I-GENOME EVOLUTION
izakhi zofuzo
Ukuhlanganiswa kofuzo lwekhwalithi ephezulu kugqamisa izici ze-rye genomic kanye nofuzo olubalulekile ngokwezolimo
PacBio |Ilumina |Imephu ye-Bionano Optical |I-Hi-C Genome Assembly |Imephu Yofuzo |Ukushanela Okukhethiwe |I-RNA-Seq |ISO-seq |I-SLAF-seq
I-Biomarker Technologies inikeze ukusekelwa kwezobuchwepheshe ekulandeleni kwe-Pacbio, ukulandelana kwe-Hi-C nokuhlaziywa kwedatha kulolu cwaningo.
Amaphuzu avelele
1.I-Rye genome yokuqala yezinga eliphezulu yezinga le-chromosomal yatholwa, enosayizi owodwa we-chromosome omkhulu kuno-1 Gb.
2.Uma kuqhathaniswa ne-Tu, Aet kanye ne-Hv genome, izehlakalo zakamuva ze-LTR-RT eziyingqayizivele zabonwa ku-Rye genome, eyayinesibopho sokunwetshwa kosayizi we-rye genome.
3.Ukuhlukana phakathi kukakolweni we-rye kanye ne-diploid kwenzeka ngemva kokuhlukaniswa kwebhali nokolweni, nezikhathi zokuhlukana kule micimbi emibili cishe zingu-9.6 kanye ne-15 MYA.
I-FT genes phosphorylation ingase ilawule isici sokuqala se-rye.
4. Ukuhlaziya okukhethiwe kukhombisa ukubandakanyeka okungenzeka kwe-ScID1 ekulawuleni usuku lwesihloko kanye nokukhethwa kwayo okungenzeka ngokufuywa ku-rye.
Ingemuva
Ingemuva
I-Rye iyisitshalo esibalulekile sokudla neklabishi, isisetshenziswa esibalulekile sofuzo sokuthuthukiswa kukakolweni kanye ne-triticale, kanye nempahla edingekayo ukuze kuqhathaniswe izifundo ze-genomics otshanini.I-Weining rye, izinhlobonhlobo eziqhakaza zakuqala ezitshalwa eShayina, ivelele ngenxa yokumelana nobubanzi bayo kokubili isikhutha kanye nokugqwala kwemigqa.Ukuze siqonde isisekelo sofuzo namangqamuzana ezimpawu ze-rye elite nokukhuthaza izifundo ze-genomic nokuzalanisa ku-rye nezitshalo ezihlobene, lapha silandelanisa futhi sahlaziya i-genome ye-Weining rye.
Izimpumelelo
I-Rye Genome
I-genome ye-Rye yakhiwa ngokuhlanganisa ukufundwa kwe-PacBio SMRT, ukulandelana kwe-Illumina okufushane, kanye naleyo evela ku-chromatin conformation capture (Hi-C), imephu yofuzo, nokuhlaziywa kwe-BioNano.Ama-contigs ahlanganisiwe (7.74 Gb) abala u-98.47% wosayizi olinganiselwe we-genome (7.86 Gb), no-93.67% wama-contigs (7.25 Gb) anikezwe ama-chromosome ayisikhombisa.Izakhi eziphindaphindayo zenze u-90.31% we-genome ehlanganisiwe.
I-Rye Genome
Imephu yokuxhumanisa izakhi zofuzo (WJ) yathuthukiswa kusetshenziswa izitshalo ezingama-295 F2 ezithathwe ekuweleni kwezindawo ezimbili ze-rye (Weining × Jingzhou)
Imephu yokuxhumana ye-Hi-C yamakhromozomu ayisikhombisa e-Weining rye ahlanganisiwe (1R – 7R)
Ukuqondanisa phakathi kwama-chromosome ayisikhombisa ahlanganisiwe e-Weining rye kanye namaqembu ayisikhombisa okuxhumanisa ama-rye athuthukiswe kusetshenziswa inani labantu be-Lo7 x Lo255 RIL
Inani le-LTR Assembly Index (LAI) le-Rye genome litholakale liyi-18.42 kanye ne-1,393 (96.74%) yezakhi zofuzo ze-BUSCO ezingu-1,440 ezilondolozwe kakhulu. kanye nezifunda ze-genic.Isamba sezakhi zofuzo ze-protein-coding ezingama-86,991, okuhlanganisa izakhi zofuzo zokuzethemba okukhulu (HC) ezingama-45,596 kanye nezakhi zofuzo zokuzethemba okuphansi (LC) ezingama-41,395 ezabikezelwa.
2. Ukuhlaziywa kwama-TEs
Ukuhlaziywa kwama-TE.Isamba esingu-6.99 Gb, esimele u-90.31% womhlangano we-Weining, sichazelwe njengama-TE, ahlanganisa izici eziyi-2,671,941 zemindeni engama-537.Lokhu okuqukethwe kwe-TE kwakungaphezulu ngokusobala kunalokho okubikwe ngaphambilini nge-Ta (84.70%), Tu (81.42%), Aet (84.40%), WEW (82.20%), noma i-Hv (80.80%).Itheminali ende ephindayo i-retrotransposons (LTR-RTs), okuhlanganisa i-Gypsy, i-Copia kanye nezakhi ze-RT ezingafakwanga ohlwini, bekungama-TE abusayo, futhi 1athathe u-84.49% wokuqukethwe kwe-TE okuchasisiwe kanye no-76.29 % we-Weining genome ehlanganisiwe;I-CACTA DNA transposons bekungama-TE esibili ngobuningi kakhulu, akha u-11.68% wokuqukethwe kwe-TE okuchasisiwe kanye no-10.55 % we-Weining genome ehlanganisiwe.
Ukuhlaziywa kwezinto ze-transposon ze-rye
I-Weining rye yayinengxenye ephezulu ngokuqhathaniswa yokufakwa kwakamuva kwe-LTR-RTs nenani eliphakeme lokukhulisa livele eminyakeni eyizigidi ezingu-0.5 edlule (MYA), okwakungokwakamuva kakhulu phakathi kwezinhlobo ezine;elinye inani eliphakeme, lenzeka cishe nge-1.7 MYA, lalindala futhi libonakala nasebhali.Ezingeni lomndeni omkhulu, ukuqhuma kwakamuva kakhulu kwezakhi ze-Copia ku-Weining rye ngo-0.3 MYA kutholwe, kuyilapho ukukhuliswa kwe-Gypsy RTs kuyimise kakhulu iphethini yokusabalalisa i-bimodal ye-LTR-RT yokuqhuma kwamandla.
3. Uphenyo lokuvela kwe-rye genome kanye nama-chromosome syntenies
Ukwehlukana phakathi kukakolweni we-rye kanye ne-diploid kwenzeka ngemva kokuhlukaniswa kwebhali nokolweni, nezikhathi zokuhlukana kwemicimbi emibili cishe i-9.6 ne-15 MYA, ngokulandelana.I-1R, 2R, 3R yayingama-collinear ngokuphelele namaqembu 1, 2 kanye nama-chromosome angu-3 kakolweni, ngokulandelana.4R, 5R, 6R, 7R kwatholakala ukuthi kukhona ukuhlangana okukhulu namasegimenti.
4. Ukuhlaziywa kokuphindaphindeka kofuzo kanye nomthelela wako kuzakhi zofuzo ze-starch biosynthesis
Ngokuphawulekayo, izinombolo zezakhi zofuzo eziphindiwe (TDGs) kanye nezakhi zofuzo eziphindaphindekayo (PDGs) ze-Weining rye zombili zaziphezulu kunalezo ezitholakale ku-Tu, Aet, Hv, Bd kanye ne-Os.Izakhi zofuzo eziphindiwe eziphindiwe (TrDGs) nazo bezimaningi kunalezo ezitholwe ngokukhethekile i-Tu ne-Aet.Ukunwetshwa kwe-rye genome kuhambisana nezinombolo eziphakeme zokuphindaphindeka kofuzo.Ukuqhuma kwe-TE okwenyuka ku-rye kungenzeka kuholele enanini eliphakeme lama-TrDG.
Ukuhlaziywa kwe-evolutionary kanye ne-chromosome synteny ye-rye genome
Ukuhlaziywa kokuphindaphindeka kofuzo lwe-rye nomthelela wako ezinhlobonhlobo zezakhi zofuzo ezihlobene nesitashi (SBRGs)
5. Ukuhlukaniswa kwe-rye seed storage protein (SSP) gene loci
I-chromosomal loci emine (Sec-1 kuya kuSec-4) ecacisa ama-rye SSP akhonjwe ku-1R noma 2R.Izakhi zofuzo ze-α-gliadin zavela kamuva nje kukolweni nasezinhlotsheni ezihlobene eduze ngemva kokuhlukana kukakolweni ku-rye.
6. Ukuhlolwa kwe-transcription factor (TF) kanye nezakhi zofuzo zokumelana nezifo
Ukuhlaziywa kwe-rye secalin loci
I-Weining rye yayinezinhlobo eziningi zofuzo ezihambisana nezifo ezihambisana ne-(DRA) (1,989, Supplementary Data 3) kune-Tu (1,621), i-Aet (1,758), Hv (1,508), Bd (1,178), Os (1,575), kanye ne-A (1,836). ), B (1,728) kanye no-D (1,888) ama-subgenome kakolweni ovamile.
7. Uphenyo lwezici zesimo sofuzo ezihlobene nesici sesihloko sangaphambi kwesikhathi
Izakhi zofuzo ezimbili ze-FT ezinokubonakala okuphezulu kakhulu ngaphansi kwezimo zosuku olude, i-ScFT1 ne-ScFT2, zichazelwe emhlanganweni we-Weining genome.Izinsalela ezimbili ze-amino acid ze-ScFT2 (S76 ne-T132) phosphorylation zitholwe zihlobene nokunciphisa isikhathi sokulawula.
Izici zokuthuthuka nezofuzo ezihlotshaniswa nesici sesihloko sangaphambi kwesikhathi se-Weining rye
8. Ukumbiwa kwezifunda ze-chromosomal kanye ne-loci okungenzeka ihileleke ekufuyweni kwe-rye
Kwasetshenziswa ama-SNP ayi-123,647 ukwenza ukuhlaziya okukhethekile phakathi kwe-rye etshaliwe kanye ne-S. vavilovii.Izimpawu zokushanela ezikhethiwe eziyi-11 ezikhonjwe inkomba yokunciphisa (i-DRI), inkomba yokulungisa (FST) kanye nendlela ye-XP-CLR.I-ScID1 itholwe ibandakanyeka ekulawuleni usuku lwesihloko.
Ukuhlonzwa nokuhlaziywa kwezifunda ze-chromosomal kanye ne-loci okungenzeka ihlobene nokufuywa kwe-rye
Ireferensi
U-Li GW et al.Ukuhlanganiswa kofuzo lwekhwalithi ephezulu kugqamisa izici ze-rye genomic kanye nofuzo olubalulekile ngokwezolimo.I-Nature Genetics (2021)
Izindaba Namaphuzu Avelele ihlose ukwabelana ngamacala akamuva ayimpumelelo ne-Biomarker Technologies, ithwebula izimpumelelo zesayensi ezinoveli kanye nezindlela ezivelele ezisetshenziswe phakathi nocwaningo.
Isikhathi sokuthumela: Jan-05-2022