Ukulandelana Kwezakhi Zofuzo Zezitshalo/Zezilwane
Izici Zesevisi
De novo
Le ndlela iwusizo kakhulu kuma-genome ayinselele njengalawo anezinga eliphezulu le-heterozygosity, izindawo eziphindaphindayo, ama-genome e-polypoloid, okuqukethwe okungajwayelekile kwe-CG njll.
Isixazululo sethu esisodwa sinikeza izinsizakalo zokulandelana ezihlanganisiwe kanye nokuhlaziywa kwe-bioinformatic okuletha i-genome ehlanganisiwe yekhwalithi ephezulu. Ucwaningo lokuqala lwe-genome ne-Illumina lunikeza izilinganiso zobukhulu be-genome kanye nobunzima, futhi lolu lwazi lusetshenziselwa ukuqondisa isinyathelo esilandelayo sokulandelana okufundwa isikhathi eside nge-PacBio HiFi, kulandelwe yide novoukuhlanganiswa kwama-contig. Ukusetshenziswa okulandelayo kwe-HiC assembly kwenza kube lula ukunamathela kwama-contig ku-genome, kutholakale i-chromosome-level assembly. Okokugcina, i-genome ichazwa ngokubikezela izakhi zofuzo nangokulandelanisa izakhi zofuzo eziveziwe, kusetshenziswe ama-transcriptome anokufundwa okufushane nokude.
-- Ukuhlanganiswa kwezinsizakalo eziningi zokulandelana kanye ne-bioinformatic kusisombululo esisodwaIsevisi efanele inoveli yokwakha
-- ama-genome noma ukuthuthukiswa kwama-genome okubhekiselwa kuwo akhona ezinhlobo ezithakaselwayo.
Ukulandelana kabusha
-- Ukulungiselela umtapo wolwazi kungaba okujwayelekile noma okungenawo ama-PCR
-- Itholakala kumapulatifomu amane okulandelana: i-Illumina NovaSeq, i-MGI T7, i-Nanopore Promethion P48 noma i-PacBio Revio.
-- Ukuhlaziywa kwe-Bioinformatic kugxile ekubizeni okuhlukile: i-SNP, i-InDel, i-SV kanye ne-CNV
Izinzuzo Zesevisi
●Ubuchwepheshe Obubanzi kanye Nerekhodi Lokushicilela: Ngobade novoizinsizakalo, siqoqe ulwazi olukhulu ekuhlanganisweni kwe-genome esezingeni eliphezulu yezinhlobo ezahlukahlukene, kufaka phakathi ama-genome e-diploid kanye nama-genome ayinkimbinkimbi kakhulu ezinhlobo ze-polyploid kanye ne-allopolyploid. Kusukela ngo-2018, sibe negalelo ezincwadini ezingaphezu kuka-300 ezinethonya elikhulu, futhi ezingu-20+ zazo zishicilelwe ku-Nature Genetics. Ngokulandelana kabusha kwezakhi zofuzo, siqoqe izinhlobo ezingaphezu kwe-1000, okwaholela emacaleni angaphezu kwe-1000 ashicilelwe anesici somthelela esihlanganisiwe esingaphezu kwe-5000.
●Isixazululo Sokuma Kanye: Kuvuliwede novoNgokulandelana, indlela yethu ehlanganisiwe ihlanganisa ubuchwepheshe obuningi bokulandelana kanye nokuhlaziywa kwe-bioinformatic kube ukuhamba komsebenzi okuhlangene, okuletha i-genome ehlanganisiwe esezingeni eliphezulu.
●Kulungiselelwe Izidingo Zakho: Ukuhamba komsebenzi wethu wesevisi kungenziwa ngezifiso, okuvumela ukuzivumelanisa nezimo ze-genome ezinezici ezahlukahlukene kanye nezidingo ezithile zocwaningo.
●Ithimba Le-Bioinformatics Nelebhu Elinekhono Eliphezulu: Kungakhathaliseki ukuthi kungenxade novoUkulandelanisa noma ukulandelelanisa kabusha, ithimba lethu linamathuluzi nolwazi olunekhono lokuqinisekisa impumelelo yephrojekthi. Lokhu kungaqinisekiswa ngochungechunge lwama-patents kanye namalungelo okushicilela esofthiwe abawakhile.
● Usekelo Lwangemva Kokuthengisa:Ukuzibophezela kwethu kudlulela ngale kokuqedwa kwephrojekthi ngesikhathi senkonzo yezinyanga ezintathu ngemuva kokuthengisa. Phakathi nalesi sikhathi, sinikeza ukulandelwa kwephrojekthi, usizo lokuxazulula izinkinga, kanye nezikhathi zemibuzo nezimpendulo ukuze kuxazululwe noma yimiphi imibuzo ehlobene nemiphumela.
●Ukuhlaziywa Okuphelele Kwe-Bioinformatics: Kufaka phakathi ukubiza okuguquguqukayo kanye nesichasiselo somsebenzi.
●Isichasiselo Esiphelele Sokulandelana: Sisebenzisa izizindalwazi eziningi ukuze sichaze izakhi zofuzo ngendlela esebenzayo ngezinguquko ezitholakele futhi senze ukuhlaziywa kokunotha okuhambisanayo, sinikeze ulwazi ngamaphrojekthi akho ocwaningo.
Imininingwane Yesevisi
| Izinhlobo ezizobonakala | Isu lokulandelana kwezigaba | Ukujula okunconywayo |
| I-SNP ne-InDel | I-Illumina NovaSeq PE150 noma i-MGI T7 | 10x |
| I-SV ne-CNV (okunganembile kangako) | 30x | |
| I-SV ne-CNV (kunembe kakhudlwana) | I-Nanopore Prom P48 | 20x |
| Ama-SNP, ama-Indels, ama-SV kanye nama-CNV | I-PacBio Revio | 10x |
Izidingo Zesampula
| Ama-nucleic acid akhishwe ezicutshini noma ezicutshini | I-Illumina/MGI | I-Nanopore (iLabhulali engu-8 Kb) | I-PacBio (iLabhulali engu-15 Kb)
| ||
| I-Animal Viscera | ≥ 0.2 g | ≥ 0.5 g | ≥ 1 g
| ||
| Imisipha Yezilwane | |||||
| Igazi Lezilwane Ezincelisayo | ≥ 0.3 mL | ≥ 0.5 mL
| ≥ 1 mL
| ||
| Igazi Lenkukhu/Lenhlanzi | ≥ 0.05 mL | ≥ 0.1 mL
| ≥ 0.1 mL
| ||
| Isitshalo - Iqabunga Elisha | ≥ 0.5 g | ≥ 1 g
| ≥ 2 g
| ||
| Amaseli Akhuliswe | ≥ 1x106 | ≥ 5x106 | ≥ 5x106
| ||
| Izicubu ezithambile zezinambuzane/Umuntu Ngamunye | ≥ 0.2 g | ≥ 0.3 g
| ≥ 1 g
| ||
| Izinto eziphilayo zasemanzini - Izicubu zemisipha | ≥ 0.3 g | ≥ 1 g | ≥ 1.5 g | ||
| Izinto eziphilayo zasemanzini - Ulwelwe | ≥ 0.5 g | ≥ 1.5 g | ≥ 3 g | ||
| I-DNA ekhishwe
| Ukugxila: ≥ 1 ng/µL Inani: ≥ 30 ng Ukuwohloka noma ukungcola okulinganiselwe noma okungenakho
| Ukugxila Inani
OD260/280
OD260/230
Ukuwohloka noma ukungcola okulinganiselwe noma okungenakho
| ≥ 40 ng/µL 2 µg/iseli lokugeleza/isampula
1.7 - 2.2
1.5 - 3.0 | Ukugxila Inani
OD260/280
OD260/230
Ukuwohloka noma ukungcola okulinganiselwe noma okungenakho | ≥ 50 ng/µL 8 µg/iseli lokugeleza/isampula
1.7 - 2.2
1.8 - 2.5 |
| Ukulungiselela Umtapo Wolwazi Ongena-PCR: Ukugxila ≥ 40 ng/µL Inani ≥ 500 ng | |||||
Ukugeleza Komsebenzi Wesevisi
Ukulethwa kwesampula
Ukukhishwa kwe-DNA
Ukwakhiwa komtapo wolwazi
Ukulandelana
Ukuhlaziywa kwedatha
Ukulethwa kwedatha
De novoipayipi le-bioinformatics
Uma ufuna ukubona umbono ophelele wamapayipi ethu ahlukene okuhlanganisa:
Ukuhlaziywa okuphelele kwe-bioinformatic, okuhlukaniswe ngezinyathelo ezine:
1. Ucwaningo lwe-genome, olusekelwe ekuhlaziyweni kwe-k-mer nge-NGS reads.Izosinika ulwazi mayelana nalokhu:
- Ukuqagela usayizi we-genome
- Isilinganiso se-heterozygosity
- Isilinganiso sezindawo eziphindaphindayo
2. Ukuhlanganiswa kwe-Genome nge-PacBio HiFi.Ukusebenzisa ukufunda okude kuzosinika:
- De novoumhlangano
- Ukuhlolwa kokuhlanganiswa: kufaka phakathi ukuhlaziywa kwe-BUSCO kokuphelela kwe-genome kanye nokuhlela ngemuva kwe-NGS kanye ne-PacBio HiFi reads
3. Ukuhlanganiswa kwe-Hi-C.Uma sesiyihlanganisile, ukuba nolwazi ngesakhiwo se-genome 3D kuzojulisa ulwazi futhi kucebise i-genome yokubhekisela esiyakhayo.
- I-QC yelabhulali ye-Hi-C ukuze kulinganiswe ukusebenzisana kwe-Hi-C okusebenzayo.
- Ukuhlanganiswa kwe-Hi-C. Sizokwenza ukuhlanganiswa kwama-contig ngamaqembu, kulandelwe ukuhleleka kwama-contig ngaphakathi kweqembu ngalinye bese sinikeza ukuqondiswa kwama-contig.
- Ukuhlolwa kwe-Hi-C
4. Isichasiselo se-genome:
- Ukubikezela kwe-RNA okungasebenzisi ikhodi
- Ukuhlonza ukulandelana okuphindaphindiwe (ama-transposon kanye nokuphindaphinda kwe-tandem)
- Ukubikezela kwezakhi zofuzo
- De novo: ama-algorithms okuqala
- Kususelwa ku-homology
- Ngokusekelwe ku-transcriptome, ngokufundwa okude nokufushane: ukufundwa ku-de novokuhlanganiswe noma kufakwe kumephu ye-genome eklanyiwe
- Isichasiselo sezakhi zofuzo ezibikezelwe ngemininingwane eminingi
Ukulandelanisa kabushaipayipi le-bioinformatics
Kufaka phakathi ukuhlaziywa okulandelayo:
- Ukulawulwa Kwekhwalithi Yedatha Engavuthiwe
- Izibalo zokuhambisana ne-genome yokubhekisela
- Ukuhlonza okuhlukile: i-SNP, i-InDel, i-SV kanye ne-CNV
- Isichasiselo esisebenzayo sezinhlobo ezahlukene
Izibalo zokuhambisana nokusatshalaliswa kokujula kokulandelana kwe-genome
Ukubizwa kwe-SNP phakathi kwamasampula amaningi
Ukuhlonza i-InDel - izibalo zobude be-InDel esifundeni se-CDS kanye nesifunda sonke se-genome
Ukusatshalaliswa kokwehluka kulo lonke i-genome - i-Circos plot
Isichasiselo esisebenzayo sezakhi zofuzo ezinezinhlobo eziveziwe - i-Gene Ontology
UChai, Q. et al. (2023) 'I-glutathione S‐transferase GhTT19 inquma umbala wezimbali ngokulawula ukuqongelela kwe-anthocyanin kukotini',Ijenali ye-Plant Biotechnology, 21(2), p. 433. doi: 10.1111/PBI.13965.
UCheng, H. et al. (2023) 'I-genome ye-Hevea brasiliensis yasendle esezingeni le-Chromosome inikeza amathuluzi amasha okuzalanisa okusizwa yi-genomic kanye ne-loci ebalulekile yokuphakamisa isivuno senjoloba',Ijenali ye-Plant Biotechnology, 21(5), amakhasi 1058–1072. doi: 10.1111/PBI.14018.
ULi, C. et al. (2021) 'Ukulandelana kwezakhi zofuzo kwembula imizila yokusabalala komhlaba wonke futhi kusikisela ukuzivumelanisa kwezakhi zofuzo ezihambisanayo ekuguqukeni kwehhashi lasolwandle',Ukuxhumana Kwemvelo, 12(1). doi: 10.1038/S41467-021-21379-X.
ULi, Y. et al. (2023) 'Izinguquko Ezinkulu Ze-Chromosomal Ziholela Ekushintsheni Kokubonakaliswa Kwezinga Le-Genome, Ukuzivumelanisa Nemvelo, kanye Nokukhethekile ku-Gayal (Bos frontalis)',I-Molecular Biology kanye Nokuziphendukela Kwemvelo, 40(1). doi: 10.1093/MOLBEV/MSAD006.
UTian, T. et al. (2023) 'Ukuhlanganiswa kwezakhi zofuzo kanye nokwahlukaniswa kwezakhi zofuzo ze-germplasm yommbila evelele engamelani nesomiso',Izakhi Zofuzo Zemvelo 202355:3, 55(3), amakhasi 496–506. doi: 10.1038/s41588-023-01297-y.
UZhang, F. et al. (2023) 'Ukwembula ukuvela kwe-tropane alkaloid biosynthesis ngokuhlaziya ama-genome amabili emndenini wakwaSolanaceae',Ukuxhumana Kwemvelo2023 14:1, 14(1), amakhasi 1–18. doi: 10.1038/s41467-023-37133-4.
UZeng, T. et al. (2022) 'Ukuhlaziywa kwezinguquko ze-genome kanye ne-methylation ezinkukhu zomdabu zaseShayina ngokuhamba kwesikhathi kunikeza ukuqonda ngokulondolozwa kwezinhlobo',Ibhayoloji Yokuxhumana, 5(1), amakhasi 1–12. doi: 10.1038/s42003-022-03907-7.
Izifundo zamacala eziyinselele:
Ukuhlanganiswa kwe-Telomere kuya ku-telomere:UFu, A. et al. (2023) 'Ukuhlanganiswa kwe-genome ye-Telomere-kuya-telomere ye-bitter melon (i-Momordica charantia L. var. abbreviata Ser.) kwembula ukuthuthukiswa kwezithelo, ukwakheka kanye nezici zofuzo zokuvuthwa',Ucwaningo Lwezolimo, 10(1). doi: 10.1093/HR/UHAC228.
Ukuhlanganiswa kwe-Haplotype:UHu, W. et al. (2021) 'I-genome echazwe yi-allele yembula ukuhlukaniswa kwe-biliallelic ngesikhathi sokuvela kwe-cassava',Isitshalo Se-Molecular, 14(6), amakhasi 851-854. doi: 10.1016/j.molp.2021.04.009.
Ukuhlanganiswa kwe-genome enkulu:UYuan, J. et al. (2022) 'Isisekelo se-genomic sama-giga-chromosome kanye ne-giga-genome ye-tree peony Paeonia ostii',Ukuxhumana Kwemvelo2022 13:1, 13(1), amakhasi 1–16. doi: 10.1038/s41467-022-35063-1.
Ukuhlanganiswa kwe-genome ye-polyploid:UZhang, Q. et al. (2022) 'Ukuqonda kwe-genomic ekunciphiseni kwakamuva kwe-chromosome ye-autopolyploid sugarmoba Saccharum spontaneum',Izakhi Zofuzo Zemvelo 202254:6, 54(6), amakhasi 885-896. doi: 10.1038/s41588-022-01084-1.
