Isityalo / isilwanyana de novo ye-genome
De NovoUkulandelelana kubhekisa ekwakhiweni koluhlobo lwe-genome yohlobo lwe-genome kusetyenziswa itekhnoloji yokugcwala ngokungabikho kwereferensi ye-genome. Intshayelelo kunye nokwamkelwa ngokubanzi kokulandelelana kwesithathu, ukwenza ixesha elide i-genome indibano yokuphucula i-genome ngokwandisa i-overlap phakathi kufundwayo. Oku kuphuculwa kulunga kakhulu xa ujongene ne-genomes enomdla, njengale mimandla iphindaphindiweyo, imixholo ephindaphindiweyo ephindaphindiweyo, okanye i-GC engaqhelekanga esebenzisa ukulandelelana okufutshane yedwa.
Isisombululo sethu sokumisa sinike iinkonzo ezidityanisiweyo kunye nohlalutyo lwe-biincormatic oluhambisa i-genome ehlanganisiweyo ye-vinome. Uvavanyo lokuqala lwe-genome kunye ne-Ilimumina lubonelela ngoqikelelo lobungakanani be-genome kunye nobunzima, kwaye olu lwazi lusetyenziselwa ukukhokela inyathelo elilandelayo lokufunda ixesha elide kunye ne-pacbio hifi, elandelwa ngude novoINdibano ye-EndIgs. Ukusetyenziswa okulandelayo kwe-hic kwenza ukuba i-adhoring yezinto ezikhethekileyo kwi-genome, ifumana indibano yenqanaba le-chromomous. Okokugqibela, i-genome ichazelwa kwangaphambili ngoqikelelo lwemfuza kwaye ngokulandelelana kwabonisa uhlobo, ukuguqulela kwimizobo efutshane kwaye ifundwe ixesha elide.
Iimpawu zenkonzo
● Uhlanganiso lweenkonzo ezininzi zokulandelelana kunye neenkonzo ze-bioricformatic kwisisombululo esinye se-Stop:
Uvavanyo lwe-genome kunye ne-Illina ukuya kuqikelelwa ubungakanani be-genome kwaye ukhokele amanyathelo alandelayo;
Ukufunda ixesha elidede novoindibano ye-EndIgs;
Hi-c ukulandelelana kwe-chromosome;
I-MRNA Lequeeding yeNkulumbuziyo yemfuza;
Ukuqinisekiswa kweNdibano.
● Inkonzo ilungele i-Inoves yeNoves okanye ukuphuculwa kwezinto ezikhoyo zereferensi zezinto ezinomdla.
Izibonelelo zeNkonzo
Ukuphuhliswa kwamaqonga okulandelelana kunye ne-bioinformatics kwide novoI-Genome Church
(Amaramhe sl et al.,I-genome biology, 2020)
●Ingcali ebanzi kunye nerekhodi yokupapasha: I-Bmkgene iqokelele amava amakhulu kwiNdibano ye-genome ephezulu ye-genome yeentlobo ezahlukeneyo, kubandakanya i-geplomes yediplomes kunye ne-genomes yediplomes kunye ne-genomes ye-polyploid kunye ne-alfallypload. Ukusukela ngo-2018, sinegalelo kwi-OverNgama-300 upapasho oluPhezulu, kunye ne-20 + yazo ipapashwa kwindalo yendalo.
● Isisombululo sokumisa esinye: Inkqubo yethu ehlanganisiweyo idibanisa ubuchwephesha obuninzi bokugcwala kunye nokuhlalutya kwe-bioinformatic kwindawo yokuhambahamba, ukuhambisa i-genome ephezulu kakhulu.
●Ilungiselelwe iimfuno zakho: Imsebenzi yethu yenkonzo yenkonzo iyazilungisa, ivumela ukuba kulungelelwaniso lwe-genomes enezinto ezahlukeneyo kunye neemfuno ezithile zophando. Oku kubandakanya ukufumana indawo enkulu ye-genomes, i-gelyplomes genomes, i-genorozygous kakhulu ye-genomes, nangaphezulu.
●I-bioinformatics enobuchule kakhulu kunye neqela lelebhu: Ngamava amahle kuzo zombini iindlela zokuvavanywa kunye ne-bioricformatics ze-genomes ye-genome enzima kunye nothotho lwamalungelo awodwa omenzi wechiza kunye neendlela zokushicilela zesoftware.
●Inkxaso yasemva kwentengiso:Ukuzibophelela kwethu kugqitha ngaphaya kokugqitywa kweprojekthi kunye nexesha lenkonzo yenkonzo yasemva kwenkonzo emva kwenkonzo. Ngeli xesha, sinikezela ngeprojekthi yokulandela iprojekthi, uncedo lokucombulula iingxaki, kunye ne-Q & Iiseshoni zokujongana nayo nayiphi na imibuzo enxulumene neziphumo.
Inkcazo yenkonzo
| Uvavanyo lwe-genome | I-Genome Church | Inqanaba leChromomosome | Isichazi-magama se-genome |
| I-50x Invaumina Novaseq Pe150
| I-30x Pacbio CCS HIFI ifundwa | I-100x hi-c | I-RNA-Seq Inbumina Pe150 GB + (ngokuzithandela) Ubude obugcweleyo be-rna-seq pacbio i-40 GB okanye I-Nanopore 12 GB |
Iimfuneko zeNkonzo
Ngovavanyo lwe-genome, i-genome yendibano kunye ne-Hi-C indibano:
| Izicubu okanye zikhutshiwe i-acid ye-nucleic | Uvavanyo lwe-genome | I-Genome Church ene-pacbio | INdibano yeHi-C |
| I-viscera yesilwanyana | I-0.5-1 g
| ≥ 3.5 g | ≥2 g |
| Isihlunu sesilwanyana | ≥ 5 g | ||
| Igazi laseMammalian | I-1.5 ml
| ≥ 5 ml | ≥2 ml |
| Inkukhu / igazi lentlanzi | I-0.5 ml | ||
| Isityalo- amagqabi amatsha | 1-2 g | ≥ 5 g | ≥ 4 g |
| Iiseli ezikhulisiweyo |
| ≥ 1x108 | ≥ 1x107 |
| Izinambuzane | I-0.5-1 g | ≥ 3 g | ≥ 2 g |
| Ikhutshiwe i-DNA | Uxinzelelo: ≥1 Ng / μl Isixa-mali 30 NG Inqongophele okanye akukho hlazo okanye ungcoliseko | Uxinzelelo: ≥ 50 Ng / μl Imali: 10 μG / Iseli / isampulu I-OD260 / 280 = 1.7-222 I-OD260 / 230 = 1.8-2.5 Inqongophele okanye akukho hlazo okanye ungcoliseko |
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Kwi-genome inkcazo nge-transcrippices:
| Izicubu okanye zikhutshiwe i-acid ye-nucleic | I-Illumina Debripptome | I-Pacbio Tracttoptome | I-Nanopore Transpripptome |
| Ingcambu ye-Stem / stem / petal | I-450 mg | I-600 mg | |
| Isityalo-amagqabi / imbewu | I-300 mg | I-300 mg | |
| Isityalo-iziqhamo | 1.2 g | 1.2 g | |
| Intliziyo yezilwanyana / i-sine | I-300 mg | I-300 mg | |
| I-viscera yesilwanyana / ingqondo | I-240 mg | I-240 mg | |
| Isihlunu sesilwanyana | I-450 mg | I-450 mg | |
| Amathambo ezilwanyana / iinwele / ulusu | 1 g | 1 g | |
| I-Arthropod-Inambuzane | 6 | 6 | |
| I-arthropod -crestacea | I-300 mg | I-300 mg | |
| Igazi liphela | I-1 ityhubhu | I-1 ityhubhu | |
| Ikhutshiwe iRNA | Uxinzelelo: ≥ 20 Ng / μl Isixa-mali 0.3 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin≥ 6 5º28s / 18s≥1 | Uxinzelelo: I-100 NG / μl Ixabiso le-0.75 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin≥ 8 5º28s / 18s≥1 | Uxinzelelo: I-100 NG / μl Ixabiso le-0.75 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin7.5 5º28s / 18s≥1 |
Ukuhanjiswa kwesampulu
Isikhongozeli: 2 Ml Centrifuge Tube (i-tin foil ayikhuthazwanga)
(Uninzi lweesampulu, sicebisa ukuba singayigcini e-Ethanol.)
Iifayile zelebheli: Iisampulu kufuneka zibhalwe ngokucacileyo kwaye zifana kwifom yolwazi yesampulu yesampulu.
Ukuhanjiswa: Umkhenkce owomileyo: Iisampulu kufuneka zipakishwe kwiingxowa kuqala kwaye zingcwatywe kwi-ice eyomileyo.
Umsebenzi wokusebenza
Ukuhamba kwenkonzo
Uyilo lovavanyo
Ukuhanjiswa kwesampula
Ukukhutshwa kwe-DNA
Ulwakhiwo lwethala leencwadi
Ukulandelelana
Uhlalutyo lwedatha
Iinkonzo zentengiso emva
Gcwalisa uhlalutyo lwe-biinorinformatic, wahlukaniswe ngamanyathelo ama-4:
1) Uvavanyo lwe-genome, olusekwe kuhlalutyo lwe-K-PER kunye ne-NGS (
Uqikelelo lobungakanani be-genome
Uqikelelo lwe-heterozygonoity
Uqikelelo lwemimandla ephindaphindayo
2) Indibano ye-genome ene-pacbio hifi:
De Novoindibano
Uvavanyo lwendibano: kubandakanya uhlalutyo lwe-Busco lokupheliswa kwe-genome kunye ne-meppie umva kwi-NGS kunye ne-pacbio hifi
3) INdibano ye-3) INdibano yeHi-C:
I-Gha-C Ithala leencwadi QC: uqikelelo lwendlela esebenzayo ye-hi-c
INdibano ye-Hi-C: Ukuqokelelwa kweentsebenzo ngokwamaqela, kulandelwa ngu-oda kwinkcitho kwiqela ngalinye kunye nokwabela ukuqhelaniswa kwenkani
Hi-c
I-4) I-Genome Aittation:
Ukungabhakisi
Ukulandelelana kolandelelaniso
Uqikelelo
§De Novo: Ab i-algorithms
§ Isekwe kwi-homology
§ Isekwe kwi-transcripptome, enesidima eside kwaye sifundwede novoidityaniswe okanye ikhutshiwe kwi-genome
§ Inkcazo yemfuza eqikelelweyo kunye neenkcukacha ezininzi
1) Uvavanyo lwe-genome- k-k-per
2) Indibano ye-genome
2) Indibano ye-genome- pacbio hifi ifunda imephu kwindibano yokuyila
2) INdibano ye-Hi-C-uqikelelo lwee-HI-C
3) hi-c-c post-yendibano
I-4) I-Genome Asit-Ingqungquthela yeGenekisela eqikelelweyo
I-4) I-Genome Asnotition -umes eqikelelweyo
Jonga i-NVULO EQHUTYELWEYO NGEENKONZO ZE-BMKgene's De Novo Poing Ingqokelela yeempapasho ezinyanyelweyo:
Li, c. et al. . Doi: 10.1038 / S41467-021-21379-X.
Li, y. et al. . I-DoI: 10.1093 / MOLBEV / MS006.
Tian, t. et al. . Doi: 10.1038 / S41588-023-01297-y.
Zhang, f. et al. . DoI: 10.1038 / S41467-0237133-3.
Izifundo ezinzima
INdibano yeTelomere-to-TelomereFu, A. ET Al. . Doi: 10.1093 / HR / UHAC228.
Indibano ye-haplotypepe:Hu, w. et al. . Doi: 10.1016 / J.molp.2021.04.009.
Indibano enkulu ye-genome:Yuan, j. et al. . Doi: 10.1038 / S41467-0225063-1.
I-polyploid yendibano ye-geome:Zhang, Q. ET Al. . Doi: 10.1038 / S41588-022-01084-1.
