KUSINTHA KWA GENOME
chibadwa chibadwa
Msonkhano wapamwamba kwambiri wa genome umawonetsa mawonekedwe a rye genomic ndi majini ofunikira pazachuma
PacBio |Ilumina |Mapu a Bionano Optical |Hi-C Genome Assembly |Genetic Mapu |Zosankha Zosesa |RNA-Seq |ISO-seq |SLAF-seq
Biomarker Technologies idapereka chithandizo chaukadaulo pakutsata kwa Pacbio, kutsata kwa Hi-C ndi kusanthula deta mu kafukufukuyu.
Mfundo zazikuluzikulu
1.Mtundu woyamba wa chromosomal wapamwamba kwambiri wa Rye genome unapezedwa, womwe uli ndi kromosomu imodzi yokulirapo kuposa 1 Gb.
2.Poyerekeza ndi Tu, Aet ndi Hv genome, zochitika zapadera za LTR-RT zaposachedwapa zinawonedwa mu Rye genome, yomwe inali ndi udindo wowonjezera kukula kwa rye genome.
3.Kusiyanitsa pakati pa rye ndi tirigu wa diploid kunachitika pambuyo pa kulekanitsidwa kwa balere ndi tirigu, ndi nthawi zosiyana za zochitika ziwirizo pafupifupi 9.6 ndi 15 MYA.
FT gene phosphorylation imatha kuwongolera zomwe zimayambira mu rye.
4. Kusanthula kosankha kukuwonetsa kutha kukhudzidwa kwa ScID1 pakuwongolera tsiku lamutu komanso kusankhidwa kwake mwa kubzala rye.
Mbiri
Mbiri
Rye ndi chakudya chamtengo wapatali komanso mbewu ya forage, gwero lofunikira kwambiri pakukula kwa tirigu ndi triticale, komanso chinthu chofunikira kwambiri pakuyerekeza kwama genomics muudzu.Weining rye, mtundu woyamba wamaluwa womwe umabzalidwa ku China, ndiwopambana kwambiri chifukwa umalimbana ndi nkhungu ndi dzimbiri la mizere.Kuti timvetsetse chibadwa ndi mamolekyu a rye osankhika komanso kulimbikitsa maphunziro a genomic ndi kuswana mu rye ndi mbewu zofananira, apa tasanja ndi kusanthula ma genome a Weining rye.
Zopambana
Rye Genome
Rye genome idapangidwa ndikuphatikiza zowerengera za PacBio SMRT, kutsatizana kwa Illumina kwakanthawi kochepa, komanso kuchokera ku chromatin conformation capture (Hi-C), mapu amtundu, ndi kusanthula kwa BioNano.Ma contigs ophatikizidwa (7.74 Gb) anali 98.47% ya kukula kwa genome (7.86 Gb), ndi 93.67% ya contigs (7.25 Gb) yoperekedwa ku ma chromosome asanu ndi awiri.Zinthu zobwerezabwereza zimapanga 90.31% ya ma genome ophatikizidwa.
Rye Genome
Mapu olumikizana ndi ma genetic (WJ) adapangidwa pogwiritsa ntchito mbewu 295 F2 zotengedwa kuchokera pakudutsa madera awiri a rye (Weining × Jingzhou)
Mapu olumikizana a Hi-C a ma chromosome asanu ndi awiri ophatikizidwa a Weining rye (1R - 7R)
Kuyanjanitsa pakati pa ma chromosome asanu ndi awiri ophatikizidwa a Weining rye ndi magulu asanu ndi awiri olumikizirana rye adapangidwa pogwiritsa ntchito Lo7 x Lo255 RIL kuchuluka.
Mtengo wa LTR Assembly Index (LAI) wa Rye genome unapezeka kuti ndi 18.42 ndi 1,393 (96.74%) wa 1,440 wotetezedwa kwambiri wa BUSCO majini adadziwika . ndi zigawo geni.Ma jini okwana 86,991 okhala ndi mapuloteni, kuphatikiza majini 45,596 odzidalira kwambiri (HC) ndi majini 41,395 odzidalira kwambiri (LC) adanenedweratu.
2. Kusanthula kwa TEs
Kusanthula kwa TEs.Chiwerengero chonse cha 6.99 Gb, chomwe chikuyimira 90.31% ya msonkhano wa Weining, adafotokozedwa ngati ma TE, omwe adaphatikizapo zinthu 2,671,941 za mabanja 537.Zomwe zili mu TEzi zinali zapamwamba kwambiri kuposa zomwe zidanenedwapo kale za Ta (84.70%), Tu (81.42%), Aet (84.40%), WEW (82.20%), kapena Hv (80.80%).Ma retrotransposons aatali omaliza (LTR-RTs), kuphatikizapo Gypsy, Copia ndi zinthu zosadziwika za RT, anali ma TE akuluakulu, ndipo 1 inatenga 84.49% ya zolemba za TE ndi 76.29 % ya Weining genome;Ma transposon a CACTA DNA anali ma TE achiwiri ochulukirachulukira, omwe amapanga 11.68% ya TE yolembedwa ndi 10.55% ya Weining genome yophatikizidwa.
Kusanthula kwa zinthu za transposon za rye
Weining rye anali ndi gawo lalikulu kwambiri la zoyika zaposachedwa za LTR-RTs ndi nsonga ya kukulitsa zidawonekera zaka 0.5 miliyoni zapitazo (MYA), yomwe inali yaposachedwa kwambiri pakati pa mitundu inayi;nsonga ina, inachitika pafupifupi 1.7 MYA, inali yakale komanso idawonedwa mu balere.Pamabanja apamwamba, kuphulika kwaposachedwa kwa zinthu za Copia mu Weining rye pa 0.3 MYA kunapezeka, pomwe kukulitsa kwa Gypsy RTs kumakhudza kwambiri njira yogawa bimodal ya LTR-RT burst dynamics.
3. Kufufuza za kusintha kwa rye genome ndi ma chromosome syntenies
Kusiyanitsa pakati pa tirigu wa rye ndi diploid kunachitika pambuyo pa kulekanitsidwa kwa balere ndi tirigu, ndi nthawi zosiyana za zochitika ziwirizi zimakhala pafupifupi 9.6 ndi 15 MYA, motsatira.1R, 2R, 3R anali collinear kwathunthu ndi magulu 1, 2 ndi 3 ma chromosome a tirigu, motsatana.4R, 5R, 6R, 7R anapezeka alipo lalikulu maphatikizidwe ndi zigawo.
4. Kuwunika kwa kubwereza kwa majini ndi momwe zimakhudzira majini a starch biosynthesis
Makamaka, kuchuluka kwa majini obwerezabwereza (TDGs) ndi majini obwerezabwereza (PDGs) a Weining rye onse anali okwera kuposa omwe amapezeka ku Tu, Aet, Hv, Bd ndi Os.Ma genes obwerezabwereza (TrDGs) analinso ochulukirapo kuposa omwe amapezeka makamaka a Tu ndi Aet.Kukula kwa Rye genome kumatsagana ndi kuchuluka kwa kubwereza kwa majini.Kuwonjezeka kwa TE kuphulika kwa rye kungapangitse kuti chiwerengero cha TrDG chikhale chokwera.
Chisinthiko ndi chromosome synteny kusanthula kwa rye genome
Kusanthula kwa kubwereza kwa majini a rye ndi zotsatira zake pamitundu yosiyanasiyana ya majini okhudzana ndi starch biosynthesis (SBRGs)
5. Kugawanika kwa jini yosungira mbeu ya rye (SSP).
Malo anayi a chromosomal (Sec-1 mpaka Sec-4) ofotokoza ma SSP a rye adziwika pa 1R kapena 2R.Mitundu ya α-gliadin idasinthika posachedwa mu tirigu ndi mitundu yofananira pambuyo pakusiyana kwa tirigu kuchokera ku rye.
6. Kuwunika kwa transcription factor (TF) ndi majini olimbana ndi matenda
Kusanthula kwa rye secalin loci
Weining rye anali ndi mitundu yambiri yolimbana ndi matenda yokhudzana ndi (DRA) (1,989, Supplementary Data 3) kuposa Tu (1,621), Aet (1,758), Hv (1,508), Bd (1,178), Os (1,575), ndi A (1,836) ), B (1,728) ndi D (1,888) ma subgenomes a tirigu wamba.
7. Kufufuza za mawonekedwe a jini okhudzana ndi mutu woyambirira
Mitundu iwiri ya FT yokhala ndi mawonekedwe apamwamba kwambiri pamasiku atali, ScFT1 ndi ScFT2, adafotokozedwa mu msonkhano wa Weining genome.Zotsalira ziwiri za amino acid za ScFT2 (S76 ndi T132) phosphorylation zinapezeka kuti zikugwirizana ndi kuchepetsa nthawi.
Mawonekedwe achitukuko ndi ma jini okhudzana ndi mutu woyamba wa Weining rye
8. Migodi ya zigawo za chromosomal ndi loci zomwe zingathe kutenga nawo mbali pakuweta rye
Ma SNP okwana 123,647 adagwiritsidwa ntchito poyesa kusesa pakati pa rye wolimidwa ndi S. vavilovii.11 yosankha kusesa zizindikiro zodziwika ndi reduction index (DRI), fixation index (FST) ndi XP-CLR njira.ScID1 idapezeka kuti ingalowe nawo pakuwongolera tsiku lamutu.
Kuzindikiritsa ndi kusanthula madera a chromosomal ndi malo omwe angakhale okhudzana ndi kubadwa kwa rye
Buku
Li GW et al.Msonkhano wapamwamba kwambiri wa genome umawonetsa mawonekedwe a rye genomic ndi majini ofunikira pazachuma.Nature Genetics (2021)
Nkhani ndi Mfundo Zazikulu ikufuna kugawana milandu yaposachedwa kwambiri ndi Biomarker Technologies, kujambula zomwe zakwaniritsa zasayansi komanso njira zodziwika bwino zomwe zimagwiritsidwa ntchito pophunzira.
Nthawi yotumiza: Jan-05-2022