Zomera / Zinyama za De Novo Genome Sequencing
Ubwino wa Utumiki
Kukula kwamapulatifomu otsatizana ndi bioinformatics mundi novomsonkhano wa genome
(Amarasinghe SL et al.,Genome Biology, 2020)
● Kupanga ma genome atsopano komanso kuwongolera ma genome omwe alipo kuti azitha chidwi.
● Kulondola kwapamwamba, kupitiriza ndi kukwanira mu msonkhano
● Kupanga zofunikira zopangira kafukufuku wa polymorphism motsatizana, ma QTL, kusintha ma gene, kuswana, ndi zina.
● Zokhala ndi nsanja zonse za m'badwo wachitatu: njira yolumikizira ma genome imodzi.
● Masanjidwe osinthika ndi kuphatikiza njira zokwaniritsira ma genome osiyanasiyana okhala ndi mawonekedwe osiyanasiyana
● Gulu la akatswiri odziwa zambiri za sayansi ya zamoyo omwe ali ndi chidziwitso chambiri pamagulu ovuta a genome, kuphatikizapo ma polyploid, ma genome akuluakulu, ndi zina zotero.
● Milandu yoposa 100 yopambana ndipo kuchuluka kwa kufalitsa kwakhudza kupitirira 900
● Kutembenuza nthawi kufulumira kwa miyezi itatu pakuphatikiza ma chromosome genome.
● Thandizo lolimba laukadaulo lokhala ndi ma patent angapo ndi zokopera zamapulogalamu poyeserera ndi bioinformatics.
Mafotokozedwe a Utumiki
|
Zamkatimu
|
nsanja
|
Werengani Utali
|
Kufotokozera
|
| Kafukufuku wa Genome
| Illumina NovaSeq
| Mtengo wa PE150
| ≥ 50X
|
| Kutsata kwa Genome
| PacBio Revio
| 15 KB Kuwerenga kwa HiFi
| ≥30X
|
| Hi-C
| Illumina NovaSeq
| Mtengo wa PE150
| ≥100X
|
Kuyenda kwa ntchito
Zitsanzo Zofunika ndi Kutumiza
Zitsanzo Zofunika:
| Mitundu | Minofu | Za PacBio | Za Nanopore |
| Zinyama | Visceral ziwalo (chiwindi, ndulu, etc.) | ≥ 1.0 g | ≥ 3.5 g |
| Minofu | ≥ 1.5 g | ≥ 5.0 g | |
| Magazi a nyama zoyamwitsa | ≥ 1.5 mL | ≥ 5.0 mL | |
| Magazi a nsomba kapena mbalame | ≥ 0.2 mL | ≥ 0.5 mL | |
| Zomera | Masamba atsopano | ≥ 1.5 g | ≥ 5.0 g |
| Petal kapena tsinde | ≥ 3.5 g | ≥ 10.0 g | |
| Mizu kapena mbewu | ≥ 7.0 g | ≥ 20.0 g | |
| Maselo | Maselo chikhalidwe | ≥ 3 × 107 | ≥ 1 × 108 |
Kutumiza Kwachitsanzo Kovomerezeka
Chidebe: 2 ml centrifuge chubu (zojambula za malata ndizosavomerezeka)
Pazitsanzo zambiri, timalimbikitsa kuti musasunge ethanol.
Zitsanzo zolembetsera: Zitsanzo ziyenera kulembedwa momveka bwino komanso zofanana ndi zomwe zatumizidwa.
Kutumiza: Owuma-Izi: Zitsanzo ziyenera kulongedzedwa m'matumba kaye ndikukwiriridwa mu ayezi wouma.
Kuyenda kwa Ntchito Yantchito
Kuyesera kupanga
Kupereka zitsanzo
Kutulutsa kwa DNA
Kumanga laibulale
Kutsata
Kusanthula deta
Pambuyo pogulitsa ntchito
*Zotsatira zachiwonetsero zomwe zikuwonetsedwa pano zonse zidachokera ku ma genome omwe amasindikizidwa ndi Biomarker Technologies
1.Circos pa chromosome-level genome assembly waG. rotundifoliumndi Nanopore sequencing platform
Wang M ndi al.,Molecular Biology ndi Evolution, 2021
2.Statistics of Weining rye genome assembly and annotation
Li G et al.,Nature Genetics, 2021
3.Gene kulosera zaSechium edulegenome, yochokera ku njira zitatu zolosera:Pa novokulosera, kulosera motengera Homology ndi kuneneratu kwa data ya RNA-Seq
Fu A et al.,Kafukufuku wa Horticulture, 2021
4.Kuzindikiritsa materminal atali osasinthika akubwereza ma genome atatu a thonje
Wang M ndi al.,Molecular Biology ndi Evolution, 2021
5.Hi-C kutentha mapu aC. acuminatama genome omwe amawonetsa kuyanjana kwamtundu uliwonse.Kuchuluka kwa machitidwe a Hi-C ndi ofanana ndi mtunda wa mzere pakati pa ma contig.Mzere wowongoka pamapu otenthawa ukuwonetsa kukhazikika kolondola kwa ma contig pa ma chromosome.(Chiwerengero cha Contig anchoring: 96.03%)
kang M et al.,Nature Communications,2021
BMK Case
Msonkhano wapamwamba kwambiri wa genome umawonetsa mawonekedwe a rye genomic ndi majini ofunikira pazachuma
Lofalitsidwa: Nature Genetics, 2021
Njira yotsatirira:
Msonkhano wa genome: PacBio CLR mode yokhala ndi laibulale ya 20 kb (497 Gb, pafupifupi 63×)
Kuwongolera kwakanthawi: NGS yokhala ndi laibulale ya 270 bp DNA (430 Gb, pafupifupi 54×) pa nsanja ya Illumina
Contigs anchoring: Hi-C library (560 Gb, pafupifupi 71×) pa nsanja ya Illumina
Mapu owonera: (779.55 Gb, pafupifupi 99×) pa Bionano Irys
Zotsatira zazikulu
1. Msonkhano wa Weining rye genome unasindikizidwa ndi kukula kwa genome kwa 7.74 Gb (98.74% ya kukula kwa genome ndi flow cytometry).Scaffold N50 ya msonkhano uno idapeza 1.04 Gb.93.67% ya contigs adazikika bwino pa 7 pseudo-chromosomes.Msonkhanowu udawunikidwa ndi mapu olumikizana, LAI ndi BUSCO, zomwe zidapangitsa kuti pakhale zambiri pakuwunika konse.
2.Kufufuza kwina pa ma genomics ofananiza, mapu olumikizana ndi ma genetic, maphunziro a transcriptomics adachitidwa pamaziko a genome iyi.Makhalidwe osiyanasiyana okhudzana ndi ma genomic adawululidwa kuphatikiza kubwereza kwa majini amtundu wonse komanso momwe amakhudzira majini owuma a starch biosynthesis;Kukonzekera kwapang'onopang'ono kwa prolamin loci, mafotokozedwe a jini omwe ali ndi zomwe zimayambira pamutu woyambirira komanso zigawo za chromosomal zomwe zimagwirizanitsidwa ndi chromosomal ndi loci mu rye.
 Circos chithunzi pa genomic mawonekedwe a Weining rye genome |  Chisinthiko ndi chromosome synteny kusanthula kwa rye genome |
Li, G., Wang, L., Yang, J.ndi al.Msonkhano wapamwamba kwambiri wa genome umawonetsa mawonekedwe a rye genomic ndi majini ofunikira pazachuma.Nat Genet 53,574–584 (2021).
https://doi.org/10.1038/s41588-021-00808-z
