Kuenzanisa Genomics
Basa Rinobatsira
● Comprehensive analys package, ine zvisere zvinowanzodiwa ongororo
● Kuvimbika kwepamusoro pakuongorora netsanangudzo yakadzama uye inonzwisisika pamhedzisiro
● Nhamba dzakanyatsogadzirwa dzakagadzirira-kushambadza nhamba
● Chikwata chepamusoro-soro chebioinformatics chinozadzisa zvido zvekuongorora zvakasiyana-siyana
● Kupfupika-kutenderera-kutenderera nguva nepamusoro-soro yakarurama mukuongorora
● Ruzivo rwakawanda nezviitiko zvinopfuura makumi mapfumbamwe zvakabudirira zvine accumulative yakadhindwa maitiro ezvinodarika mazana mapfumbamwe
Sevhisi Zvinotsanangurwa
| Inofungidzirwa kutendeuka-nguva | Nhamba yemhando | Anoongorora |
| 30 mazuva ekushanda | 6 - 12 | Gene mhuri kuungana Gene mhuri yekuwedzera uye kuputika Phylogenetic muti kuvaka Divergence nguva fungidziro (Fossil calibration inodiwa) Nguva yekuisa LTR (Yezvirimwa) Yese genome duplication (Yezvirimwa) Selective pressure Synteny analysis |
Bioinformatics inoongorora
● Gene mhuri
● Phylogenetics
● Nguva yekusiyana
● Madzvinyiriro ekusarudza
● Synteny kuongorora
Sample Zvinodiwa uye Delivery
Sample Zvinodiwa:
Tissue kana DNA ye genome sequencing uye kusangana
For Tissue
| Zvisikwa | Tissue | Survey | PacBio CCS |
| Mhuka | Visceral tishu | 0.5 ~ 1g | ≥ 3.5g |
| Tsandanyama | |||
| ≥ 5.0g | |||
| ≥ 5.0mL | |||
| Ropa reMammalian | |||
| ≥ 0.5mL | |||
| Huku/Hove ropa | |||
| Plant | Fresh Leaf | 1 ~ 2g | ≥ 5.0g |
| Petal/Stem | 1 ~ 2g | ≥ 10.0g | |
| Mudzi/Mbeu | 1 ~ 2g | ≥ 20.0g | |
| Masero | Cultured sero | - | ≥ 1 x 108 |
Data
Genome sequence files(.fasta) uye annotation mafaira (.gff3) emhando dzakanyanya hukama
Kuyerera Kwebasa Rebasa
Kuedza kugadzira
Muenzaniso wekutumira
Kuvakwa kweraibhurari
Sequencing
Data analysis
Mushure mekutengesa masevhisi
*Demo mhedzisiro inoratidzwa pano yese kubva kugenomes yakaburitswa neBiomarker Technologies
1.LTR isa fungidziro yenguva: Nhamba yakaratidza kugoverwa kwakasiyana kwebimodal muLTR-RTs nguva dzekuisa muWeining rye genome, zvichienzaniswa nemamwe marudzi.Iyo yepamusoro-soro yazvino yakaonekwa makore anosvika miriyoni 0.5 apfuura.
Li Guang et al.,Nature Genetics, 2021
2.Phylogeny uye gene mhuri yekuongorora pa chayote (Sechium edule) : Nokuongorora chayote nemamwe marudzi ane 13 ane hukama mumhuri yejeni, Chayote yakawanikwa ichinyanya kushamwaridzana nenyoka gourd (Trichosanthes anguina).Chayote inotorwa kubva kugourd renyoka mukati me27-45 Mya uye yakazara genome duplication(WGD) yakaonekwa mu chayote mu25±4 Mya, inova yechitatu WGD chiitiko mucucuibitaceae.
Fu A et al.,Horticulture Research, 2021
3.Synteny analysis: Mamwe majini ane chokuita ne phytohormones mukukura kwemichero akawanikwa mu chayote, nyoka gourd uye squash.Hukama huripo pakati pechayote ne squash hwakakwira zvishoma pane huri pakati pechayote negourd renyoka.
Fu A et al.,Horticulture Research, 2021
4.Gene mhuri yekuongorora: KEGG kupfumisa pamusoro pekuwedzera kwemhuri yejeni uye kuputika muG.thurberi uye G.davidsonii genomes yakaratidza kuti steroid biosynthesis uye brassinosteroid biosynthesis ane chokuita nemajini akawedzerwa.
Yang Z et al.,BMC Biology, 2021
5.Whole genome duplication analysis: 4DTV uye Ks ongororo yekugovera yakaratidza chiitiko chose chekudzokorora kwegenome.Peaks of intraspecies anoratidzwa kudzokorora zviitiko.Peaks of interspecies akaratidzwa speciation zviitiko.Ongororo iyi yakaratidza kuti tichienzanisa nemamwe marudzi matatu ane hukama zvakanyanya, O. europaea yakapfuura nemumwero mukuru wekudzokororwa kwemajini munguva pfupi yapfuura.
Rao G et al.,Horticulture Research, 2021
Nyaya yeBMK
Rose isina prickle: genomic manzwisisiro akabatana nekunyorova kugadzirisa
Rakatsikiswa: National Science Ongororo, 2021
Sequencing strategy:
'Basye'sisina minzwa' (R.Wichurainan) genome:
Approx.93 X PacBio + approx.90 X Nanopore + 267 X Illumina
Mibairo yakakosha
1.High quality R.wichuraiana genome yakavakwa pachishandiswa nzira dzekuverenga kwenguva refu, izvo zvinopa musangano we 530.07 Mb (Inofungidzirwa genome saizi yaive ingangoita 525.9 Mb nekuyerera kwe cytometry uye 525.5 nekuongorora genome; Heterozygosity yaive yakapoteredza 1.03%).BUSCO inofungidzirwa chibodzwa chaive 93.9%.Kuenzanisa ne "Old blush" (haploOB), kunaka uye kukwana kweiyi genome kwakasimbiswa ne base single-base accuracy uye LTR assembly index (LAI = 20.03).R.wichuraiana genome ine 32,674 mapuroteni ekukodha majini.
2.Multi-omics joint analysis, inosanganisira kuenzanisa genomics, transcriptomics, QTL kuongororwa kwemajini evanhu, yakaratidza kukosha kwakakosha pakati peR. wichuraiana naRosa chinensis.Zvakare, kusiyanisa kwekutaura kwemajini ane hukama muQTL angangove akabatana ne stem prickle patterning.
Kuenzanisa genomics anaysis pakati peBasye;'s Thornless naRosa chinensis inosanganisira synteny ongororo, gene mhuri cluster, kuwedzera uye chibvumirano chekuongorora, yakaratidza huwandu hukuru hwekusiyana, hune hukama nehunhu hwakakosha mumaruva.Kuwedzera kwakasarudzika muNAC uye FAR1/FRS gene mhuri yaigona kuve yakabatana nekupokana nenzvimbo dema.
Kuenzanisa genomics kuongororwa pakati peBT uye haploOB genomes.
Zhong, M., nevamwe."Rose isina prickle: genomic manzwisisiro akabatana nekugadzirisa hunyoro"National Science Ongororo, 2021;, nwb092.
