GENOME EVOLUTION
ntuj genetics
Kev sib sau ua ke genome zoo qhia txog rye genomic yam ntxwv thiab cov noob tseem ceeb agronomically
PacBio |Illumina |Bionano Optical Map |Hi-C Genome Assembly |Daim ntawv qhia caj ces |Xaiv Sweeps |RNA-Seq |ISO-seq |SLAF-sib
Biomarker Technologies tau muab kev txhawb nqa rau Pacbio sequencing, Hi-C sequencing thiab cov ntaub ntawv tsom xam hauv txoj kev tshawb no.
Qhov tseem ceeb
1.Qhov thawj chromosomal-theem zoo Rye genome tau txais, uas muaj ib qho chromosome loj dua 1 Gb.
2.Piv rau Tu, Aet thiab Hv genome, ib qho tshwj xeeb tsis ntev los no LTR-RT cov xwm txheej tau pom hauv Rye genome, uas yog lub luag haujlwm rau kev txuas ntxiv ntawm rye genome loj.
3.Qhov sib txawv ntawm rye thiab diploid nplej tau tshwm sim tom qab kev sib cais ntawm barley los ntawm cov nplej, nrog rau lub sijhawm sib txawv ntawm ob qhov xwm txheej yog kwv yees li 9.6 thiab 15 MYA.
FT noob phosphorylation tuaj yeem tswj tau qhov zoo ntawm lub taub hau thaum ntxov hauv rye.
4.Selective cheb tsom xam qhia tau hais tias muaj peev xwm koom tes ntawm ScID1 nyob rau hauv cov kev cai ntawm lub npe hnub thiab nws tej zaum xaiv los ntawm domestication nyob rau hauv rye
Keeb kwm
Keeb kwm
Rye yog ib qho khoom noj muaj txiaj ntsig thiab cov qoob loo qoob loo, ib qho tseem ceeb ntawm cov noob qoob loo rau kev txhim kho cov nplej thiab triticale, thiab cov khoom siv tseem ceeb rau kev sib piv genomics kev tshawb fawb hauv cov nyom.Weining rye, ib qho kev cog qoob loo thaum ntxov hauv Suav teb, yog qhov zoo heev vim nws qhov dav-spectrum tsis kam rau ob qho tib si powdery mildew thiab kab txaij xeb.Txhawm rau kom nkag siab txog cov noob caj noob ces thiab molecular hauv paus ntawm rye cov neeg tseem ceeb zoo thiab txhawb cov kev tshawb fawb genomic thiab kev yug me nyuam hauv rye thiab cov qoob loo uas muaj feem xyuam, peb ntawm no tau ua ntu zus thiab txheeb xyuas cov genome ntawm Weining rye.
Kev ua tiav
Rye Genome
Lub Rye genome tau tsim los ntawm kev sib txuas PacBio SMRT nyeem, nyeem luv luv Illumina sequencing, nrog rau cov los ntawm chromatin conformation capture (Hi-C), genetic mapping, thiab BioNano tsom xam.Cov contigs sib sau ua ke (7.74 Gb) suav txog 98.47% ntawm qhov kwv yees genome loj (7.86 Gb), nrog 93.67% ntawm contigs (7.25 Gb) muab rau xya chromosomes.Cov ntsiab lus rov ua dua yog 90.31% ntawm cov genome sib sau ua ke.
Rye Genome
Genetic linkage map (WJ) tsim siv 295 F2 nroj tsuag tau los ntawm kev hla ntawm ob lub rye landraces (Weining × Jingzhou)
Hi-C daim ntawv qhia ntawm xya sib sau ua ke Weining rye chromosomes (1R - 7R)
Kev sib xyaw ntawm xya chromosomes ntawm Weining rye thiab xya pawg rye linkage tsim siv Lo7 x Lo255 RIL cov pej xeem
Qhov LTR Assembly Index (LAI) tus nqi ntawm Rye genome tau pom tias yog 18.42 thiab 1,393 (96.74%) ntawm 1,440 BUSCO cov noob tau txais txiaj ntsig zoo tau txheeb xyuas .Cov txiaj ntsig no qhia tias Weining rye genome sequence yog qhov zoo hauv ob qho tib si intergenic. thiab thaj chaw genic.Tag nrho ntawm 86,991 protein-coding genes, suav nrog 45,596 high-confidence (HC) genes thiab 41,395 low-confidence genes (LC) noob tau kwv yees.
2. Kev soj ntsuam ntawm TEs
Analysis ntawm TEs.Tag nrho ntawm 6.99 Gb, sawv cev rau 90.31% ntawm Weining los ua ke, tau sau tseg raws li TEs, uas suav nrog 2,671,941 cov ntsiab lus ntawm 537 tsev neeg.Cov ntsiab lus TE no tau meej meej siab dua qhov uas tau tshaj tawm yav dhau los rau Ta (84.70%), Tu (81.42%), Aet (84.40%), WEW (82.20%), lossis Hv (80.80%).Lub davhlau ya nyob twg ntev rov ua dua retrotransposons (LTR-RTs), suav nrog Gypsy, Copia thiab cov ntsiab lus RT tsis suav nrog, yog cov tseem ceeb TEs, thiab 1ccupied 84.49% ntawm cov ntsiab lus TE thiab 76.29% ntawm kev sib sau Weining genome;CACTA DNA transposons yog qhov thib ob ntau tshaj TEs, suav nrog 11.68% ntawm cov ntsiab lus TE cov ntsiab lus thiab 10.55% ntawm kev sib sau ua ke Weining genome.
Analysis ntawm transposon ntsiab ntawm rye
Weining rye muaj qhov sib piv siab ntawm qhov tsis ntev los no ntawm LTR-RTs nrog lub ncov ntawm amplification tshwm sim nyob ib ncig ntawm 0.5 lab xyoo dhau los (MYA), uas yog qhov tsis ntev los no ntawm plaub hom;lwm lub ncov, tshwm sim kwv yees li 1.7 MYA, laus dua thiab tseem pom hauv barley.Nyob rau theem superfamily, qhov tawg tsis ntev los no ntawm Copia cov ntsiab lus hauv Weining rye ntawm 0.3 MYA tau pom, thaum lub zog ntawm Gypsy RTs dominantly zoo li tus bimodal faib qauv ntawm LTR-RT tawg dynamics.
3. Kev soj ntsuam ntawm rye genome evolution thiab chromosome syntenies
Qhov sib txawv ntawm rye thiab diploid nplej tau tshwm sim tom qab kev sib cais ntawm barley los ntawm cov nplej, nrog rau lub sij hawm sib txawv ntawm ob qhov xwm txheej yog kwv yees li 9.6 thiab 15 MYA, feem.1R, 2R, 3R yog tag nrho collinear nrog pawg 1, 2 thiab 3 chromosomes ntawm cov nplej, feem.4R, 5R, 6R, 7R tau pom muaj cov fusions loj thiab ntu.
4. Kev soj ntsuam ntawm cov noob duplications thiab lawv cov kev cuam tshuam rau cov hmoov txhuv nplej siab biosynthesis noob
Qhov tseem ceeb, cov lej ntawm cov noob caj noob ces (TDGs) thiab cov noob sib xws (PDGs) ntawm Weining rye yog ob qho tib si siab dua cov uas pom rau Tu, Aet, Hv, Bd thiab Os.Transposed duplicated genes (TrDGs) kuj muaj ntau dua li qhov tshwj xeeb pom rau Tu thiab Aet.Rye genome expansion yog nrog los ntawm ntau dua ntawm cov noob duplications.Qhov nce TE tawg nyob rau hauv rye tej zaum yuav ua rau kom nce tus naj npawb ntawm TrDGs.
Evolutionary thiab chromosome synteny tsom xam ntawm rye genome
Kev soj ntsuam ntawm rye noob duplications thiab lawv cov kev cuam tshuam rau ntau haiv neeg ntawm starch biosynthesis ntsig txog cov noob (SBRGs)
5. Kev txiav cov noob qoob loo khaws cia protein (SSP) gene loci
Plaub chromosomal loci (Sec-1 txog Sec-4) qhia rye SSPs tau raug txheeb xyuas ntawm 1R lossis 2R.α-gliadin noob tau hloov zuj zus tsis ntev los no nyob rau hauv hom qoob mog thiab ze ze rau hom tom qab sib txawv ntawm cov nplej los ntawm rye.
6. Kev soj ntsuam ntawm qhov transcription factor (TF) thiab kab mob tiv thaiv kab mob
Analysis ntawm rye secalin loci
Weining rye muaj ntau yam kab mob tiv thaiv kab mob (DRA) noob (1,989, Cov Ntaub Ntawv Ntxiv 3) dua li Tu (1,621), Aet (1,758), Hv (1,508), Bd (1,178), Os (1,575), thiab A (1,836). ), B (1,728) thiab D (1,888) subgenomes ntawm hom nplej.
7. Kev soj ntsuam ntawm cov noob qhia cov yam ntxwv cuam tshuam nrog cov ncauj lus thaum ntxov
Ob FT noob uas muaj kev qhia siab nyob rau hauv ib hnub ntev, ScFT1 thiab ScFT2, tau sau tseg hauv Weining genome los ua ke.Ob qho amino acid residues ntawm ScFT2 (S76 thiab T132) phosphorylation tau pom muaj kev sib raug zoo nrog txo qis lub sijhawm tswj
Kev loj hlob thiab noob qhia cov yam ntxwv cuam tshuam nrog lub ntsiab lus thaum ntxov ntawm Weining rye
8. Mining ntawm cheeb tsam chromosomal thiab loci muaj peev xwm koom nrog hauv rye domestication
Tag nrho ntawm 123,647 SNPs tau siv los ua selevtive sweep tsom xam ntawm cultivated rye thiab S. vavilovii.11 xaiv cheb teeb liab pom los ntawm kev txo qis (DRI), kho qhov ntsuas (FST) thiab XP-CLR txoj kev.ScID1 tau pom tias muaj peev xwm koom nrog hauv txoj cai ntawm hnub tim.
Kev txheeb xyuas thiab kev txheeb xyuas ntawm thaj chaw chromosomal thiab loci muaj feem cuam tshuam rau rye domestication
Kev siv
Li GW et al.Kev sib sau ua ke ntawm genome zoo qhia txog cov yam ntxwv ntawm rye genomic thiab agronomically tseem ceeb cov noob.Nature Genetics (2021)
Xov xwm thiab qhov tseem ceeb 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-05-2022