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Imikhiqizo

Isitshalo / isilwane devo genome

Isitshalo / isilwane devo sogen tequency isithombe esifakiwe

De NovoUkulandelana kubhekiselwa ekwakhiweni kwezinhlobo 'zofuzo lonke usebenzisa ubuchwepheshe bokulandelana kokungabikho kwe-genome teference. Isingeniso kanye nokwamukelwa okuphezulu kakhulu kokulandelana kwezizukulwane zesithathu, okubandakanya ukufundwa isikhathi eside, bathuthukise kakhulu umhlangano we-genome ngokwandisa ukugqagqana phakathi kokufunda. Lokhu kuthuthukiswa kubaluleke kakhulu lapho usebenzelana ne-getomes eyinselele, efana naleyo ekhombisa i-heterozyuzytuty ephezulu, isilinganiso esiphakeme sezifunda eziphindaphindayo, okuqukethwe okuphindaphindayo, okuqukethwe okuphezulu kakhulu, noma ubunzima obukhulu obuhlangene kakhulu besebenzisa ukulandelana okufundwa okufushane yedwa.

Isixazululo sethu esisodwa sokuma sinikeza izinsizakalo ezihlanganisiwe zokulandelana nokuhlaziywa kwe-bioinformatic eletha i-de Novo ephezulu esezingeni eliphakeme. Inhlolovo yokuqala ye-genome ene-Illinan ihlinzeka ngokulinganiswa kosayizi we-genome nobunzima, futhi lolu lwazi lusetshenziselwa ukuqondisa igxake elilandelayo lokulandelana okulindelwe isikhathi eside ngePacBio Hifi, kulandelwade NovoUmhlangano we-Contigs. Ukusetshenziswa okulandelayo kwe-hic assembly kunika amandla ama-incussoli e-genome, ukuthola umhlangano we-chromosome-level. Ekugcineni, i-genome ichazwa ukubikezela kofuzo kanye nokulandelana kwazo kwavezwa, kuguqukela ekuhambeni kwama-transcriptomes ngokufunda okufushane nokude.

Xhumana nathi

Imininingwane ye-Service

Bioinformatics

Imiphumela yedemo

Izincwadi Ezifakiwe

Izici Zensizakalo

● Ukuhlanganiswa kokulandelana okuningi kanye nezinsizakalo ze-bioinchatic zesixazululo esisodwa:

Ucwaningo lwe-Genome nge-Illina ukukala usayizi we-genome futhi uqondise izinyathelo ezalandela;

Ukufundwa okudede NovoUmhlangano we-Contigs;

I-Hi-C ukulandelana kwe-chromosome anchloring;

I-MRNA ihlehlizela ukuthola isichasiselo sezakhi zofuzo;

Ukuqinisekiswa komhlangano.

● Insizakalo ilungele inoveli yokwakha i-genomes noma ukuthuthukiswa kwe-tyference ekhona yezinhlobo zezinto ezithakazelayo.

Izinzuzo zensizakalo

I-1Development-of-requencing-and-bioinformatics-in-de-novo-genome-sollog

Ukuthuthukiswa kwamapulatifomu okulandelana kanye nama-bioinformatics kude NovoUmhlangano we-Genome

(Amarasinghe SL et al.,I-Genome Biology, 2020)

●Ubuchwepheshe obubanzi kanye nerekhodi lokushicilelaI-BMKGENEE ihlanganise isipiliyoni esikhulu se-genome esezingeni eliphakeme lezinhlobo ezahlukahlukene zohlobo oluhlukahlukene, kufaka phakathi uhlobo lwe-dipoloid kanye nezinhlobo eziyinkimbinkimbi ze-plyploid kanye ne-alepolyploid nezinhlobo ze-allopolyploid. Kusukela ngo-2018, siba negalelo ngaphezuluIzincwadi ezingama-300 ezinomthelela omkhulu, kanye ne-20 + yazo zishicilelwa ku-genetics yendalo yendalo.

● Isixazululo esisodwa sokuma: Indlela yethu ehlanganisiwe ihlanganisa ubuchwepheshe obuningi bokulandelana kwezindawo zokulandelana kanye nokuhlaziywa kwe-bioinformatic ku-genome ebumbene yokusebenza, ukuletha i-genome esezingeni eliphakeme kakhulu.

●Ihambisana nezidingo zakho: Ukuchitheka kwethu komsebenzi wethu kuyathandeka, kuvumela ukuzivumelanisa nohlobo lwe-genomes olunezici ezahlukahlukene kanye nezidingo ezithile zocwaningo. Lokhu kufaka phakathi ukuhlalisa i-Giant genomes, i-polyploid genomes, i-getomes ephakeme kakhulu, nokuningi.

●Iqembu elinamakhono amakhulu amakhono kanye neqembu labandlululo: Ngolwazi olukhulu kuzo zombili izilingo kanye ne-bioinformatics ngaphambili kwemihlangano eyinkimbinkimbi ye-genome kanye nochungechunge lwamalungelo obunikazi namalungelo obunikazi wesoftware.

●Ukusekelwa kokuthengisa ngemuva:Ukuzibophezela kwethu kunwebeka ngaphezu kokuphothulwa kwephrojekthi ngesikhashana sezinyanga ezi-3 ngemuva kokuthengisa. Ngalesi sikhathi, sinikezela ngokulandela iphrojekthi, usizo lokuxazulula inkinga, kanye ne-q & amaseshini ukubhekana nanoma yimiphi imibuzo ehlobene nemiphumela.

Ukucaciswa Kwensiza

UHLOME SHROVENER

Umhlangano we-Genome

I-Chromosome-Level

Isichasiso se-Genome

I-50X I-Illina Novaseq PE150

I-30x Pacbio CCS HiFi Iyafunda

I-100x Hi-C

I-RNA-SEQ Illinina Pe150 10 GB

(Ngokuzithandela)

Ubude obugcwele rna-seq pacbio 40 GB noma

I-Nanopore 12 GB

Izidingo Zenkonzo

Okwenhlolovo yaseGenome, umhlangano we-Genome Assembly kanye ne-HI-C:

Izicubu noma ama-nucleic acid ama-nucleic	UHLOME SHROVENER	I-Genome Assembly nePacbio	HI-C UMLANDO
Isilwane se-viscera	0.5-1 g	≥ 3.5 g	≥2 g
Izicubu zezilwane	0.5-1 g	≥ 5 g	≥2 g
Igazi LaseMammalian	1.5 ml	≥ 5 ml	≥2 ml
I-PoulTry / Igazi Lezinhlanzi	1.5 ml	≥ 0.5 ml	≥2 ml
Isitshalo- iqabunga elisha	1-2 g	≥ 5 g	≥ 4 g
Amaseli abunjiwe		≥ 1x10⁸	≥ 1x10⁷
Isilokazane	0.5-1 g	≥ 3 g	≥ 2 g
Kukhishwe i-DNA	Ukuhlushwa: ≥1 ng / μl Inani ≥ 30 ng Kukhawulelwe noma akukho ukucekelwa phansi noma ukungcoliswa	Ukugxila: ≥ ≥ ≥ ng / μl Inani: 10 μg / ukugeleza iselula / isampula I-OD260 / 280 = 1.7-2.2 I-OD260 / 230 = 1.8-2.5 Kukhawulelwe noma akukho ukucekelwa phansi noma ukungcoliswa	-

Ukuchazwa kwe-genome nge-transcriptomics:

Izicubu noma ama-nucleic acid ama-nucleic	I-Illumina Transcripmeme	I-Pacbio i-Transcripmeme	I-Nanopore Transcripmeme
I-FACT- ROOT / STEM / PELAL	450 mg	I-600 mg
Isitshalo - iqabunga / imbewu	300 mg	300 mg
Isitshalo - izithelo	1.2 g	1.2 g
Inhliziyo Yezilwane / Amathumbu	300 mg	300 mg
Isilwane se-viscera / ubuchopho	240 mg	240 mg
Izicubu zezilwane	450 mg	450 mg
Amathambo ezilwane / izinwele / isikhumba	1 g	1 g
I-Arthropod - Isinambuzane	6	6
I-Arthropod -Cropacea	300 mg	300 mg
Igazi lonke	1 ishubhu	1 ishubhu
Kukhishwe i-rna	Ukuhlushwa: ≥ ≥ 10 μL Inani ≥ 0.3 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin≥ 6 5≥28s / 18S≥1	Ukuhlushwa: ≥ 100 ngl Inani ≥ 0.75 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin≥ 8 5≥28s / 18S≥1	Ukuhlushwa: ≥ 100 ngl Inani ≥ 0.75 μg I-OD260 / 280 = 1.7-2.5 I-OD260 / 230 = 0.5-2.5 Rin≥ 7.5 5≥28s / 18S≥1

Kunconywe ukulethwa kwezinkampu

Isitsha: 2 ml centrifuge tube (i-tin foil ayinconywa)

(Kwamasampula amaningi, sincoma ukuthi singagcini e-ethanol.)

Ilebula yesampula: Amasampula kufanele abhalwe ngokucacile futhi afane nefomu lolwazi lesampula elihanjisiwe.

Ukuhanjiswa: I-Dry-Ice: Amasampula adinga ukupakishwa ezikhwameni kuqala futhi angcwatshwe eqhweni eyomile.

Ukuflow

Ukugeleza komsebenzi wesevisi

Idizayini yokuhlola

Ukulethwa kwesampula

Ukukhishwa kwe-DNA

Ukwakhiwa Kwelabhulali

Ukulandelana

Ukuhlaziywa kwedatha

Services After-Sale

Okwedlule: Ukuhlelwa kabusha komuntu wonke

Olandelayo: I-HI-C esekwe eGenome Assembly

Qedela ukuhlaziywa kwe-bioinformatic, kuhlukaniswe ngezinyathelo ezi-4:

1) Ucwaningo lwe-Genome, olususelwa ekuhlaziyweni kwe-K-RAL nge-NGS Reads:

Ukulinganiselwa kosayizi we-genome

Isilinganiso se-heterozyasity

Ukulinganisa kwezifunda eziphindayo

2) I-Genome Assembly nePacbio HIFI:

De Novoumbuthano

Ukuhlolwa Komhlangano: Kubandakanya Ukuhlaziywa kweBusco kwe-Genome Ukuphelela kanye neMephu emuva kwe-NGS kanye nePacbio Hifi Reads

3) HI-C Umhlangano:

I-Hi-C Library qc: Ukulinganisa kokusebenzisana okuvumelekile kwe-Hi-C

Umhlangano weHi-C: Ukuhlanganiswa kwezindawo zokuxhumana ngamaqembu, kulandelwa uku-oda kwe-congig eqenjini ngalinye futhi kwabelwe ukuqondiswa kwe-congig

Ukuhlolwa kwe-Hi-C

4) Isichasiso se-genome:

Isibikezelo se-RNA esingewona amakhodi

Ukuphikisana okuphindaphindwayo (okuguqulwayo kanye nokuphindaphinda)

Ukubikezela kofuzo

+кDe Novo: ab initio algorithms

§ Ngokusekelwe kwi-Homology

§ Ngokusekelwe ku-transcriptipmeme, ngokufundwa okude nokufushane: Kufundwade Novobabuthene noma bahlangene ku-genome okusalungiswa

§ Isichasiselo sezakhi zofuzo ezibikezelwe ezinemininingwane eminingi

1) I-Genome Survery- k-HLA UKUHLAZIYA

2) I-Genome Assembly

2) I-Genome Assembly - I-PACBIO HIFI ifunda ukumenyelela ku-Draft Assembly

2) I-HI-C UMLANDE - Ukulinganisa kokusebenzisana kwe-Hi-C okuvumelekile ngababili

3) Ukuhlolwa kwangemva kwe-Hi-C

4) Isichasiselo se-genome - ukuhlanganiswa kwezinhlobo ezibikezelwe

4) Isichasiso se-Genome - Isichasiso seGene ebikezelwe

Hlola intuthuko elungiswe yi-BMKGENE's de Novo Geneno Geneno Geneno gerger Services ngeqoqo elikhethiwe lokushicilelwa:

I-LI, C. et al. . Doi: 10.1038 / S41467-021-11379-X.

I-LI, Y. et al. (2023) 'Izinguquko ezinkulu ze-chromosomal ziholela ekushintsheni kwezinga le-genome-level, ukuvumelanisa kwezemvelo kanye nokuvalwa kwe-gayal (BOS Fradis), i-molefanele biology kanye nokuziphendukela kwemvelo, 40). Doi: 10.1093 / Molbev / MSAD006.

UTian, uT. Et al. (2023) Umhlangano woGenome kanye nofuzo lwezakhi zofuzo lwe-gerplasm evelele yesomiso esivimbela imvula ', izifukofuzo zemvelo 2023 55: 3, 55 (3), PP. 496-506. Doi: 10.1038 / S41588-023-01297-Y.

UZhang, F. et al. . Doi: 10.1038 / S41467-023-37133-4.

Izifundo ezinzima - Izifundo:

Umhlangano weTelomere-to-telomere:Fu, A. et al. (2023) 'I-Telomere-to-telomere genome solon of melon (Momordica Charantia L. var. I-ABBREVIATA SER.) Iveze ukuthuthukiswa kwezithelo, ukwakheka kwezimpawu zofuzo ", 10 (1). Doi: 10.1093 / HR / UDAC228.

Umhlangano weHaplotype:Hu, W. et al. . Doi: 10.1016 / J.molp.204.004.009.

Umhlangano omkhulu waseGenome:Yuan, J. et al. . DOI: 10.1038 / S41467-022-35063-1.

I-POLYPLOID Genecme Assembly:UZhang, Q. et al. . DOI: 10.1038 / S41588-022201084-1.