GENOME EVOLUTION
PNAS
Keeb kwm evolutionary thiab domestication keeb kwm ntawm goldfish (Carassius auratus)
PacBio |Illumina |Bionano Genome daim ntawv qhia |Hi-C Genome Assembly |Daim ntawv qhia caj ces |GWAS |RNA-Sib
Qhov tseem ceeb
1.Goldfish genome tau hloov kho nrog cov khoom sib dhos ua tau zoo, ua rau 95.75% ntawm cov kab mob mus rau 50 pseudochromosomes (Scaffold N50 = 31.84 Mb).Ob tug subgenomes tau disentangled.
2.Genomic cheeb tsam ntawm kev xaiv sweeps thaum lub sij hawm domestication raug txheeb xyuas los ntawm resequencing cov ntaub ntawv ntawm 201 tus neeg, unveiling tshaj 390 tus neeg sib tw genes uas yuav txuam nrog domestication zoo.
3.GWAS ntawm dorsal fin nyob rau hauv domesticated goldfish qhia 378 tus neeg sib tw genes uas muaj feem cuam tshuam.Tus kws tshaj xov xwm tyrosine-protein kinase tau txheeb xyuas tias yog tus neeg sib tw cov noob caj noob ces cuam tshuam nrog pob tshab
Keeb kwm
Goldfish (Carassius auratus) yog ib qho ntawm cov ntses ua liaj ua teb tseem ceeb tshaj plaws, uas tau ua los ntawm crucian carp hauv Suav teb thaum ub.Lawv tau tawm tswv yim los ntawm Charles Darwin li "Kev hla dhau qhov yuav luag tsis muaj qhov sib txawv ntawm cov xim, peb ntsib nrog cov kev hloov pauv txawv tshaj plaws ntawm cov qauv".Cov yam ntxwv sib txawv heev thiab keeb kwm ntev ntawm kev yug me nyuam thiab yug me nyuam ua rau cov ntses goldfish ua qauv zoo heev rau cov ntses physiology thiab evolution.
Kev ua tiav
Goldfish genome
Joint tsom xam ntawm PacBio thiab Illumina khub-kawg sequencing cov ntaub ntawv yields thawj 1.657 G kev sib sau ua ke (Contig N50 = 474 Kb).Bionano kho qhov muag daim ntawv qhia tau tsim thiab kho lub rooj sib txoos rau hauv 1.73 Gb loj (kwv yees genome loj: 1.8 Gb).Hi-C raws li kev sib dhos ntxiv txhim kho scaffold N50 los ntawm 606 Kb rau 31.84 Mb thiab ua tiav 95.75% (1.65 Gb) taw qhia thiab txiav txim siab tus nqi.Cov genome suav nrog 56,251 coding genes thiab 10,098 ntev tsis-coding transcript.Ntxiv mus, 38 lub peev xwm centromeric cheeb tsam tau kwv yees tawm ntawm 50 chromosomes.
Fig.1 Kub ntses Genome
Two clear sets of subgenomes tau txheeb pom nyob rau hauv 50 goldfish chromosomes uas tshwm sim los ntawm ib tug ancient hybridization tshwm sim.Cov txheej txheem ntawm chromosomes nrog ntau dua ntawm kev nyeem raws li cov ntses kub thiab Barbinae tau txhais tias yog subgenome A (ChrA01 ~ A25), piv txwv li subgenome rau Barbinae, thiab cov seem li subgenome B (ChrB01 ~ B25).
Domestication thiab xaiv sweeps
Atag nrho ntawm 16 hom tsiaj qus crucian carps thiab 185 tus neeg sawv cev kub ntses variants tau tshwm sim nrog qhov nruab nrab qhov sib txawv ntawm kwv yees li 12.5X, tsim 4.3 terabases ntawm cov ntaub ntawv.Phylogenetic reconstruction thiab PCA tsom xam tau lees paub tias muaj kev sib raug zoo ntawm cov ntses kub thiab crucian carp dua li lwm cov ntses kub, uas tom qab muab faib ua ob kab.
LD decay tsom rau saum plaub subpopulations txhawb lub hav zoov ntawm cov pej xeem caj ces caj dab thaum lub sij hawm lub domestication thiab muaj zog dag xaiv nyob rau hauv goldfish.Ua kom muaj ntau haiv neeg sib txawv (π) los ntawm crucian carp mus rau cov ntses kub ntau ntxiv mus rau Wen goldfish thiab Qe goldfish qhia tau hais tias muaj kev cuam tshuam loj ntawm kev hloov pauv caj ces thaum lawv nyob hauv tsev.50 xaiv cheb genomic cheeb tsam npog 25.2 Mb thiab 946 noob tau txheeb xyuas los ntawm cov ntaub ntawv sawv cev (33 goldfish thiab 16 crucian crap).Kev tsom xam nthuav dav rau 201 tus neeg, 393 cov noob qhia txog thaj tsam ntawm kev ua tiav kev xaiv cheb.Cov noob no tau pom muaj ntau haiv neeg tsawg, uas yuav muaj feem cuam tshuam rau cov phenotypes cuam tshuam nrog cov yam ntxwv tseem ceeb hauv cov ntses kub.
Fig.3 Genome-wide domestication-associated analysis
GWAS ntawm domesticated goldfish
Dorsal fin yog ib qho tseem ceeb feature distinguishes Wen goldfish los ntawm qe goldfish.GWAS ntawm dorsal fin ntawm 96 Wen goldfish thiab 87 Qe goldfish qhia 378 tus neeg sib tw genes kis thoob plaws 13 chromosomes thiab kev faib tsis sib xws ntawm cov noob ntawm cov subgenomes tau pom.Kev tsom xam ua haujlwm ntawm cov noob neeg sib tw no tau hais txog cov txheej txheem lom neeg suav nrog "Cell nto receptor signaling", "Transmembrane thauj", "Skeletal system development", thiab lwm yam.
Fig.4 GWAS ntawm dorsal fin on domesticated goldfish
In GWAS ntawm pob tshab nplai muaj feem cuam tshuam, ib qho kev sib koom ua ke muaj zog tshaj plaws tau kuaj pom.Ib lub noob encoding tyrosine-protein kinase receptor tau txheeb xyuas nyob rau hauv ib qho ntawm cov neeg sib tw.
Fig.5 GWAS ntawm pob tshab nplai ntsig txog qhov zoo
Kev siv
Chen D et al.Keeb kwm evolutionary thiab domestication keeb kwm ntawm goldfish (Carassius auratus).NPAS (2020)
Xov xwm Lub hom phiaj ntawm kev sib koom cov xwm txheej ua tiav tshiab nrog Biomarker Technologies, khaws cov kev tshawb fawb tshiab thiab cov txuj ci tseem ceeb siv thaum kawm.
Post lub sij hawm: Jan-04-2022