Mea kanu/holoholona De Novo Genome Sequencing
Pono lawelawe
Ka hoʻomohala ʻana o nā kahua hoʻonohonoho sequencing a me nā bioinformatics made novohui genome
(Amarasinghe SL et al.,ʻO ke ola kino Genome, 2020)
● Ke kūkulu ʻana i nā genomes hou a me ka hoʻomaikaʻi ʻana i nā genomes kuhikuhi no nā ʻano mea hoihoi.
● ʻOi aku ka pololei, ka hoʻomau a me ka piha i ka hui
● Ke kūkulu ʻana i nā kumuwaiwai kumu no ka noiʻi ʻana ma ka sequence polymorphism, QTLs, gene editing, breeding, etc.
● Hoʻolako ʻia me ke kiko kiko piha o nā papa hana hoʻonohonoho ʻekolu o nā hanauna: hoʻokahi-stop genome assembly solution
● ʻO ka hoʻonohonoho ʻana a me ka hoʻohui ʻana i nā hoʻolālā e hoʻokō ana i nā genome like ʻole me nā hiʻohiʻona like ʻole
● ʻO ka hui bioinformatician akamai loa me ka ʻike nui i nā hui genome paʻakikī, me nā polyploids, giant genomes, etc.
● ʻOi aku ma mua o 100 mau hihia kūleʻa me kahi kumu hoʻohālikelike i hoʻopuka ʻia ma mua o 900
● ʻO ka wikiwiki o ka manawa hoʻohuli e like me 3 mahina no ka hui genome pae chromosome.
● Kākoʻo ʻenehana paʻa me ke ʻano o nā patent a me nā kope kope polokalamu ma ka ʻaoʻao hoʻokolohua a me nā bioinformatics.
Nā kikoʻī lawelawe
|
Maʻiʻo
|
Papahana
|
Heluhelu Length
|
Ka uhi
|
| Nānā Genome
| ʻO Illumina NovaSeq
| PE150
| ≥ 50X
|
| Ka Hoʻopili Genome
| PacBio Revio
| Heluhelu 15 kb HiFi
| ≥ 30X
|
| Hi-C
| ʻO Illumina NovaSeq
| PE150
| ≥100X
|
Ka holo hana
Nā Koina Laʻana a me ka Hoʻouna ʻana
Nā Koina Laʻana:
| ʻAnoʻano | Kiʻi | No PacBio | No Nanopore |
| Holoholona | ʻO nā kino visceral (ake, spleen, etc.) | ≥ 1.0 g | ≥ 3.5 g |
| ʻiʻo | ≥ 1.5 g | ≥ 5.0 g | |
| Koko o nā mea momona | ≥ 1.5 mL | ≥ 5.0 mL | |
| Koko iʻa a manu paha | ≥ 0.2 mL | ≥ 0.5 mL | |
| Nā mea kanu | Lau hou | ≥ 1.5 g | ≥ 5.0 g |
| Petal a kumu paha | ≥ 3.5 g | ≥ 10.0 g | |
| Nā aʻa a i ʻole nā hua | ≥ 7.0 g | ≥ 20.0 g | |
| Nā pūnaewele | Moʻomeheu kelepona | ≥ 3×107 | ≥ 1×108 |
Manaʻo ʻia ka hāʻawi laʻana
ʻO ka pahu: 2 ml centrifuge tube (ʻAʻole ʻōlelo ʻia ʻo Tin foil)
No ka hapa nui o nā laʻana, paipai mākou ʻaʻole e mālama i loko o ka ethanol.
Laʻana hōʻailona: Pono e hōʻailona ʻia nā laʻana a e like me ka palapala ʻike hāpana i waiho ʻia.
Hoʻouna: Ka hau maloʻo: Pono e hoʻopili mua ʻia nā laʻana i loko o nā ʻeke a kanu ʻia i loko o ka hau maloʻo.
Holo Hana Hana
Hoʻolālā hoʻokolohua
Hāʻawi laʻana
Ka unuhi ʻana o DNA
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 aneʻi mai nā genome i paʻi ʻia me Biomarker Technologies
1.Circos ma chromosome-level genome hui oG. rotundifoliumna Nanopore sequencing platform
Wang M et al.,Molecular Biology and Evolution, 2021
2. Heluhelu o ka Weining rye genome hui a me ka hoike
Li G et al.,Nature Genetics, 2021
3.Gene wanana oSechium edulegenome, i loaʻa mai ʻekolu mau ʻano wānana:De novowanana, wanana e pili ana i ka Homology a me ka wanana e pili ana i ka ikepili RNA-Seq
Fu A et al.,ʻImi Horticulture, 2021
4. Identification of intact long terminal repeats in ekolu pulupulu genomes
Wang M et al.,Molecular Biology and Evolution, 2021
5.Hi-C wela palapala o kaC. acuminataka genome e hōʻike ana i nā pilina genome-ākea.ʻO ka ikaika o nā pilina Hi-C e like me ka laina laina ma waena o nā contigs.ʻO kahi laina pololei maʻemaʻe ma kēia palapala wela e hōʻike ana i kahi heleuma pololei loa o nā contigs ma nā chromosomes.(Laki pili pili: 96.03%)
kang M et al.,Nature Communications,2021
Hihia BMK
Hōʻike ka hui genome kiʻekiʻe i nā ʻano genomic rye a me nā genes koʻikoʻi agronomically
Paʻi ʻia: Nature Genetics, 2021
Hoʻolālā kaʻina hana:
Hui Genome: PacBio CLR mode me 20 kb waihona (497 Gb, ma kahi o 63×)
Hoʻoponopono kaʻina: NGS me ka waihona DNA 270 bp (430 Gb, ma kahi o 54 ×) ma ke kahua ʻo Illumina
Contigs heleuma: Hi-C hale waihona puke(560 Gb, ma kahi o 71×) ma Illumina platform
Palapala 'opika: (779.55 Gb, ma kahi o 99×) ma Bionano Irys
Nā hopena koʻikoʻi
1. Ua paʻi ʻia kahi hui o Weining rye genome me ka nui o ka genome he 7.74 Gb(98.74% o ka nui genome i manaʻo ʻia e ka cytometry kahe).Loaʻa ka Scaffold N50 o kēia hui i ka 1.04 Gb.93.67% o nā contigs i hoʻopaʻa pono ʻia ma 7 pseudo-chromosomes.Ua loiloi ʻia kēia hui e ka palapala loulou, LAI a me BUSCO, i loaʻa ai nā helu kiʻekiʻe ma nā loiloi āpau.
2. Ua hana ʻia nā haʻawina hou aku e pili ana i nā genome hoʻohālikelike, ka palapala ʻāina pili genetic, nā haʻawina transcriptomics ma ke kumu o kēia genome.Ua hōʻike ʻia kekahi ʻano o nā hiʻohiʻona e pili ana i ka genomic e pili ana i ka hoʻololi ʻana o ka genome-wide gene a me ko lākou hopena i nā genes biosynthesis starch;ʻO ka hui kino o ka loci prolamin paʻakikī, nā hiʻohiʻona hōʻike gene i lalo o ke ʻano poʻomanaʻo mua a me nā wahi chromosomal pili i ka home a me ka loci i ka rai.
 Diagram Circos ma nā hiʻohiʻona genomic o Weining rye genome |  ʻO nā loiloi evolutionary a me chromosome synteny o ka genome rye |
Li, G., Wang, L., Yang, J.et al.Hōʻike ka hui genome kiʻekiʻe i nā ʻano genomic rye a me nā genes koʻikoʻi agronomically.Nat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
