Chirimwa / mhuka de novo genome sekuseka
De novoSEQUENCE inoratidza kuvakwa kwemarudzi 'ese genome uchishandisa tekinoroji ekusavapo genice genome. Nhungamidzo uye kugoverwa kwakapararira kwechitatu-kutururwa kwekutsakatiswa, kunevererwa kwenguva refu, kuve nekuvandudzwa kweGenome gungano nekuwedzera kuwanda pakati pekuverenga. Uku kusimudzira kunonyanya kukanganisika kana vachinetseka nekuita genomes dzakasimba, dzakadai sokuratidzira heterozygossity, polyploids, kana kuomarara kwezvinhu zvakadzora, kana kuomarara kwakadzokororwa kunowanzoita zvisina kufanira kwekuverenga ndega.
Yedu-yekumira mhinduro inopa yakabatanidzwa sequencing masevhisi uye Bioinformatic kuongorora iyo inounza yakakwirira-mhando de Novo yakaunganidzwa genome. Ongororo yekutanga yeGenome ine Illumina inopa kufungidzira kweiyo genome salution uye kuoma, uye ruzivo urwu rwunoshandiswa kutungamira iyo inotevera nhanho yekuverengera yekuverenga nePacbio Hifi, ichiteverwa nede novoUngano yeConigs. Kushandisa kwakazotevera kwegungano reHIC kunoita kuti isimbiswe yeiyo contig kune genome, kuwana genomeosome-level gungano. Pakupedzisira, genome inotsanangurwa neye gene kufanotaura uye nekutsakatisa yakaratidza majini, kushanduka kushandurwa uye kuverenga kwenguva pfupi uye kureba kuverenga.
Service maficha
● Kubatanidzwa kweakawanda soquencing uye bioinformatic services mune imwe-yekumisa mhinduro:
Genome ongororo ine Illumina yekufungidzira kukura kweGenome uye kutungamira nhanho dzinotevera;
Kuverengera kuverenga kutevedzana kwede novoUngano yeCligs;
Mhoro-c sequencing for chromosome chinja;
MrNN seequencing yekuzivisa majini;
Kusimbiswa kwegungano.
● Shumiro yakakodzera kuvaka nerevel genvels kana kuvandudzwa kwezvirevo zviripo zvemarudzi ekufarira.
Zvigadzirwa zvebasa
Kuvandudzwa kwekutsvagira mapuratifomu uye bioinformatics mukatide novoGENGORO Gungano
(Amorashee Sl et al.,Genome Biology, 2020)
●Yakawedzera hunyanzvi uye rekodhi rekodhi. Kubva 2018, isu takapa kupfuuraMabhuku mazana matatu ezvipingwo anokanganiswa, uye 20+ zvazvo zvinoburitswa mune zvakasikwa genetics.
● Imwe-yekumira mhinduro.
●Yakagadzirirwa kune zvaunoda: Yedu yebasa rebasa ndeyechiitiko, kubvumira kuomerera kune genomes ine dzakasiyana siyana maficha uye zvakananga zvekutsvagisa zvinodiwa. Izvi zvinosanganisira pekugara geniant geniomes, polyploadiz genomes, hetecheygous genomes, uye zvimwe.
●Ane hunyanzvi bioinformatics uye labatorial timu.
●Post-Kutengesa Tsigiro:Kuzvipira kwedu kunowedzera kupfuura purojekiti kupedzisa nemwedzi mitatu-mushure-yekutengesa basa nguva. Pakati peino nguva, isu tinopa chirongwa chekutevera-up, kugadzirisa dambudziko rekubatsira, uye Q & zvikamu zvekugadzirisa chero mibvunzo zvine chekuita nemhedzisiro.
Service Rudzidziso
| Genome ongororo | GENGORO Gungano | Chromosome-level | Genome Antotation |
| 50x Illumina Nevaaseq Pe150
| 30x Pacbio CCS Hifi Inoverenga | 100x hi-c | Rna-seq Illumina pe150 10 GB + (Inesarudzo) Yakazara kureba rna-seq pacbio 40 gb kana Nanopore 12 GB |
Zvinodiwa Nebasa
Zvekuongorora genome, genome gungano uye Hi-c musangano:
| Tishu kana kuburitsa nucleic acids | Genome ongororo | Genome Assembly nePacbio | Hi-c musangano |
| Animal viscera | 0.5-1 g
| ≥ 3.5 g | ≥2 g |
| Mhasuru yemhuka | ≥ 5 g | ||
| Mammalian Ropa | 1.5 ml
| ≥ 5 ml | ≥2 ML |
| Rufu / rehove reropa | ≥ 0.5 ml | ||
| Mashizha matsva | 1-2 g | ≥ 5 g | ≥ 4 g |
| Masero eCustomer |
| ≥ 1x108 | ≥ 1x107 |
| Chipembenene | 0.5-1 g | ≥ 3 g | ≥ 2 g |
| Kunowedzera DNA | Kusimbisa: ≥1 Ng / μL Mari ≥ 30 ng Mashoma kana kusasvibiswa kana kusvibiswa | Kusimbisa: ≥ 50 NG / μL Mari: 10 μg / cell Cell / sampuli Od260 / 280 = 1,7-22.2 Od260 / 230 = 1.8-2.5 Mashoma kana kusasvibiswa kana kusvibiswa |
-
|
Ye genome annotation ine transpric crubleptomics:
| Tishu kana kuburitsa nucleic acids | Illumina Transptome | Pacbio Transptome | Nanopore transptome |
| Midzi- midzi / stem / petal | 450 mg | 600 mg | |
| Chirimwa - mashizha / mbeu | 300 mg | 300 mg | |
| Chirimwa - michero | 1.2 g | 1.2 g | |
| Mhuka yemhuka / mudumbu | 300 mg | 300 mg | |
| Animal viscera / uropi | 240 mg | 240 mg | |
| Mhasuru yemhuka | 450 mg | 450 mg | |
| Mhuka pfupa / bvudzi / ganda | 1 g | 1 g | |
| Arthropod - chipembenene | 6 | 6 | |
| Arthropod -crustacea | 300 mg | 300 mg | |
| Ropa rese | 1 tube | 1 tube | |
| Inobviswa rna | Kusimbisa: ≥ 20 NG / μL Mari ≥ 0.3 μg Od260 / 280 = 1.7-2.5 Od260 / 230 = 0.5-2.5 Rin≥ 6 5828s / 18s≥1 | Kusimbisa: ≥ 100 NG / μL Mari ≥ 0,75 μg Od260 / 280 = 1.7-2.5 Od260 / 230 = 0.5-2.5 Rin≥ 8 5828s / 18s≥1 | Kusimbisa: ≥ 100 NG / μL Mari ≥ 0,75 μg Od260 / 280 = 1.7-2.5 Od260 / 230 = 0.5-2.5 Rin≥ 7.5 5828s / 18s≥1 |
Yakakurudzirwa Samplumple Kutumira
Mudziyo: 2 ml centrifige tube (tin foil haina kukurudzirwa)
(Kune mazhinji emasampuli, tinokurudzira kuti tirege kuchengeta muEthanol.)
SAMPLE LABLEYS: SAMPLES inofanirwa kuve yakanyatsotaurwa uye yakafanana kune yakatumirwa sample ruzivo fomu.
Kutumira: Dry-Ice: samples dzinoda kutariswa mumabhegi kutanga uye kuvigwa mune yakaoma-ice.
Workflow
Basa rebasa rinoyerera
Kuedza Dhizaini
Muenzaniso
Satchection
Raibhurari Kuvaka
Kutevedzana
Kuongororwa kwedata
Mushure mekutengesa-kutengesa masevhisi
Yakazara Bioinformatic analyis, yakaparadzaniswa mune 4 nhanho:
1) genome ongororo, yakavakirwa pane k-mer ongororo neNGS inoverenga:
Kufungidzira kweiyo genome saizi
Fungidziro ye heterozygosity
Fungidzira nezve kudzokorora matunhu
2) Genome Assembly nePacbio Hifi:
De novogungano
Kuongorora kwegungano: Kusanganisira Busco kuongororwa kweGenome kuzara uye mamepu kumashure kweNGS uye PACBOO Hifi kuverenga
3) Hi-c musangano:
Hi-c raibhurari QC: fungidziro yeiyo inoshanda hi-c kudyidzana
Hi-C musangano: kubatanidzwa kwezvemapoka mumapoka, kuteverwa ne contig kuraira mukati meboka rimwe nerimwe uye kugovera kutarisisa
Hi-C ongorora
4) Genome Antotation:
Isiri-Coding RNA kufanotaura
Kudzokorora kutevedzana kuzivikanwa (transposons uye tandem kudzokorora)
Gene Gene
§De novo: AB Initio Algorithms
§ Kubva pane Homology
§ Kubva pane Transptome, ine refu uye pfupi kuverenga: kuverenga ndeyede novoakaunganidzwa kana kuti akapetwa kujira genome
§ Anotaurwa NezveMajini Akafanotaura neDhatabhesi akawanda
1) genome ong-k-mer ongororo
2) Genome Assembly
2) Genome Assembly - Pacbio Hifi Inoverenga Mepu kuDhipatimendi Gungano
2) Hi-c musangano - fungidziro yeHi-c inoshanda yekudyidzana vaviri vaviri
3) Hi-C Post-Compass Kuongorora
4) genome annotation - kubatanidzwa kweiyo yakafanotaurwa geny
4) genome chinzwi - yakafanotaura geny
Ongorora kufambira mberi kwakabatanidzwa neBMKGE 'DE Novo Genema Systems Services kuburikidza neyekuunganidzwa muunganidzwa wezvinyorwa:
Li, C. et Al. . Doi: 10.1038 / S41467-02111-21379-x.
Li, Y. et Al. . Doi: 10.1093 / Molbev / Msad006.
Tian, T. et Al. (2023) Doi: 10.1038 / s415888833-01297-y.
Zhang, F. et Al. . Doi: 10.1038 / S41467-023-37133-4.
Zvinetso Zvinokosha-Zvidzidzo:
Telomere-kuna-Telomere gungano:Fu, A. et al. . Doi: 10.1093 / hr / uhac228.
Haplotype gungano:Hu, w. et al. . Doi: 10.1016 / j.molp.2021.04.009.
Geant Genyke Gungano:Yuan, J. et al. . Doi: 10.1038 / S41467-0220063-1.
Polyploid genome gungano:Zhang, Q. et Al. . Doi: 10.1038 / S41588-02-01084-1.
