Hoʻohālikelike Genomics
Pono lawelawe
● pūʻolo hoʻopaʻa ʻana piha, aia nā ʻewalu i makemake nui ʻia
● ʻO ka hilinaʻi kiʻekiʻe i ka nānā ʻana me ka wehewehe kikoʻī a maʻalahi hoʻi i nā hopena
● Ua hoʻolālā maikaʻi ʻia nā kiʻi mākaukau e hoʻolaha
● Hoʻokō ka hui bioinformatics akamai loa i nā koi noiʻi pilikino like ʻole
● ʻOi aku ka pōkole o ka manawa huli me ka ʻoi aku ka pololei o ka nānā ʻana
● Nui ka ʻike me ka ʻoi aku o 90 mau hihia kūleʻa me ka nui o ka hopena i hoʻopuka ʻia ma luna o 900
Nā kikoʻī lawelawe
| Kuhi ʻia ka manawa huli | Ka helu o nā ʻano | Nānā |
| 30 mau lā hana | 6 - 12 | Hui ʻohana Gene ʻO ka hoʻonui a me ka hoʻopaʻa ʻana o ka ʻohana Gene Ke kūkulu lāʻau phylogenetic Manaʻo manawa ʻokoʻa (pono ka calibration fossil) Ka manawa hoʻokomo LTR (No nā mea kanu) Ka hoʻopāpā ʻana o ka genome holoʻokoʻa (No nā mea kanu) Pumi koho ʻIkepili Synteny |
Nā loiloi bioinformatics
● ʻohana Gene
● Phylogenetics
● Ka manawa like ʻole
● kaomi koho
● Kānāwai Synteny
Nā Koina Laʻana a me ka Hoʻouna ʻana
Nā Koina Laʻana:
Tissue a i ʻole DNA no ka hoʻonohonoho ʻana a me ka hui ʻana
No ka Tissue
| ʻAnoʻano | Kiʻi | Nānā | PacBio CCS |
| Holoholona | ʻiʻo visceral | 0.5 ~ 1g | ≥ 3.5g |
| ʻiʻo ʻiʻo | |||
| ≥ 5.0g | |||
| ≥ 5.0mL | |||
| Koko momona | |||
| ≥ 0.5mL | |||
| Koko moa/i'a | |||
| Meakanu | Lau Hou | 1 ~ 2g | ≥ 5.0g |
| Petal/Stem | 1 ~ 2g | ≥ 10.0g | |
| Aʻa/Hua | 1 ~ 2g | ≥ 20.0g | |
| Nā pūnaewele | Cell moʻomeheu | - | ≥ 1 x 108 |
ʻIkepili
Nā waihona kaʻina genome(.fasta) a me nā faila hōʻike (.gff3) o nā ʻano pili pili loa
Holo Hana Hana
Hoʻolālā hoʻokolohua
Hāʻawi laʻana
Kūkulu hale waihona puke
Ke kaʻina ʻana
ʻIkepili ʻikepili
Nā lawelawe ma hope o ke kūʻai aku
*ʻO nā hopena demo i hōʻike ʻia ma ʻaneʻi mai nā genome i paʻi ʻia me Biomarker Technologies
1.LTR hoʻokomo manawa manaʻo: Ua hōʻike ʻia ke kiʻi i kahi mahele bimodal kūʻokoʻa i nā manawa hoʻokomo LTR-RTs ma Weining rye genome, i hoʻohālikelike ʻia me nā ʻano ʻano ʻē aʻe.Ua ʻike ʻia ka piko hope loa ma kahi o 0.5 miliona mau makahiki i hala.
Li Guang et al.,Nature Genetics, 2021
2. Ka nānā 'ana o Phylogeny a me ka 'ohana gene ma ka chayote (Sechium edule): Ma ka 'ana'ana i ka chayote a me nā mea 'ē a'e he 13 e pili ana i ka 'ohana gene, ua 'ike 'ia he pili pili loa 'o Chayote me ka snake gourd (Trichosanthes anguina).Loaʻa ʻia ka Chayote mai ka ʻumeke nahesa ma kahi o 27-45 Mya a ua ʻike ʻia ka hoʻopiʻi genome holoʻokoʻa (WGD) i ka chayote ma 25±4 Mya, ʻo ia ke kolu o ka hanana WGD ma cucuibitaceae.
Fu A et al.,ʻImi Horticulture, 2021
3. ʻIkepili Synteny: Ua loaʻa kekahi mau genes e pili ana i nā phytohormones i ka ulu ʻana o ka hua i loko o ka chayote, snake gourd a me ka ʻōpala.ʻOi aku ka kiʻekiʻe o ka pilina ma waena o ka chayote a me ka ʻōpala ma mua o ka hui ʻana ma waena o ka chayote a me ka ʻumeke nahesa.
Fu A et al.,ʻImi Horticulture, 2021
4.Gene Family Analysis: KEGG enrichment on gene family expansion and contraction in G.thurberi and G.davidsonii genomes i hōʻike ʻia ua hoʻonui ʻia nā genes pili i ka biosynthesis steroid a me ka brassinosteroid biosynthesis.
ʻO Yang Z et al.,BMC Biology, 2021
5. Ka nānā 'ana i ka ho'opā'ālua genome holo'oko'a: 4DTV a me Ks hō'ike 'ana i hō'ike 'ia ka hanana ho'opālua genome holo'oko'a.Ua hōʻike ʻia nā kiʻekiʻe o nā intraspecies i nā hanana kope.Hōʻike ʻia nā kiʻekiʻe o nā interspecies i nā hanana speciation.Ua hōʻike ʻia ka hōʻike ʻana i ka hoʻohālikelike ʻana me nā ʻano ʻano ʻekolu pili pili, ua hele ʻo O. europaea i kahi hana hoʻopāpā nui i kēia manawa.
Rao G et al.,ʻImi Horticulture, 2021
Hihia BMK
ʻO Rose me ka ʻole o ka prickle: nā ʻike genomic e pili ana i ka hoʻololi ʻana i ka wai
Paʻi ʻia: National Science Review, 2021
Hoʻolālā kaʻina hana:
'O Basye'sʻaʻohe kākalaioa' (R.Wichurainan) genome:
Ma kahi.93 X PacBio + ma kahi o.90 X Nanopore + 267 X Illumina
Nā hopena koʻikoʻi
1. Ua kūkulu ʻia ka genome R.wichuraiana kūlana kiʻekiʻe me ka hoʻohana ʻana i nā ʻenehana kaʻina heluhelu lōʻihi, kahi e loaʻa ai kahi hui o 530.07 Mb (ʻO ka nui o ka genome i manaʻo ʻia he 525.9 Mb ma ka cytometry kahe a me 525.5 ma ka anana genome; Heterozygosity ma kahi o 1.03%).ʻO ka helu helu BUSCO he 93.9%.Ke hoʻohālikelike ʻia me ka "Old blush" (haploOB), ua hōʻoia ʻia ka maikaʻi a me ka hoʻopiha piha ʻana o kēia genome e ka base one-base accuracy a me LTR assembly index (LAI=20.03).Loaʻa iā R.wichuraiana genome he 32,674 mau genes coding protein.
2. ʻO ka loiloi hui pū ʻana o nā multi-omics, ʻo ia hoʻi nā genomic comparative, transcriptomics, QTL analysis of genetic population, i hōʻike i ka speciation koʻikoʻi ma waena o R. wichuraiana a me Rosa chinensis.Eia kekahi, pili ʻia ka hoʻololi ʻana o nā genes pili i ka QTL me ka hoʻohālikelike ʻana i ka stem prickle.
ʻO ka loiloi genomics hoʻohālikelike ma waena o Basye;s Thornless a me Rosa chinensis me ka synteny analysis, gene family cluster, expansion and contraction analysis, i hōʻike ʻia i nā ʻano like ʻole, pili i nā ʻano koʻikoʻi o nā rosa.ʻO ka hoʻonui kūʻokoʻa i ka ʻohana gene NAC a me FAR1/FRS i pili pū me ke kū'ē i kahi ʻeleʻele.
Ka hoʻohālikelike ʻana i nā genomics ma waena o BT a me haploOB genomes.
Zhong, M. , et al."Rose me ka ʻole o ka prickle: nā ʻike genomic i pili i ka hoʻololi ʻana i ka wai"National Science Review, 2021;, nwab092.
