DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation,development,and evolution.However,the dynamics of cytonuclear interaction during crop domestication have still been rarely ...DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation,development,and evolution.However,the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated.Here,we examine cytonuclear interactions during grapevine domestication using pan-mitogenome,pan-plastome,and haplotype-resolved nuclear genomes,all assembled from long-read sequences across 33 wild and domesticated grapevine accessions.Structural variation shaped the mitogenomic variation in gene contents,leading to duplications of three specific genes during grapevine domestication(one cox and two rpl genes).Extensive genomic signals of cytonuclear interactions were detected,including a total of212–431 nuclear–mitochondrial segments(NUMTs)and 95–205 nuclear–plastid segments(NUPTs).These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes,whereas NUPTs dominated in wild grapes,indicating the evolutionary trajectories of cytonuclear interactions during grape domestication.Through Genome-Wide Association Study(GWAS),we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions.Among these,the PFD1 gene acts as a signaling regulator,modulating specific signaling pathways regulated by the mitochondria.Interestingly,there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions,suggesting NUMTmediated interactions between the nuclear and mitochondrial genomes.Overall,our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication,offering new insight into the impact of cytonuclear interactions on plant evolution,genetics,and breeding.展开更多
基金financial y supported by Shenzhen Polytechnic University Research Project(Grant No.6024330001K)to Ling Tianthe National Natural Science Foundation of China(No.32372662)+2 种基金the Science Fund Program for Distinguished Young Scholars of the National Natural Science Foundation of China(Overseas)to Yongfeng Zhouthe National Key Research and Development Program of China(No.2023YFD2200700)supported by the project of State Key Laboratory of Tropical Crop Breeding(No.NKLTCB-RC202501,No.NKLTCBCXTD40,No.SKLTCBBSH202501)。
文摘DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation,development,and evolution.However,the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated.Here,we examine cytonuclear interactions during grapevine domestication using pan-mitogenome,pan-plastome,and haplotype-resolved nuclear genomes,all assembled from long-read sequences across 33 wild and domesticated grapevine accessions.Structural variation shaped the mitogenomic variation in gene contents,leading to duplications of three specific genes during grapevine domestication(one cox and two rpl genes).Extensive genomic signals of cytonuclear interactions were detected,including a total of212–431 nuclear–mitochondrial segments(NUMTs)and 95–205 nuclear–plastid segments(NUPTs).These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes,whereas NUPTs dominated in wild grapes,indicating the evolutionary trajectories of cytonuclear interactions during grape domestication.Through Genome-Wide Association Study(GWAS),we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions.Among these,the PFD1 gene acts as a signaling regulator,modulating specific signaling pathways regulated by the mitochondria.Interestingly,there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions,suggesting NUMTmediated interactions between the nuclear and mitochondrial genomes.Overall,our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication,offering new insight into the impact of cytonuclear interactions on plant evolution,genetics,and breeding.
