Chirimwa/Mhuka Yese Genome Sequencing
Zvimiro Zvebasa
● Kugadzirira raibhurari kunogona kuva kwakajairika kana kuti PCR-isina
● Inowanikwa mu 4 sequencing platforms: Illumina NovaSeq, MGI T7, Nanopore Promethion P48, kana PacBio Revio.
● Kuongorora kweBioinformamatic kwakanangana nekuonekwa kwezvinhu zvakasiyana-siyana: SNP, InDel, SV uye CNV
Basa Rinobatsira
●Hunyanzvi Hwakawanda uye Zvinyorwa Zvinyorwa: Kuwedzera ruzivo mukutevedzana kwegenome kune anopfuura zana emarudzi kwakonzera pamusoro pe1000 dzakaburitswa makesi ane cumulative kukanganisa chinhu chinodarika zviuru zvishanu.
●Comprehensive Bioinformatics Analysis: Kusanganisira mutsauko wekufona uye chirevo chebasa.
● Kutsigira Kwepashure-Kutengesa:Kuzvipira kwedu kunowedzera kupfuura kupera kweprojekiti nemwedzi mitatu mushure mekutengesa sevhisi nguva. Munguva ino, tinopa kutevedza kweprojekiti, rubatsiro rwekugadzirisa matambudziko, uye maQ&A masesheni kugadzirisa chero mibvunzo ine chekuita nemhedzisiro.
●Comprehensive Annotation+
Sevhisi Zvinotsanangurwa
| Variants kuti zvizivikanwe | Sequencing strategy | Yakakurudzirwa kudzika |
| SNP uye InDel | Illumina NovaSeq PE150 kana MGI T7 | 10x |
| SV uye CNV (zvishoma zvishoma) | 30x | |
| SV uye CNV (zvakawanda chaizvo) | Nanopore Prom P48 | 20x |
| SNPs, Indels, SV uye CNV | PacBio Revio | 10x |
Muenzaniso Zvinodiwa
| Tissue kana kubviswa nucleic acids | Illumina/MGI | Nanopore | PacBio
| ||
| Animal Viscera | 0.5-1 g | ≥ 3.5 g
| ≥ 3.5 g
| ||
| Tsandanyama dzemhuka | ≥ 5 g
| ≥ 5 g
| |||
| Ropa reMammalian | 1.5 mL | ≥ 0.5 mL
| ≥ 5 mL
| ||
| Huku/Hove Ropa | ≥ 0.1 mL
| ≥ 0.5 mL
| |||
| Chirimwa- Fresh Leaf | 1-2 g | ≥ 2 g
| ≥ 5 g
| ||
| Cultured Cells |
| ≥ 1x107
| ≥ 1x108
| ||
| Insect soft tissue/Munhu oga | 0.5-1 g | ≥ 1 g
| ≥ 3 g
| ||
| DNA yakabviswa
| Kuisa pfungwa: ≥ 1 ng/ µL Kuwanda: ≥ 30 ng Yakaganhurirwa kana isina kudzikisira kana kusvibiswa
| Concentration Mari
OD260/280
OD260/230
Yakaganhurirwa kana isina kudzikisira kana kusvibiswa
| ≥ 40 ng/µL 4 µg/flow cell/sample
1.7-2.2
≥1.5 | Concentration Mari
OD260/280
OD260/230
Yakaganhurirwa kana isina kudzikisira kana kusvibiswa | ≥ 50 ng/µL 10 µg/flow cell/sample
1.7-2.2
1.8-2.5 |
| PCR-isina Raibhurari Gadziriro: Concentration≥ 40 ng/µL Kuwanda≥ 500 ng | |||||
Kuyerera Kwebasa Rebasa
Muenzaniso wekutumira
Kutorwa kweDNA
Kuvakwa kweraibhurari
Sequencing
Data analysis
Data delivery
Inosanganisira ongororo inotevera:
- Raw Data Quality Control
- Statistics of alignment to reference genome
- Kuzivikanwa kwakasiyana: SNP, InDel, SV uye CNV
- Kushanda annotation yezvakasiyana
Nhamba dzekugadzirisa kune referensi genome - kutevedza kudzika kwekugovera
SNP kufona pakati peakawanda samples
InDel chiziviso - nhamba dzehurefu hweInDel mudunhu reCDS uye genome-yakafara dunhu.
Kugovera kwakasiyana kune genome - Circos plot
Inoshanda tsinhiro yemajini ane akasiyana akaonekwa - Gene Ontology
Chai, Q. et al. (2023) 'A glutathione S-transferase GhTT19 inosarudza ruva petal pigmentation kuburikidza nekugadzirisa anthocyanin kuunganidza mukotoni', Plant Biotechnology Journal, 21 (2), p. 433. doi: 10.1111/PBI.13965.
Cheng, H. et al. (2023) 'Chromosome-level wild Hevea brasiliensis genome inopa midziyo mitsva yekuberekesa inobatsirwa nejenomic uye nzvimbo yakakosha yekusimudza goho rerabha', Plant Biotechnology Journal, 21(5), mapeji 1058–1072. doi: 10.1111/PBI.14018.
Li, A. nevamwe. (2021) 'Genome of the estuarine oyster inopa ruzivo rwemamiriro ekunze uye adaptive plasticity', Communications Biology 2021 4: 1, 4 (1), mapeji 1-12. doi: 10.1038/s42003-021-02823-6.
Zeng, T. et al. (2022) 'Ongororo yekuchinja kwegenome uye methylation muhuku dzechiChinese nekufamba kwenguva inopa ruzivo rwekuchengetedza mhuka', Communications Biology, 5 (1), mapeji 1–12. doi: 10.1038/s42003-022-03907-7.
