GENOME EVOLUTION
nature genetics
Musangano wepamusoro-soro wegenome unoratidza rye genomic maitiro uye agronomically akakosha majini
PacBio |Ilumina |Bionano Optical Map |Hi-C Genome Assembly |Genetic Map |Selective Sweeps |RNA-Seq |ISO-seq |SLAF-seq
Biomarker Technologies yakapa rutsigiro rwehunyanzvi pakutevedzana kwePacbio, kutevedzana kweHi-C uye kuongororwa kwedata muchidzidzo ichi.
Pfungwa huru
1.Yekutanga chromosomal-level high quality Rye genome yakawanikwa, iyo ine chromosome imwe yakakura kupfuura 1 Gb.
2.Kuenzaniswa neTu, Aet uye Hv genome, chiitiko chakasiyana chekupedzisira cheLTR-RT chakaonekwa muRye genome, iyo yaiva nebasa rekuwedzera kwehukuru hwejenome rye.
3.Kusiyana pakati pe rye uye diploid gorosi kwakaitika mushure mekuparadzaniswa kwebhari kubva gorosi, pamwe nekusiyana nguva dzezviitiko zviviri zvinenge 9.6 uye 15 MYA.
FT majini phosphorylation inogona kudzora yekutanga musoro hunhu mu rye.
4.Selective sweep analysis inoratidza zvinogona kubatanidzwa kweScID1 mukutonga kwemusoro wemusoro uye kusarudzwa kwayo kungangoitwa nekuchengetwa mu rye.
Background
Background
Rye chikafu chakakosha uye chirimwa cheforogo, yakakosha genetic sosi yekuvandudza gorosi uye triticale, uye chinhu chakakosha pakuenzanisa zvidzidzo zvegenomics muuswa.Weining rye, rudzi rwekutanga maruva rwakarimwa kuChina, rwakatanhamara nekuda kwehupamhi hwekudzivirira kwayo kuvhuvhu uye mutsara.Kuti tinzwisise genetic uye molecular hwaro hweiyo rye elite hunhu uye kusimudzira genomic uye kupfuya zvidzidzo mu rye uye zvirimwa zvine hukama, isu pano takatevedzana nekuongorora genome yeWeining rye.
Zvakabudirira
Rye Genome
Iyo Rye genome yakagadzirwa nekubatanidza PacBio SMRT kuverenga, pfupi-kuverenga Illumina kutevedzana, pamwe neayo kubva kuchromatin conformation capture (Hi-C), genetic mepu, uye BioNano ongororo.Iwo akaunganidzwa contigs (7.74 Gb) akaverengera 98.47% yeanofungidzirwa genome saizi (7.86 Gb), aine 93.67% yemacontigs (7.25 Gb) akaiswa kune manomwe makromosomes.Zvinhu zvinodzokororwa zvakaumba 90.31% ye genome yakaungana.
Rye Genome
Genetic linkage mepu (WJ) yakagadziridzwa ichishandisa 295 F2 zvirimwa zvakatorwa kubva mukuyambuka kwembiri rye landraces (Weining × Jingzhou)
Hi-C yemepu yekubatanidza yeanomwe akaungana Weining rye chromosomes (1R - 7R)
Kurongeka pakati pemakromosomes manomwe akaunganidzwa eWeining rye uye mapoka manomwe ekubatanidza rye akagadzirwa achishandisa Lo7 x Lo255 RIL huwandu.
Iyo LTR Assembly Index (LAI) kukosha kweRye genome yakawanikwa iine 18.42 uye 1,393 (96.74%) ye1,440 yakachengetedzwa zvakanyanya BUSCO genes yakaonekwa kunze .Izvi zvinobuda zvinoratidza kuti Weining rye genome sequence ndeyemhando yepamusoro mune zvese intergenic. uye genic regions.Huwandu hwe86,991 mapuroteni-coding genes, anosanganisira 45,596 high-confidence (HC) genes uye 41,395 low-confidence genes (LC) genes akafanotaurwa.
2. Kuongororwa kweTEs
Ongororo yeTEs.Huwandu hwe6.99 Gb, inomiririra 90.31% yemusangano weWeining, yakatsanangurwa seTEs, iyo inosanganisira 2,671,941 zvinhu zvemhuri mazana mashanu nemakumi matatu nenomwe.Izvi zvinyorwa zveTE zvaive zvakakwirira zvakanyanya kupfuura izvo zvakambotaurwa nezveTa (84.70%), Tu (81.42%), Aet (84.40%), WEW (82.20%), kana Hv (80.80%).Iyo refu terminal inodzokorora retrotransposons (LTR-RTs), kusanganisira Gypsy, Copia uye unclassified RT zvinhu, ndizvo zvaive zvakanyanya TEs, uye 1 yakabata 84.49% yezvinyorwa zveTE zvinyorwa uye 76.29% yeakaungana Weining genome;CACTA DNA transposons yaive yechipiri kuwanda kweTEs, ichiita 11.68% yezvinyorwa zveTE zvinyorwa uye 10.55% yeWeining genome yakaungana.
Kuongororwa kwezvinhu zve transposon zve rye
Weining rye yakanga ine chikamu chepamusoro chekuiswa kweLTR-RTs nepamusoro-soro yekuwedzera yakaonekwa makore anosvika mamiriyoni 0.5 apfuura (MYA), iyo yakanga ichangopfuura pakati pemarudzi mana;imwe peak, yakaitika ingangoita 1.7 MYA, yaive yakura uye yakaonekwawo mubhari.Padanho repamusoro-soro, nguva pfupi yadarika kuputika kwezvinhu zveCopia muWeining rye pa0.3 MYA kwakawanikwa, ukuwo maamplification eGypsy RTs ainyanya kuumba bimodal yekugovera maitiro eLTR-RT burst dynamics.
3. Kuferefetwa kweiyo rye genome evolution uye machromosome syntenies
Kusiyana pakati pe rye uye diploid gorosi kwakaitika mushure mekuparadzaniswa kwebhari kubva kugorosi, uye nguva dzekusiyana kwezviitiko zviviri izvi zvinenge 9.6 uye 15 MYA, maererano.1R, 2R, 3R aive akazara collinear nemapoka 1, 2 uye 3 machromosome egorosi, zvichiteerana.4R, 5R, 6R, 7R yakawanikwa iripo yakakura-yakakura fusions uye zvikamu.
4. Ongororo yekudzokororwa kwemajini uye mabatiro azvinoita pa starch biosynthesis genes
Zvikuru, huwandu hwetandemly duplicated genes (TDGs) uye proximally duplicated genes (PDGs) eWeining rye ese aive akakwira kupfuura akawanikwa kuTu, Aet, Hv, Bd uye Os.Transposed duplicated genes(TrDGs) aivewo akawanda kupfuura ayo akanyatsowanikwa Tu neAet.Rye genome yekuwedzera inoperekedzwa nenhamba dzepamusoro dzekudzokororwa kwemajini.Iyo yakawedzera TE kuputika mu rye inogona kunge yakatungamira kune yakakwira nhamba yeTrDGs.
Evolutionary uye chromosome synteny inoongorora ye rye genome
Ongororo ye rye gene duplications uye maitiro avo pane zvakasiyana-siyana zve starch biosynthesis inoenderana genes (SBRGs)
5. Kutsemura rye seed storage protein (SSP) gene loci
Ina chromosomal loci (Sec-1 kusvika Sec-4) inotsanangura rye SSPs yakaonekwa pa1R kana 2R.α-gliadin majini akavepo nguva pfupi yadarika mugorosi uye mhando dzine hukama zvakanyanya mushure mekusiyana kwegorosi kubva ku rye.
6. Kuongororwa kwezvinyorwa zvinyorwa (TF) uye zvirwere zvekudzivirira zvirwere
Kuongororwa kwe rye secalin loci
Weining rye yaive neakawanda kurwisa zvirwere zvinoenderana (DRA) majini (1,989, Supplementary Data 3) kupfuura Tu (1,621), Aet (1,758), Hv (1,508), Bd (1,178), Os (1,575), uye A (1,836) ), B (1,728) uye D (1,888) subgenomes yezviyo zvakajairika.
7. Kuferefeta kwemajini ekutaura zvinhu zvine chekuita nekutanga musoro maitiro
Majini maviri eFT ane kutaura kwakanyanya pasi pemamiriro ezuva refu, ScFT1 uye ScFT2, akatsanangurwa muWeining genome assembly.Maviri amino acid akasara eScFT2 (S76 uye T132) phosphorylation akawanikwa aine hukama nekudzikisa nguva kutonga.
Kuvandudza uye gene kutaura maficha ane chekuita neiyo yekutanga musoro hunhu hweWeining rye
8. Kucherwa kwenzvimbo dzechromosomal uye loci zvinogona kubatanidzwa mukuchengetwa kwe rye
Huwandu hwe123,647 SNPs dzakashandiswa kuita selevtive sweep analysis pakati peirimwa rye neS. vavilovii.11 yakasarudzika masaini ekutsvaira anoonekwa nekuderedza index (DRI), fixation index (FST) uye XP-CLR nzira.ScID1 yakawanikwa inogona kubatanidzwa mukugadzirisa kwezuva remusoro.
Kuzivikanwa uye kuongororwa kwenzvimbo dzechromosomal uye loci ingangove yakabatana neiyo rye kuchengetwa
Reference
Li GW nevamwe.Musangano wepamusoro-soro wegenome unoratidza rye genomic maitiro uye agronomically akakosha majini.Nature Genetics (2021)
Nhau Nezvakakosha inovavarira kugovera nyaya dzichangoburwa dzakabudirira neBiomarker Technologies, kutora budiriro yesainzi pamwe nemaitiro ane mukurumbira akashandiswa panguva yekudzidza.
Nguva yekutumira: Jan-05-2022