Seboka sa Novo Fungal Genome
BMKGENE e fana ka litharollo tse fapaneng bakeng sa liphatsa tsa lefutso tsa fungal, ho fana ka litlhoko tse fapaneng tsa lipatlisiso le botlalo bo lakatsehang ba genome. Ho sebelisa tatellano e khuts'oane ea Illumina feela ho lumella ho hlahisa genome ea moralo. Tatelano ea ho bala nako e khuts'oane le ea nako e telele e sebelisang Nanopore kapa Pacbio e kopantsoe bakeng sa genome e ntlafalitsoeng ea fungal e nang le li-contig tse telele. Ho feta moo, ho kopanya tatellano ea Hi-C ho eketsa bokhoni le ho feta, ho nolofalletsa ho fihlella genome e felletseng ea boemo ba chromosome.
Likarolo tsa Tšebeletso
Ka likhetho tse tharo tseo u ka khethang ho tsona ho latela tekanyo e lakatsehang ea botlalo ba genome:
● Tlhophiso ea Khetho ea Genome: Tatelano ea nako e khuts'oane le Illumina NovaSeq PE150.
● Khetho ea Fungul Fine Genome:
Patlisiso ea Genome: Illumina NovaSeq PE150.
Kopano ea Genome: PacBio Revio (HiFi e bala) kapa Nanopore PromethION 48.
● Fungal Genome ea boemo ba Chromosome:
Patlisiso ea Genome: Illumina NovaSeq PE150.
Kopano ea Genome: PacBio Revio (HiFi e bala) kapa Nanopore PromethION 48.
Ho kopanya anchoring ka kopano ea Hi-C.
Melemo ea Tšebeletso
●Multiple Sequencing Strategies A fumaneha: Bakeng sa lipheo tse fapaneng tsa lipatlisiso le litlhoko tsa botlalo ba genome
●Tlatsa Bioinformatics Workflow:Sena se kenyelletsa kopano ea liphatsa tsa lefutso le bokhopo ba likarolo tse ngata tsa genomic, tlhaloso ea liphatsa tsa lefutso, le contig anchoring.
●Tsebo e Pharalletseng: Ka liphatsa tsa lefutso tse fetang 12,000 tse kopaneng, re tlisa boiphihlelo ba lilemo tse fetang leshome, sehlopha sa bahlahlobisisi ba nang le boiphihlelo, litaba tse felletseng, le ts'ehetso e ntle haholo ea kamora thekiso.
●Tšehetso ea Ka mor'a Thekiso:Boitlamo ba rona bo fetela ka nģ'ane ho ho phethoa ha morero ka nako ea tšebeletso ea likhoeli tse 3 ka mor'a thekiso. Nakong ena, re fana ka tatellano ea projeke, thuso ea ho rarolla mathata, le linako tsa Q&A ho araba lipotso life kapa life tse amanang le sephetho.
Litlhaloso tsa Tšebeletso
| Tshebeletso | Leano la Tatelano | Taolo ea Boleng |
| Moralo oa Genome | Illumina PE150 100x | Q30≥85% |
| Genome e ntle | Phuputso ea Genome: Illumina PE150 50 x Kopano: PacBio HiFi 30x kapa Nanopore 100x | contig N50 ≥1Mb (Pacbio Unicellular) contig N50 ≥2Mb (ONT Unicellular) contig N50 ≥500kb (Tse ling) |
| Genome ea boemo ba chromosome | Phuputso ea Genome: Illumina PE150 50 x Kopano: PacBio HiFi 30x kapa Nanopore 100x Kopano ea Hi-C 100x | Contig anchoring ratio>90%
|
Litlhoko tsa Tšebeletso
| Khokahano (ng/µL) | Kakaretso (µg) | Bolumo (µL) | OD260/280 | OD260/230 | |
| PacBio | ≥20 | ≥2 | ≥20 | 1.7-2.2 | ≥1.6 |
| Nanopore | ≥40 | ≥2 | ≥20 | 1.7-2.2 | 1.0-3.0 |
| Illumina | ≥1 | ≥0.06 | ≥20 | - | - |
Fungus ea Unicellular: ≥3.5x1010 lisele
Macro Fungus: ≥10 g
Phallo ea Mosebetsi oa Ts'ebeletso
Mohlala oa thomello
Kaho ea laebrari
Tatelano
Tlhahlobo ea lintlha
Litšebeletso tsa ka mor'a thekiso
E kenyelletsa Tlhahlobo e Latelang:
Patlisiso ea Genome:
- Ho hlophisa taolo ea boleng ba data
- Khakanyo ea Genome: boholo, heterozygosity, likarolo tse pheta-phetoang
Kopano e Ntle ea Genome:
- Ho Sequencing Taolo ea Boleng ba Boitsebiso
- De novoKopano
- Genome Component Analysis: Polelo ea CDS le likarolo tse ngata tsa genomic
- Tlhaloso e sebetsang e nang le li-database tse ngata tse akaretsang (GO, KEGG, joalo-joalo) le li-database tse tsoetseng pele (CARD, VFDB, joalo-joalo)
Kopano ea Hi-C:
- Tekolo ea Laebrari ea Hi-C.
- Contigs anchoring clustering, ordering and orienting
- Tekolo ea Kopano ea HI-C: E ipapisitse le genome ea litšupiso le 'mapa oa mocheso
Tlhahlobo ea Genome: kabo ea k-mer
Kopano ea Genome: gene homologous annotation (NR database)
Kopano ea Genome: Tlhaloso e sebetsang ea liphatsa tsa lefutso (GO)
Lekola tsoelopele e tsamaisoang ke litšebeletso tsa kopano ea fungal genome ea BMKGene ka pokello e hlophisitsoeng ea lingoliloeng.
Hao, J. et al. (2023) 'Profiling e kopantsoeng ea omic ea mushroom ea meriana Inotus obliquus tlas'a maemo a tlas'a metsi',BMC Genomics, 24(1), leqepheng la 1–12. doi: 10.1186/S12864-023-09656-Z/FIGURES/3.
Lu, L. et al. (2023) 'Tlhaloso ea liphatsa tsa lefutso e senola ho iphetola ha lintho le mekhoa ea likokoana-hloko ea koro e bohale ea mahlo a pathogen Rhizoctonia cerealis',The Crop Journal, 11(2), leqepheng la 405-416. doi: 10.1016/J.CJ.2022.07.024.
Zhang, H. et al. 2023Lefu la Semela, 107(3), leqepheng la 929-934. doi: 10.1094/PDIS-08-22-1921-A
Zhang, SS et al. (2023) 'Bopaki ba liphatsa tsa lefutso le limolek'hule tsa Tetrapolar Mating System ho Edible Mushroom Grifola frondosa',Journal ea Li-fungus, 9(10), leq. 959. doi: 10.3390/JOF9100959/S1.
