganiselweyo okanye okungekhoyo
| ≥ 40 ng/µL 4 µg/iseli yokuhamba/isampulu
1.7-2.2
≥1.5 | Ukugxila Isixa
OD260/280
OD260/230
Ukonakala okanye ukungcola okulinganiselweyo okanye okungekhoyo | ≥ 50 ng/µL 10 µg/iseli yokuhamba/isampulu
1.7-2.2
1.8-2.5 |
| Ukulungiswa kweThala leeNcwadi elingenayo i-PCR: Uxinzelelo≥ 40 ng/ µL Isixa≥ 500 ng | |||||
Ukuhamba komsebenzi wenkonzo
Ukuhanjiswa kwesampulu
Ukukhupha i-DNA
Ukwakhiwa kweThala leeNcwadi
Ukulandelelana
Uhlalutyo lwedatha
Ukuhanjiswa kwedatha
De novoumbhobho we-bioinformatics
Ukuba ufuna ukubona umbono jikelele wemibhobho yethu eyahlukeneyo yokuhlanganisa:
Uhlalutyo olupheleleyo lwe-bioinformatic, olwahlulwe ngamanyathelo ama-4:
1. Uphando lwe-genome, olusekelwe kuhlalutyo lwe-k-mer olune-NGS reads.Iza kusinika ulwazi malunga:
- Uqikelelo lobungakanani be-genome
- Uqikelelo lwe-heterozygosity
- Uqikelelo lweendawo eziphindaphindayo
2. Ukuhlanganiswa kweGenome ngePacBio HiFi.Ukusebenzisa ukufundwa okude kuya kusinika:
- De novoindibano
- Uvavanyo lokuhlanganisa: kuquka uhlalutyo lweBUSCO lokugqibelela kwe-genome kunye nokumakisha ngasemva kwe-NGS kunye ne-PacBio HiFi reads
3. Indibano yeHi-C.Nje ukuba sibe nendibano, ukuba nolwazi malunga nesakhiwo se-genome 3D kuya kuyenza nzulu ulwazi kwaye kutyebise i-genome ebhekisayo esiyakhayo.
- I-QC yelayibrari ye-Hi-C ukuze kuqikelelwe unxibelelwano olusebenzayo lwe-Hi-C.
- Indibano ye-Hi-C. Siza kwenza ukuhlanganiswa kwee-contigs ngokwamaqela, kulandele ukucwangciswa kwee-contig kwiqela ngalinye kunye nokwabela ulwalathiso lwe-contig.
- Uvavanyo lwe-Hi-C
4. Isichazi-magama sejini:
- Uqikelelo lwe-RNA olungabhalwanga kwikhowudi
- Ukuchongwa kokulandelelana okuphindaphindwayo (ii-transposons kunye nokuphindaphinda kwe-tandem)
- Uqikelelo lwe-gene
- De novo: ii-algorithms ze-ab initio
- Isekelwe kwi-homology
- Isekelwe kwi-transcriptome, enee-reads ezinde nezimfutshane: ii-reads zi-de novoidityaniswe okanye idweliswe kwi-genome eyilwayo
- Inkcazo yezakhi zofuzo eziqikelelweyo ezineedathabheyisi ezininzi
Ukulandelelanisa kwakhonaumbhobho we-bioinformatics
Kubandakanya uhlalutyo olulandelayo:
- Ulawulo loMgangatho weDatha eluhlaza
- Izibalo zokulungelelaniswa kwi-genome yesalathiso
- Ukuchonga okwahlukileyo: i-SNP, i-InDel, i-SV kunye ne-CNV
- Isichazi-magama esisebenzayo seenguqu ezahlukeneyo
Izibalo zokulungelelaniswa nokusasazwa kobunzulu be-genome yesalathiso
Ukubizwa kwe-SNP phakathi kweesampulu ezininzi
Ukuchongwa kwe-InDel – izibalo zobude be-InDel kummandla we-CDS kunye nommandla wonke we-genome
Ukusasazwa kokwahluka kwi-genome - iploti yeCircos
Isichazi-magama esisebenzayo sezakhi zofuzo ezineenguqu ezichongiweyo – iGene Ontology
UChai, Q. et al. (2023) 'I-glutathione S‐transferase GhTT19 imisela umbala weentyatyambo ngokulawula ukuqokelelwa kwe-anthocyanin kwikotoni',Ijenali yeZityalo zeBiotechnology, 21(2), iphe. 433. doi: 10.1111/PBI.13965.
UCheng, H. et al. (2023) 'I-genome yeHevea brasiliensis yasendle ekwinqanaba leChromosome ibonelela ngezixhobo ezintsha zokuzala ezincediswa yi-genomic kunye neendawo ezixabisekileyo zokuphakamisa isivuno serabha',Ijenali yeZityalo zeBiotechnology, 21(5), iphe. 1058–1072. doi: 10.1111/PBI.14018.
ULi, C. et al. (2021) 'Ulandelelwano lwee-genome lubonisa iindlela zokusasazeka kwehlabathi kwaye lucebisa uhlengahlengiso lwe-genetic oluhambelanayo kwinguquko yehashe lolwandle',Unxibelelwano lweNdalo, 12(1). doi: 10.1038/S41467-021-21379-X.
ULi, Y. et al. (2023) 'Utshintsho olukhulu lweChromosomal lukhokelela ekuTshintsheni kweNqanaba leGenome, uLungiso lweNdalo, kunye neSpeciation kwiGayal (Bos frontalis)',Ibhayoloji yeMolekyuli kunye nokuZivela kweMvelo, 40(1). doi: 10.1093/MOLBEV/MSAD006.
UTian, T. et al. (2023) 'Ukuhlanganiswa kwejini kunye nokwahlulwa kwemfuza ye-germplasm yombona ebalaseleyo enganyangekiyo yimbalela',I-Nature Genetics 202355:3, 55(3), iphepha 496–506. doi: 10.1038/s41588-023-01297-y.
UZhang, F. et al. (2023) 'Ukutyhila uphuhliso lwe-tropane alkaloid biosynthesis ngokuhlalutya ii-genomes ezimbini kusapho lweSolanaceae',Unxibelelwano lweNdalo2023 14:1, 14(1), iphe. 1–18. doi: 10.1038/s41467-023-37133-4.
UZeng, T. et al. (2022) 'Uhlalutyo lotshintsho lwe-genome kunye ne-methylation kwiinkukhu zaseTshayina zemveli ngokuhamba kwexesha lubonelela ngengqiqo ngokugcinwa kweentlobo',Ibhayoloji yoNxibelelwano, 5(1), iphe. 1–12. doi: 10.1038/s42003-022-03907-7.
Izifundo zetyala ezinzima:
Indibano yeTelomere-ukuya kwiTelomere:UFu, A. et al. (2023) 'I-Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) ityhila uphuhliso lwesiqhamo, ukwakheka kunye neempawu zemfuza ezivuthwayo',Uphando lwezoLimo, 10(1). doi: 10.1093/HR/UHAC228.
Indibano yeHaplotype:UHu, W. et al. (2021) 'I-genome echazwe yi-allele ityhila ukwahluka kwe-biallelic ngexesha lokuvela kwe-cassava',Isityalo seMolekyuli, 14(6), iphepha 851–854. doi: 10.1016/j.molp.2021.04.009.
Ukuhlanganiswa kwe-genome enkulu:UYuan, J. et al. (2022) 'Isiseko se-genomic se-giga-chromosomes kunye ne-giga-genome ye-tree peony Paeonia ostii',Unxibelelwano lweNdalo2022 13:1, 13(1), iphe. 1–16. doi: 10.1038/s41467-022-35063-1.
Ukuhlanganiswa kwe-genome ye-polyploid:UZhang, Q. et al. (2022) 'Iingcamango ze-genomic malunga nokunciphisa kwe-chromosome yakutshanje ye-autopolyploid sugarcane Saccharum spontaneum',I-Nature Genetics 202254:6, 54(6), iphepha 885–896. doi: 10.1038/s41588-022-01084-1.
