GENOME EVOLUTION
PNAS
Iyo yekushanduka-shanduka uye nhoroondo yekuchengetwa kwegoldfish (Carassius auratus)
PacBio |Ilumina |Bionano Genome Map |Hi-C Genome Assembly |Genetic Map |GWAS |RNA-Seq
Pfungwa huru
1.Goldfish genome yakagadziridzwa nemhando yepamusoro yegungano shanduro, inotsigira 95.75% ye contigs mu 50 pseudochromosomes (Scaffold N50 = 31.84 Mb).Ma subgenomes maviri akaparadzaniswa.
2. Nzvimbo dzeGenomic dzekutsvaira kwakasarudzika panguva yekugara dzakaonekwa kubva mukutevedzana kwedata revanhu 201, kuvhenekerwa pamusoro pe390 emajeni evamiriri ayo angangove ane chekuita nehunhu hwekugara.
3.GWAS padorsal fin mugoldfish inochengetwa yakaratidza 378 magene genes angangove akabatana.Mutori wenhau we tyrosine-protein kinase akaonekwa semumiriri causal gene ane chekuita nekujeka.
Background
Goldfish (Carassius auratus) imwe yehove dzakanyanya kukosha dzakarimwa, dzakachengetwa kubva kucrucian carp muChina yekare.Vakataurirwa naCharles Darwin se "Tichipfuura nemusiyano usingaperi weruvara, tinosangana neakanyanya kugadziridzwa chimiro".Zvakanyanya kusiyanisa maficha uye nhoroondo refu yekupfuya nekupfuya inoita kuti goldfish ive yakanakisa genetic modhi system yehove physiology uye shanduko.
Zvakabudirira
Goldfish genome
JOint analysis of PacBio uye Illumina pair-end sequencing data inobereka yekutanga 1.657 G draft assembly (Contig N50=474 KB).Bionano optical mepu yakagadzirwa uye yakagadzirisa gungano kuita 1.73 Gb muhukuru (Inofungidzirwa genome size: 1.8 Gb).Hi-C yakavakirwa musangano yakawedzera kuvandudza scaffold N50 kubva pa606 Kb kusvika 31.84 Mb uye yakawana 95.75% (1.65 Gb) yakatarisana uye yakaodha anchoring rate.Iyo genome inoumbwa ne56,251 coding genes uye 10,098 refu isina-coding transcript.Zvakare, makumi matatu nemasere anogona kuita centromeric matunhu akafanotaurwa kubva mumakumi mashanu echromosomes.
Fig.1 Goridhe hove Genome
Tnhamo seti dzakajeka dzemasubgenomes dzakaonekwa mumakromosomes egoldfish makumi mashanu akakonzerwa nechiitiko chekare chekusanganiswa.Seti yemakromosomes ane chikamu chepamusoro chezviverengero zvakabatanidzwa pakati pegoldfish neBarbinae akatsanangurwa se subgenome A (ChrA01~A25), kureva subgenome inowanikwa kuBarbinae, uye akasara se subgenome B (ChrB01~B25).
Kutsvaira mudzimba uye kusarudza
Ahwerengedzo yemhando gumi nenhanhatu dzemhando dzecrucian carps uye 185 dzinomiririra goldfish dzakasiyana dzaive dzakatevedzana neavhareji yehupamhi hwekutevedzana hunosvika 12.5X, ichigadzira 4,3 terabases yedata.Phylogenetic reconstruction uye PCA kuongororwa kwakasimbisa hukama hwepedyo pakati pezvakajairwa goldfish uye crucian carp pane dzimwe hove dzegoridhe, dzakazopatsanurwa kuita mitsara miviri.
LD kuongororwa kwekuora kwepamusoro pezvikamu zvina zvakatsigira kuvapo kwehuwandu hwemajini ebhodhoro panguva yekuchengetwa uye kusarudzwa kwakasimba kwekugadzira mugoldfish.Kuwedzera kusiana kwemajini (π) kubva kucrucian carp kuenda kune yakajairika goldfish kuenda kuWen goldfish uye Egg goldfish kwakaratidza kuunganidzwa kwakakura kwekusiyana kwemajini panguva yekuchengetwa kwavo.50 yakasarudzwa kutsvaira genomic nzvimbo dzinofukidza 25.2 Mb uye 946 majini akaonekwa kubva kune anomiririra data (33 goldfish uye 16 crucian crap).Kuwedzera ongororo kune 201 vanhu, 393 majini airatidza matunhu akapedzwa akasarudzika kutsvaira.Aya majini akawanikwa akaderera-akasiyana, ayo anogona kunge akakonzeresa kune phenotypes ane hukama nehukuru hunhu hwekumba mugoldfish.
Fig.3 Genome-wide domestication-associated analysis
GWAS pahove dzegoridhe dzakachengetwa
Dorsal fin chinhu chakakosha chinosiyanisa Wen goldfish kubva Egg goldfish.GWAS yedorsal fin pa96 Wen goldfish uye 87 Egg goldfish yakaburitsa magene 378 akapararira mumakromosomes gumi nematatu uye kugoverwa kusina kuenzana kwemajini aya pakati pemasubgenomes kwakaonekwa.Ongororo yekushanda pane aya majini emumiriri yakaratidza maitiro ebhayoloji anosanganisira "Cell surface receptor signing", "Transmembrane transportation", "Skeletal system development", nezvimwe.
Fig.4 GWAS yedorsal fin pahove dzegoridhe dzinopfuyiwa
In GWAS yemaitiro akajeka ane hukama, imwe chete yakasimba yemubatanidzwa peak yakaonekwa.Jeni inokodha tyrosine-protein kinase receptor yakaonekwa mune imwe yenzvimbo dzevamiriri.
Fig.5 GWAS yezvakajeka-zvine chokuita nechiyero
Reference
Chen D et al.Iyo yekushanduka-shanduka uye nhoroondo yekuchengetwa kwegoldfish (Carassius auratus).PNAS (2020)
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Nguva yekutumira: Jan-04-2022