La'au/Manu De Novo Genome Sequencing
Tulaga Auaunaga
Atina'e o fa'asologa fa'asologa ma bioinformatics io le foufa'apotopotoga o genome
(Amarasinghe SL et al.,Genome Biology, 2020)
● Fausia genomes fou ma faʻaleleia genomes o loʻo i ai nei mo ituaiga e fiafia i ai.
● Sili atu le saʻo, faʻaauau ma le atoatoa i le faʻapotopotoga
● Fausia punaoa faʻavae mo suʻesuʻega i le faʻasologa o polymorphism, QTLs, faʻasologa o kene, faʻatupuina, ma isi.
● Fa'aauupegaina i alaleo atoa o fa'asologa fa'asologa o augatupulaga lona tolu: fofo fa'apotopotoga tasi-stop genome
● Fuafuaga fetuutuunai ma le tuufaatasia o taʻiala e faʻataunuʻu ai genomes eseese ma foliga eseese
● Vaega o le bioinformatician sili ona tomai ma le poto masani i faʻapotopotoga faʻapitoa genome, e aofia ai polyploid, genomes lapoa, ma isi.
● E silia ma le 100 mataupu fa'amanuiaina fa'atasi ai ma le fa'aputuina o fa'aaafiaga fa'asalalau e silia ma le 900
● Taimi liliu i le vave e pei o le 3 masina mo le fa'apotopotoina o le genome tulaga o le chromosome.
● lagolago fa'atekinisi fa'atasi ma se fa'asologa o pateni ma puletaofia polokalame i le itu fa'ata'ita'i ma bioinformatics.
Fa'amatalaga Auaunaga
|
Anotusi
|
Fa'avae
|
Faitau Umi
|
Ufiufi
|
| Su'esu'ega Genome
| Illumina NovaSeq
| PE150
| ≥ 50X
|
| Genome Sequencing
| PacBio Revio
| 15 kb HiFi Faitau
| ≥ 30X
|
| Talofa-C
| Illumina NovaSeq
| PE150
| ≥100X
|
Fa'agasologa o galuega
Fa'ata'ita'iga Mana'oga ma le Tu'uina atu
Fa'ata'ita'iga Mana'oga:
| Ituaiga | Tisu | Mo PacBio | Mo Nanopore |
| Manu | Tokeni Visceral (ate, spleen, etc.) | ≥ 1.0 g | ≥ 3.5 g |
| Musele | ≥ 1.5 g | ≥ 5.0 g | |
| Toto o mamame | ≥ 1.5 mL | ≥ 5.0 mL | |
| Le toto o i'a po o manulele | ≥ 0.2 mL | ≥ 0.5 mL | |
| La'au | Laulaau fou | ≥ 1.5 g | ≥ 5.0 g |
| Petal po'o le 'au | ≥ 3.5 g | ≥ 10.0 g | |
| A'a po'o fatu | ≥ 7.0 g | ≥ 20.0 g | |
| sela | Aganu'u sela | ≥ 3×107 | ≥ 1×108 |
Fautuaina Fa'ata'ita'iga Tu'uina atu
Containe: 2 ml centrifuge tube (E le fautuaina le pepa apa)
Mo le tele o faʻataʻitaʻiga, matou te fautuaina e aua le faʻasaoina i le ethanol.
Fa'ailoga fa'ata'ita'iga: E mana'omia le fa'ailoga manino o fa'ata'ita'iga ma ia tutusa ma fa'amatalaga fa'ata'ita'iga ua tu'uina atu.
La'uina: Fa'amamago-aisa: Fa'ata'ita'iga e mana'omia ona teu muamua i taga ma tanu i le aisa-mago.
Auala o Galuega Au'aunaga
Fa'ata'ita'iga mamanu
Fa'ata'ita'iga tu'uina atu
Su'ega DNA
Fausia faletusi
Fa'asologa
Iloiloga fa'amaumauga
Au'aunaga pe a uma ona fa'atau
*O fa'ai'uga fa'aalia o lo'o fa'aalia iinei e mai genomes na lomia fa'atasi ma Biomarker Technologies
1.Circos i chromosome-tulaga genome potopotoga oG. rotundifoliume Nanopore sequencing platform
Wang M et al.,Molecular Biology ma le Evolution, 2021
2. Fa'amaumauga o Weining rye genome fa'apotopotoga ma fa'amatalaga
Li G et al.,Natura Genetics, 2021
3. Gene vavalo oSechium edulegenome, e maua mai i auala vavalo e tolu:De novovalo'aga, fa'asologa fa'avae Homology ma fa'amaumauga fa'amaumauga RNA-Seq
Fu A et al.,Su'esu'ega Fa'ato'aga, 2021
4. Fa'ailoaina o le fa'amaufa'ailoga umi umi toe fai i le tolu genomes cotton
Wang M et al.,Molecular Biology ma le Evolution, 2021
5.Hi-C vevela faafanua o leC. acuminatagenome fa'aalia le genome-lautele fegalegaleai uma-ma-uma.Ole malosi ole feso'ota'iga Hi-C e fa'atatau ile laina ole mamao ile va o contigs.O se laina sa'o mama i luga o lenei faafanua vevela o lo'o fa'ailoa mai ai se fa'amauga sa'o lelei o contigs i chromosomes.(Fa'atatau fa'amau fa'amau: 96.03%)
kang M et al.,Fesootaiga Natura,2021
BMK mataupu
O se fa'apotopotoga genome maualuga e fa'amanino ai uiga fa'agenomic rye ma kenera taua tele
Lolomiina: Natura Genetics, 2021
Fuafuaga fa'asologa:
Genome assembly: PacBio CLR mode ma le 20 kb faletusi (497 Gb, pe tusa 63×)
Fa'asa'oga fa'asologa: NGS fa'atasi ma le 270 bp DNA library (430 Gb, approx. 54×) i luga o le Illumina platform
Contigs taula: faletusi Hi-C(560 Gb, tusa. 71×) i luga ole tulaga Illumina
Fa'afanua fa'apitoa: (779.55 Gb, pe tusa o le 99×) ile Bionano Irys
I'uga autu
1.O se fa'apotopotoga o Weining rye genome na lomia fa'atasi ma le aofa'i atoa o le genome o le 7.74 Gb(98.74% o le fua fa'atatau o le genome e ala i le tafe cytometry).Scaffold N50 o lenei faʻapotopotoga na ausia le 1.04 Gb.93.67% o contigs na taulau manuia i le 7 pseudo-chromosomes.O lenei fa'apotopotoga sa su'esu'eina ile fa'afanua so'otaga, LAI ma BUSCO, lea na maua ai le maualuga o togi i iloiloga uma.
2. Fa'aopoopo su'esu'ega ile fa'atusatusaga o genomics, fa'afanua feso'ota'iga fa'asologa, su'esu'ega transcriptomics sa fa'atinoina ile fa'avae o lenei genome.Na fa'aalia se fa'asologa o uiga e feso'otai i le genomic e aofia ai le fa'aluaina o kenera lautele ma lo latou a'afiaga i kenera biosynthesis masoa;fa'alapotopotoga fa'aletino o lo'o lavelave prolamin loci, fa'aaliga fa'agagana o lo'o fa'avae i lalo o uiga fa'auluuluga muamua ma fa'ailoga fa'a-fa'aiga-feso'ota'i itulagi chromosomal ma loci i le rye.
 Circos fa'ata'ita'iga ile genomic features of Weining rye genome |  Evolutionary ma chromosome synteny au'ili'iliga o le genome rai |
Li, G., Wang, L., Yang, J.ma isi.O se fa'apotopotoga genome maualuga e fa'amanino ai uiga fa'agenomic rye ma kenera taua tele.Nat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
