条形 ibhanile-03

Iimveliso

De novo Fungal Genome Assembly

Umfanekiso we53

 

 

I-BMKGENE ibonelela ngezisombululo eziguquguqukayo kwiigenomes zokungunda, ukulungiselela iimfuno zophando ezahlukeneyo kunye nokugqibelela kwegenome enqwenelekayo. Ukusebenzisa ukulandelelana kwe-Illumina okufutshane kuvumela ukuveliswa kwe-genome eyidrafti. Ukufundwa okufutshane kunye nokulandelelana kwexesha elide usebenzisa i-Nanopore okanye i-Pacbio zidityanisiwe kwi-genome yefungal esulungekileyo kunye ne-contigs emide. Ngaphezu koko, ukudibanisa ulandelelwano lwe-Hi-C kuphucula ngakumbi amandla, okwenza ukuba kufunyanwe igenome yomgangatho wechromosome epheleleyo.


Iinkcukacha zeNkonzo

Bioinformatics

Iziphumo zeDemo

Iimpapasho ezikhoyo

Iimpawu zeNkonzo

Ngeendlela ezintathu ezinokuthi ukhethe kuzo ngokuxhomekeke kwinqanaba elifunekayo lokugqibelela kwegenome:

● I-Draft Genome Option: Ulandelelwano lokufunda elifutshane kunye ne-Illumina NovaSeq PE150.

● UKhetho lweFungal Fine Genome:

Uvavanyo lweGenome: Illumina NovaSeq PE150.

INdibano yeGenome: I-PacBio Revio (i-HiFi ifundeka) okanye i-Nanopore PromethION 48.

● IFungal Genome yenqanaba leChromosome:

Uvavanyo lweGenome: Illumina NovaSeq PE150.

INdibano yeGenome: I-PacBio Revio (i-HiFi ifundeka) okanye i-Nanopore PromethION 48.

Ukudibanisa i-ankile ngendibano ye-Hi-C.

Iinkonzo eziluncedo

IiNdlela ezininzi zokuSelenza ziyafumaneka: Ngeenjongo ezahlukeneyo zophando kunye neemfuno zokugqibelela kwegenome

Gqibezela i-Bioinformatics Workflow:Oku kubandakanya ukudibanisa i-genome kunye nokuqikelelwa kwezinto ezininzi ze-genomic, inkcazo yemfuza esebenzayo, kunye ne-contig anchoring.

UbuGcisa obuBanzi: Ngaphezulu kwe-12,000 yee-microbial genomes ezidityanisiweyo, sizisa ngaphezulu kweminyaka elishumi yamava, iqela lohlalutyo elinezakhono eziphezulu, umxholo obanzi, kunye nenkxaso egqwesileyo emva kokuthengisa.

Inkxaso yasemva kwentengiso:Ukuzinikela kwethu kudlulela ngaphaya kokugqitywa kweprojekthi kunye neenyanga ezi-3 emva kokuthengiswa kwenkonzo. Ngeli xesha, sinikezela ngokulandelelana kweprojekthi, uncedo lokusombulula ingxaki, kunye neeseshoni ze-Q&A ukujongana nayo nayiphi na imibuzo enxulumene neziphumo.

IiNgcaciso zeNkonzo

Inkonzo

Isicwangciso solandelelwano

Ulawulo lwemeko

Uyilo lweGenome

Illumina PE150 100x

Q30≥85%

IGenome entle

Uphando lweGenome: Illumina PE150 50 x

INdibano: PacBio HiFi 30x okanye Nanopore 100x

contig N50 ≥1Mb (Pacbio Unicellular)

contig N50 ≥2Mb(ONT Unicellular)

contig N50 ≥500kb (Abanye)

I-genome yenqanaba leChromosome

Uphando lweGenome: Illumina PE150 50 x

INdibano: PacBio HiFi 30x okanye Nanopore 100x

Hi-C Assembly 100x

Contig anchoring ratio>90%

 

IiMfuno zeNkonzo

 

Ugxininiso (ng/µL)

Imali iyonke (µg)

Umthamo (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

-

-

I-Unicellular Fungus: ≥3.5x1010 iiseli

I-Macro Fungus: ≥10 g

 

Ukuhamba komsebenzi weNkonzo

ukuhanjiswa kwesampuli

Ukuhanjiswa kwesampuli

ULungiselelo lweThala leeNcwadi

Ukwakhiwa kwethala leencwadi

Ukulandelelanisa

Ukulandelelanisa

Uhlalutyo lwedatha

Uhlalutyo lwedatha

Emva kweeNkonzo zentengiso

Iinkonzo emva kokuthengisa


  • Ngaphambili:
  • Okulandelayo:

  • 未标题-1-01

    Ibandakanya uHlahlelo Olulandelayo:

    UPhando lweGenome:

    • Ukulandelelanisa ulawulo lomgangatho wedatha
    • Uqikelelo lweGenome: ubukhulu, i-heterozygosity, izinto eziphindaphindayo

    INdibano yeGenome entle:

    • Ukulandelelanisa Ulawulo Lomgangatho Wedatha
    • De novoINdibano
    • Uhlalutyo lwecandelo leGenome: Ukubikezelwa kweCDS kunye nezinto ezininzi ze-genomic
    • Uhlaziyo olusebenzayo olunoovimba beenkcukacha ezininzi (GO, KEGG, njl.) kunye nogcino-lwazi oluphambili (iCARD, VFDB, njl.)

    INdibano ye-Hi-C:

    • UVavanyo lweThala leeNcwadi le-Hi-C.
    • I-Contigs i-ankile idibanisa, uku-odola kunye nokuqhelanisa
    • Uvavanyo lweNdibano ye-HI-C: Ngokusekwe kwireferensi yegenome kunye nemephu yobushushu

    Uphando lweGenome: ukuhanjiswa kwe-k-mer

     

     Umfanekiso we54

    Indibano yeGenome: gene homologous annotation (NR database)

     

     图片55

     

    Indibano yeGenome: Inkcazo yemfuza esebenzayo (GO)

     

    Umfanekiso we56

    Phonononga inkqubela phambili eququzelelwa yi-BMKGene yeenkonzo zokudityaniswa kofuzo lomngundo ngengqokelela egciniweyo yopapasho.

     

    Hao, uJ. et al. (2023) 'Iprofayili ye-omic edibeneyo ye-mushroom yamayeza i-Inonotus obliquus phantsi kweemeko eziphantsi kwamanzi',I-BMC Genomics, 24(1), iphepha 1–12. doi: 10.1186/S12864-023-09656-Z/IMIFANEKISO/3.

    Lu, L. et al. (2023) 'Ulandelelwano lweGenome lutyhila ukuvela kunye neendlela ze-pathogenic zengqolowa ebukhali yamehlo e-pathogen Rhizoctonia cerealis',Ijenali yezityalo, 11(2), iphepha 405–416. doi: 10.1016/J.CJ.2022.07.024.

    UZhang, H. et al. (2023) 'Izixhobo zeGenome kwiintlobo ezine zeClarireedia ezibangela indawo yeDola kwiiTurfgrasses ezahlukeneyo',Izifo zezityalo, 107(3), iphepha 929-934. doi: 10.1094/PDIS-08-22-1921-A

    UZhang, SS et al. (2023) 'Ubungqina beGenetic kunye neMolekyuli yeTetrapolar Mating System kwi-Edible Mushroom Grifola frondosa',Ijenali yeFungi, 9(10), iphe. 959. doi: 10.3390/JOF9100959/S1.

    fumana isicatshulwa

    Bhala umyalezo wakho apha kwaye uwuthumele kuthi

    Thumela umyalezo wakho kuthi: