I-Novo Fungal Genome Assembly
I-BMKGENE inikeza izixazululo eziguquguqukayo zezakhi zofuzo zesikhunta, ihlinzekela izidingo zocwaningo ezihlukahlukene kanye nokuphelela kofuzo olufiswayo. Ukusebenzisa ukulandelana kwe-Illumina yokufunda okufushane kuphela kuvumela ukukhiqizwa kwe-genome esalungiswa. Ukufunda okufushane nokufunda isikhathi eside kusetshenziswa i-Nanopore noma i-Pacbio kuhlanganiswe ukuze kube nofuzo lwesikhunta olucwengisiswe kakhulu olunama-contig amade. Ngaphezu kwalokho, ukuhlanganisa ukulandelana kwe-Hi-C kuthuthukisa futhi amandla, kuvumela ukutholwa kwegenome yeleveli ye-chromosome ephelele.
Izici Zesevisi
Ngezinketho ezintathu ongakhetha kuzo kuye ngezinga elifiswayo lokuphelela kofuzo:
● Inketho ye-Genome Esalungiswa: Ukulandelana kokufunda okufushane nge-Illumina NovaSeq PE150.
● Inketho ye-Fungal Fine Genome:
I-Genome Survey: I-Illumina NovaSeq PE150.
I-Genome Assembly: I-PacBio Revio (i-HiFi ifundeka) noma i-Nanopore PromethION 48.
● I-Fungal Genome yeleveli ye-Chromosome:
I-Genome Survey: I-Illumina NovaSeq PE150.
I-Genome Assembly: I-PacBio Revio (i-HiFi ifundeka) noma i-Nanopore PromethION 48.
I-Contig anchoring nge-Hi-C assembly.
Izinzuzo Zesevisi
●Amasu Okulandelana Okuningi Ayatholakala: Ngezinhloso ezahlukene zocwaningo kanye nezidingo zokuphelela kofuzo
●Qedela ukugeleza kokusebenza kwe-Bioinformatics:Lokhu kufaka phakathi ukuhlanganiswa kofuzo kanye nokubikezelwa kwezinto eziningi ze-genomic, isichasiselo sofuzo esisebenzayo, kanye ne-contig anchoring.
●Ubungcweti Olubanzi: Njengoba kuhlanganiswe ama-microbial genomes angaphezu kuka-12,000, siletha isipiliyoni esingaphezu kweshumi leminyaka, ithimba lokuhlaziya elinekhono eliphezulu, okuqukethwe okuphelele, nokusekelwa okuhle kakhulu kwangemva kokuthengisa.
●Ukusekelwa Kwangemva Kokuthengisa:Ukuzinikela kwethu kudlulela ngalé kokuphothulwa kwephrojekthi ngenkathi yesevisi yezinyanga ezi-3 ngemva kokuthengisa. Ngalesi sikhathi, sinikezela ngokulandelelwa kwephrojekthi, usizo lokuxazulula inkinga, namaseshini e-Q&A ukuze siphendule noma yimiphi imibuzo ehlobene nemiphumela.
Imininingwane Yesevisi
| Isevisi | Isu Lokulandelanisa | Ikhwalithi yokulawula |
| I-Genome esalungiswa | I-Illumina PE150 100x | Q30≥85% |
| IGenome Enhle | Inhlolovo ye-Genome: I-Illumina PE150 50 x Umhlangano: I-PacBio HiFi 30x noma i-Nanopore 100x | contig N50 ≥1Mb (Pacbio Unicellular) contig N50 ≥2Mb (ONT Unicellular) contig N50 ≥500kb (Abanye) |
| I-genome yezinga le-Chromosome | Inhlolovo ye-Genome: I-Illumina PE150 50 x Umhlangano: I-PacBio HiFi 30x noma i-Nanopore 100x I-Hi-C Assembly 100x | I-Contig anchoring ratio>90%
|
Izidingo Zesevisi
| Ukugxila (ng/µL) | Inani eliphelele (µg) | Ivolumu (µL) | OD260/280 | OD260/230 | |
| I-PacBio | ≥20 | ≥2 | ≥20 | 1.7-2.2 | ≥1.6 |
| I-Nanopore | ≥40 | ≥2 | ≥20 | 1.7-2.2 | 1.0-3.0 |
| Illumina | ≥1 | ≥0.06 | ≥20 | - | - |
Ukhunta Unicellular: ≥3.5x1010 amaseli
Isikhunta esikhulu: ≥10 g
Ukugeleza Komsebenzi Wesevisi
Ukulethwa kwesampula
Ukwakhiwa komtapo wolwazi
Ukulandelanisa
Ukuhlaziywa kwedatha
Amasevisi angemuva kokuthengisa
Kubandakanya Ukuhlaziya Okulandelayo:
I-Genome Survey:
- Ilandelanisa ukulawulwa kwekhwalithi yedatha
- Ukulinganisa kwe-genome: usayizi, i-heterozygosity, izakhi eziphindaphindayo
I-Fine Genome Assembly:
- Ilandelanisa Ukulawulwa Kwekhwalithi Yedatha
- De novoUmhlangano
- I-Genome Component Analysis: Ukubikezelwa kwe-CDS nezici eziningi ze-genomic
- Isichasiselo esisebenzayo esinemininingwane eminingi ejwayelekile (GO, KEGG, njll.) kanye nemininingwane yolwazi ethuthukile (i-CARD, VFDB, njll.)
I-Hi-C Assembly:
- I-Hi-C Library Assessment.
- Ama-Contigs ahlanganisa ukuhlanganisa, ukuhleleka kanye nokuma
- Ukuhlolwa Komhlangano we-HI-C: Ngokusekelwe ku-genome eyinkomba nemephu yokushisa
Inhlolovo ye-genome: ukusatshalaliswa kwe-k-mer
Ukuhlanganiswa kwe-genome: isichasiselo se-gene homologous (isizindalwazi se-NR)
Ukuhlanganiswa kwe-genome: isichasiselo sofuzo esisebenzayo (GO)
Hlola intuthuko egqugquzelwa izinsizakalo zokuhlanganiswa kofuzo lwefungal ye-BMKGene ngeqoqo elikhethiwe lokushicilelwe.
Hao, J. et al. (2023) 'Iphrofayili ye-omic ehlanganisiwe yekhowe lezokwelapha i-Inonotus obliquus ngaphansi kwezimo ezingaphansi kwamanzi',I-BMC Genomics, 24(1), amakhasi 1-12. doi: 10.1186/S12864-023-09656-Z/IZIBALO/3.
Lu, L. et al. (2023) 'Ukulandelana kwe-genome kuveza ukuziphendukela kwemvelo kanye nezindlela ze-pathogenic ze-eyepot ebukhali kakolweni pathogen i-Rhizoctonia cerealis',I-Crop Journal, 11(2), amakhasi 405-416. doi: 10.1016/J.CJ.2022.07.024.
U-Zhang, H. et al. (2023) 'Izinsiza zeGenome Zezinhlobo Ezine ze-Clarireedia Ezibangela I-Dollar Spot Kuma-Turfgrasses Ahlukahlukene',Izifo Zezitshalo, 107(3), amakhasi 929-934. doi: 10.1094/PDIS-08-22-1921-A
Zhang, SS et al. (2023) 'Ubufakazi beGenetic kanye Nemolekyuli Yesistimu Yokukhwelana Kwe-Tetrapolar ku-Edible Mushroom Grifola frondosa',Ijenali Yesikhunta, 9(10), p. 959. doi: 10.3390/JOF9100959/S1.
