Chomera / Chinyama de Novon Genome
De novoKuberekera kumatanthauza kupanga mitundu yonse ya mitundu yonse pogwiritsa ntchito matekinoloje osapezeka pakadali pano. Kuyambika komanso kufalikira kwa mawonekedwe am'badwo wachitatu, monganso kuwerenga kwanthawi yayitali, kumakhala ndi msonkhano waukulu kwambiri pochulukitsa pakati pa kuwerenga. Kuchulukitsa kumeneku kuli makamaka polimbana ndi ma genomes otsutsa, monga omwe akuwonetsa nyengo yayitali, ma polyploids omwe amapezeka mobwerezabwereza, kapena malo ovuta omwe amasonkhana mobwerezabwereza pogwiritsa ntchito zingwe zazifupi Pa yekhayo.
Njira yathu yoyimilira imapereka ntchito zophatikizira ndi kusanthula kwa bioninformatic komwe kumaperekanso mtundu wapamwamba wa de Novome. Kafukufuku woyambirira wa genome yemwe ali ndi Audina amapereka masitepe a generome kukula ndi zovuta, ndipo chidziwitsochi chimagwiritsidwa ntchito potsogolera gawo lotsatira la mipando yayitali ndi Pacbio HIFI, kutsatiridwa ndide novomisonkhano yamisonkhano. Kugwiritsa ntchito msonkhano wa Hic kumathandiza kuchonderera kwa zigawengazo ku genomes, kupeza msonkhano wa chromosome. Pomaliza, genome imadziwika ndi gene yolosera komanso kutengera majini, kusintha ma transcript ndi nthawi yayitali.
Mawonekedwe antchito
● Kuphatikiza kwa magawo angapo osokosera ndi bioinfoctic ntchito mu yankho limodzi:
Kafukufuku wamtundu wa Genome ndi Audina kuti awerenge kukula kwa genome ndi kuwongolera njira zotsatila;
Kuwerenga motalikade novomsonkhano wamisonkhano;
Hi-C obermining ya chithokomiro cha chromosome;
Kusintha kwa mrna kuti chibadwa kwa majini;
Kutsimikizika kwa msonkhano.
● Utumiki woyenera kuwongolera kwa genomes kapena kusintha kwa geni otchulidwa komwe kulipo kwa mitundu ya chidwi.
Ubwino Wantchito
Kukula kwa nsanja zotsekemera ndi bioinformocticde novoMsonkhano waukulu
(Amarasing s sno et al.,Biology biology2020)
●Ukadaulo Wambiri ndi Zolemba: BMKgene wapeza zokumana nazo zazikuluzikulu zamisonkhano yapamwamba kwambiri ya mitundu yosiyanasiyana, kuphatikizapo geniveloid genomes ndi ziphuphu zovuta kwambiri za mitundu ya polyploid ndi alpoulyploid. Kuyambira 2018, taperekaMabuku 300 okwera kwambiri, ndipo 20+ amafalitsidwa mu chilengedwe.
● Yankho Loyimira: Njira zathu zophatikizira kuphatikiza matekinoloje angapo ndi bioinformatic imasanthula yolumikizira yolumikizira, ndikupereka mtundu wapamwamba kwambiri wophatikizidwa.
●Zogwirizana ndi zosowa zanu: Ntchito yathu ya ntchito ndiyotha kwambiri, kulola kusintha kwa genomes ndi mawonekedwe osiyanasiyana komanso kufufuza kwakanthawi. Izi zimaphatikizapo zokhala ndi zimphona zazikulu za polyploid polyploid, geyurozygous kwambiri, ndi zina zambiri.
●Gulu laukadaulo wambiri ndi laboratorial: Ndi zokumana nazo kwambiri pagulu lankhondo komanso ma bioninformatic patsogolo pa zovuta zamisonkhano yovuta komanso misonkhano yambiri.
●Thandizo la Kugulitsa:Kudzipereka kwathu kumapitilira kumaliza ntchito ndi mwezi wachitatu - nthawi yogulitsa ntchito. Panthawi imeneyi, timapereka thandizo lotsatira, kuvutitsa, ndi magawo kuti athetse mafunso okhudzana ndi zotsatira zake.
Zolemba
| Kafukufuku wamtunduwu | Msonkhano waukulu | Chromosome-mulingo | Nanu Mwachizolowezi |
| 50xillina novaseq pe150
| 30x pacbio ccs hifi amawerenga | 100x hi-c | RNA-SUQUIGIINE Pe150 10 GB + (kusankha) Kutalika kwathunthu RNA-seq Pacbio 40 GB kapena Nanopore 12 GB |
Zofunikira
Mwachitsanzo, kafukufuku wa Genome, Msonkhano Waukulu ndi Msonkhano wa Hi-C Morm:
| Minofu kapena kuchotsa ma acid acid | Kafukufuku wamtunduwu | Msonkhano waukulu ndi Pacbio | HI-C Msonkhano |
| Nyama viscera | 0.5-1 g
| ≥ 3.5 g | ≥2 g |
| Minofu yanyama | ≥ 5 g | ||
| Magazi a Mammalian | 1.5 ml
| ≥ 5 ml | ≥2 ml |
| Magazi / magazi a nsomba | ≥ 0,5 ml | ||
| Zomera | 1-2 g | ≥ 5 g | ≥ 4 g |
| Maselo odziwika |
| ≥ 1x108 | ≥ 1x107 |
| Tizilombo | 0.5-1 g | ≥ 3 g | ≥ 2 g |
| Anatulutsa DNA | Kuzindikira: ≥1 ng / μl Kuchuluka ≥ 30 z Kuperewera kapena kuwonongeka kapena kuipitsidwa | Kuzindikira: ≥ 50 ng / μl Kuchuluka: 10 μg / flow cell / chitsanzo Ode260 / 280 = 1.7-2.2 Ode260 / 230 = 1.8-2.5 Kuperewera kapena kuwonongeka kapena kuipitsidwa |
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Kwa mtundu wa genome ndi transcriptrics:
| Minofu kapena kuchotsa ma acid acid | Audino Transcript | Pacbio Omasulira | Nanopore transcript |
| Zomera- muzu / tsinde | 450 mg | 600 mg | |
| Chomera - tsamba / mbewu | 300 mg | 300 mg | |
| Chomera - Zipatso | 1.2 g | 1.2 g | |
| Mtima wanyama / matumbo | 300 mg | 300 mg | |
| Nyama viscera / ubongo | 240 mg | 240 mg | |
| Minofu yanyama | 450 mg | 450 mg | |
| Mafupa a nyama / tsitsi / khungu | 1 g | 1 g | |
| Arthropod - kachilombo | 6 | 6 | |
| Arthropod --crustacea | 300 mg | 300 mg | |
| Mwazi wonse | 1 chubu | 1 chubu | |
| Zopangidwa RNA | Kuzindikira: ≥ 20 Ng / μl Kuchuluka ≥ 0,3 μg Ode260 / 280 = 1.7-2.5 Ode260 / 230 = 0,5-2.5 Khwangwala≥ 6 5≥28s / 18s≥1 | Kuzindikira: ≥ 100 Ng / μl Kuchuluka ≥ 0.75 μg Ode260 / 280 = 1.7-2.5 Ode260 / 230 = 0,5-2.5 Khwangwala≥ 8 5≥28s / 18s≥1 | Kuzindikira: ≥ 100 Ng / μl Kuchuluka ≥ 0.75 μg Ode260 / 280 = 1.7-2.5 Ode260 / 230 = 0,5-2.5 Khwangwala≥ 7.5 5≥28s / 18s≥1 |
Kulimbikitsidwa Kwambiri
Chidebe: 2 ml centrifuge chubu (chinimba cha tin sichikulimbikitsidwa)
(Pa zitsanzo zambiri, timalimbikitsa kuti tisateteze ku Ethanol.)
Kulemba zitsanzo: Zitsanzo ziyenera kulembedwa momveka bwino komanso zofanana ndi mawonekedwe omwe adatumizidwa.
Kutumiza: Madzi oundana: zitsanzo zimafunikira kuti zikhale m'matumba oyamba ndikuikidwa m'manda oundana.
Wanchito
Ntchito Yogwira Ntchito
Mapangidwe a kuyesa
Kutumiza kwachitsanzo
DNA Kuchotsa
Ntchito Yomanga Laibulale
Kusazidza
Kusanthula kwa data
Ntchito Zogulitsa Pambuyo
Kusanthula kwa bioinformic, opatukana mu magawo 4:
1) Kafukufuku wamtunduwu, kutengera ndi K-Mer Kusanthula ndi NGS amawerenga:
Kuwerengera kwa mtundu wa genome
Kuyerekeza kwa Heterozyglence
Kuwerengetsa zigawo zobwereza
2) Msonkhano wa Genome ndi Pacbio Hifi:
De novomsonkhano
Kuwunika Kwamsonkhano
3) HI-C Msonkhano:
Moni-C Library QC: Kuwerengera kwa Hi-C
HI-C Msonkhano: Kusokoneza magulu m'magulu, kutsatiridwa ndi controg Resip mkati mwa gulu lirilonse ndikugawa
Moni-C
4) Malingaliro:
Kulosera kwa RNA
Kubwereza zidziwitso (Transposon ndi Tandem Kubwereza)
MABUKU
§De novo: Ab algorithms
§ Kutengera ku Hologrology
§ Kutengera omasulira, motalika komanso kanthawi kochepa: amawerengade novoanasonkhana kapena kusinthidwa ku genome
Zosakaniza za majini onenedweratu okhala ndi database angapo
1) Genome Janome- K-K-Mgwirizano
2) Msonkhano waukulu
2) Msonkhano waukulu - Pacbio Hifi amawerenga mapu okwerera msonkhano
2) HI-C Msonkhano - Kutalika kwa Hi-C ovomerezeka awiri
3) Moni-C-Cistly Kuzindikira
4) Nambala Yodziwitsa - Kuphatikiza kwa Zifaniziro Zonenedweratu
4) Nambala ya Ndondomeko - Kunenedweratu Zakale
Funsani zomwe zikuchitika ndi BMKGE Ge Novo 10
Li, C. et al. . Doi: 10.1038 / S41467-021-21379-X.
Li, y. et al. . Doi: 10.1093 / Molbev / Msad006.
Tian, T. et al. . Doi: 10,1038 / S41588-023-0129-y.
Zhang, F. et al. . Doi: 10.1038 / S41467-023-37133*-4.
Kafukufuku Wovuta:
Tlomere-to-telomeres:Fu, A. A. . Doi: 10,1093 / hr / uhac228.
Msonkhano wa Haplotype:Hu, W. et al. (2021) 'Ndege yodziwika bwino yomwe imatanthauzira imavumbula kusasiyanitsa kwa bialleva kusinthika kwa chisinthiko,', mbewu yazomera, 14 (6), mas. Doi: 10,1016 / J.Molp.2021.04.009.
Msonkhano waukulu kwambiri:Yuan, J. et al. . Doi: 10,1038 / S41467-022-35063-1.
Msonkhano wa Gelyploid Genome:Zhang, Q. et al. (Melc. Doi: 10,1038 / S4158-022-01084-1.
