Kuyerekeza kwa Genomics
Ubwino wa Utumiki
●Mbiri Yambiri Yaukatswiri ndi zofalitsa: ndi zosonkhanitsa, BMKGene yamaliza ma projekiti ofananiza a genomics opitilira 90, ndipo chiwonjezeko chafika pa 900.
●Kusanthula kwatsatanetsatane kwa bioinformatics: phukusi lowunikira lili ndi zowunikira zisanu ndi zitatu zomwe zimafunikira kwambiri, kupereka ziwerengero zokonzedwa bwino zokonzeka kusindikiza ndikulola kutanthauzira kosavuta kwa zotsatira.
●Gulu laluso laukadaulo la bioinformatics komanso kuzungulira kwakanthawi kochepa: odziwa zambiri pakuwunika kufananiza kwa ma genomics, gulu la BMKGene limakwaniritsa zowunikira zosiyanasiyana pakanthawi kochepa.
●Thandizo Pambuyo Pakugulitsa:Kudzipereka kwathu kumapitilira kutha kwa projekiti ndi nthawi ya miyezi itatu mutagulitsa. Panthawiyi, timapereka zotsatila za polojekiti, chithandizo chazovuta, ndi magawo a Q&A kuti tiyankhe mafunso aliwonse okhudzana ndi zotsatira.
Mafotokozedwe a Utumiki
| Nthawi yoyerekeza yozungulira | Chiwerengero cha mitundu | Amasanthula |
| 30 masiku ogwira ntchito | 6-12 | Gene family clustering Kukula kwa banja la Gene ndi kuchepetsedwa Kupanga mitengo ya Phylogenetic Kuyerekeza kwa nthawi ya Divergence (Kulinganiza kwa zinthu zakale kumafunikira) Nthawi yoyika LTR (Yazomera) Kubwereza kwamtundu wonse (Kwa zomera) Kukakamiza kosankha Kusanthula kwa Synteny |
Bioinformatics kusanthula
● Banja la Gene
● Phylogenetics
● Nthawi yosiyana
● Kukakamiza kusankha
● Kusanthula kwa mawu
Zitsanzo Zofunika ndi Kutumiza
Zitsanzo Zofunika:
Tissue kapena DNA yotsatizana ndi ma genome
Za Tissue
| Mitundu | Minofu | Kafukufuku | PacBio CCS |
| Nyama | Matenda a Visceral | 0.5-1 g | ≥ 3.5 g |
| Minofu ya minofu | |||
| ≥ 5.0 g | |||
| ≥ 5.0 mL | |||
| Magazi a mammalian | |||
| ≥ 0.5 mL | |||
| Magazi a Nkhuku/Nsomba | |||
| Chomera | Tsamba Latsopano | 1-2g pa | ≥ 5.0 g |
| Petal / tsinde | 1-2g pa | ≥ 10.0 g | |
| Muzu/Mbewu | 1-2g pa | ≥ 20.0 g | |
| Maselo | Selo yachikhalidwe | - | ≥ 1 x 108 |
Deta
Mafayilo amtundu wa genome(.fasta) ndi mafayilo ofotokozera (.gff3) amitundu yofananira
Kuyenda kwa Ntchito Yantchito
Kuyesera kupanga
Kupereka zitsanzo
Kumanga laibulale
Kutsata
Kusanthula deta
Pambuyo pogulitsa ntchito
*Zotsatira zowonetsedwa pano zonse zidachokera ku ma genome omwe amasindikizidwa ndi Biomarker Technologies
1.LTR ikani chiyerekezo cha nthawi: Chiwerengero chomwe chikuwonetsa kugawa kwapadera kwa bimodal mu nthawi zoyika za LTR-RTs mu Weining rye genome, poyerekeza ndi zamoyo zina. Chiwopsezo chaposachedwa kwambiri chidawoneka pafupifupi zaka 0.5 miliyoni zapitazo.
Li Guang et al.,Nature Genetics, 2021
2.Phylogeny and gene family analysis on chayote (Sechium edule) : Pofufuza chayote ndi mitundu ina ya 13 yokhudzana ndi jini, Chayote anapezeka kuti ali pafupi kwambiri ndi njoka ya njoka (Trichosanthes anguina). Chayote yochokera ku mphonda ya njoka mozungulira 27-45 Mya ndi kubwereza kwamtundu wonse (WGD) idawonedwa mu chayote mu 25±4 Mya, chomwe ndi chochitika chachitatu cha WGD ku cucuibitaceae.
Fu A et al.,Kafukufuku wa Horticulture, 2021
3.Kusanthula kwa Synteny: Majini ena okhudzana ndi phytohormones mu chitukuko cha zipatso adapezeka mu chayote, mphodza ya njoka ndi sikwashi. Kugwirizana pakati pa chayote ndi sikwashi ndikokwera pang'ono kuposa pakati pa chayote ndi mphonda wa njoka.
Fu A et al.,Kafukufuku wa Horticulture, 2021
Kusanthula kwa banja la 4.Gene: Kuchulukitsa kwa KEGG pakukula kwa banja la jini ndi kuchepetsedwa mu G.thurberi ndi G.davidsonii genomes zasonyeza kuti steroid biosynthesis ndi brassinosteroid biosynthesis zokhudzana ndi majini zinakulitsidwa.
Yang Z et al.,BMC Biology, 2021
5.Kusanthula kwamtundu wonse wa ma genome: Kusanthula kwa 4DTV ndi Ks kukuwonetsa zochitika zonse zobwereza ma genome. Kuchuluka kwa intraspecies kumawonetsa zochitika zobwerezabwereza. Kuchuluka kwa mitundu yamitundu yosiyanasiyana kumawonetsa zochitika zapadera. Kufufuzaku kunasonyeza kuti poyerekezera ndi mitundu ina itatu yogwirizana kwambiri, O. europaea inadutsa m'kubwereza kwa majini ambiri posachedwapa.
Rao G ndi al.,Kafukufuku wa Horticulture, 2021
BMK Case
Rose wopanda prickle: chidziwitso cha genomic cholumikizidwa ndi kusintha kwa chinyezi
Lofalitsidwa: National Science Review, 2021
Njira yotsatirira:
'Basye'sZopanda minga' (R.Wichurainan) genome:
Pafupifupi. 93 X PacBio + pafupifupi. 90 X Nanopore + 267 X Illumina
Zotsatira zazikulu
1.Mawonekedwe apamwamba a R.wichuraiana genome adapangidwa pogwiritsa ntchito njira zowerengera nthawi yayitali, zomwe zimapereka kuphatikiza kwa 530.07 Mb (Kuyerekeza kwa kukula kwa genome kunali pafupifupi 525.9 Mb ndi flow cytometry ndi 525.5 ndi kafukufuku wa genome Heterozygosity inali pafupifupi 1.03%). BUSCO ikuyerekeza kuti inali 93.9%. Poyerekeza ndi "Old blush" (haploOB), ubwino ndi kukwanira kwa genome iyi kunatsimikiziridwa ndi kulondola kwa maziko amodzi ndi LTR assembly index (LAI = 20.03). R.wichuraiana genome ili ndi ma gene 32,674 a protein coding.
2.Kusanthula kophatikizana kwa ma multi-omics, kuphatikiza ma genomics, transcriptomics, kusanthula kwa QTL kwa kuchuluka kwa majini, kunavumbulutsa tsatanetsatane wofunikira pakati pa R. wichuraiana ndi Rosa chinensis. Komanso, kusiyanasiyana kwa ma jini okhudzana ndi QTL kumayenera kulumikizidwa ndi mawonekedwe a tsinde.
Kuyerekeza kwa genomics pakati pa Basye;'s Thornless ndi Rosa chinensis kuphatikiza kusanthula kwa synteny, gulu la mabanja a jini, kusanthula kwakukula ndi kutsika, kudawonetsa kusiyanasiyana kwakukulu, komwe kumakhudzana ndi mikhalidwe yofunika kwambiri yamaluwa. Kukula kwapadera mu NAC ndi FAR1/FRS banja la jini linali lotheka kulumikizidwa ndi kukana kwakuda.
Kuyerekeza kwa genomics pakati pa BT ndi haploOB genomes.
Zhong, M., ndi al. "Rose wopanda prickle: chidziwitso cha genomic cholumikizidwa ndi kusintha kwa chinyezi"National Science Review, 2021;, mba092.
