Akebia trifoliata subsp.australis is a well-known medicinal and potential woody oil plant in China.The limited genetic information available for A.trifoliata subsp.australis has hindered its exploitation.Here,a high-q...Akebia trifoliata subsp.australis is a well-known medicinal and potential woody oil plant in China.The limited genetic information available for A.trifoliata subsp.australis has hindered its exploitation.Here,a high-quality chromosomelevel genome sequence of A.trifoliata subsp.australis is reported.The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb.The genome includes 25,598 protein-coding genes,and 71.18%(485.55 Mb)of the assembled sequences were identi fi ed as repetitive sequences.An ongoing massive burst of long terminal repeat(LTR)insertions,which occurred~1.0 million years ago,has contributed a large proportion of LTRs in the genome of A.trifoliata subsp.australis.Phylogenetic analysis shows that A.trifoliata subsp.australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera,which supports the well-established hypothesis of a close relationship between basal eudicot species.The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and fi-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A.trifoliata subsp.australis.Furthermore,the acyl-ACP desaturase gene family,including 12 stearoyl-acyl-carrier protein desaturase(SAD)genes,has expanded exclusively.A combined transcriptome and fatty-acid analysis of seeds at fi ve developmental stages revealed that homologs of SADs,acyl-lipid desaturase omega fatty acid desaturases(FADs),and oleosins were highly expressed,consistent with the rapid increase in the content of fatty acids,especially unsaturated fatty acids.The genomic sequences of A.trifoliata subsp.australis will be a valuable resource for comparative genomic analyses and molecular breeding.展开更多
Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value,especially because of the high content of vitamin C in its fruit.In this study,we de novo assembled two tel...Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value,especially because of the high content of vitamin C in its fruit.In this study,we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var.‘Donghong’(DH)and Actinidia latifolia‘Kuoye’(KY),with total lengths of 608327852 and 640561626 bp for 29 chromosomes,respectively.With a burst of structural variants involving inversion,translocations,and duplications within 8.39 million years,the metabolite content of DH and KY exhibited differences in saccharides,lignans,and vitamins.A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha,both of which have ultra-high vitamin C content.With each assembly phased into two complete haplotypes,we identified allelic variations between two sets of haplotypes,leading to protein sequence variations in 26494 and 27773 gene loci and allele-specific expression of 4687 and 12238 homozygous gene pairs.Synchronized metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents;free fatty acids and flavonols accumulated in the early stages,but sugar substances and amino acids accumulated in the late stages.The AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in fruit.Compared with wild varieties and other Actinidia species,AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content,providing a possible explanation on why red-flesh kiwifruits are sweeter.Collectively,these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.展开更多
The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis(Ac)which may bring risks such as canker disease.Introgression of desired traits from wild relatives is an im...The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis(Ac)which may bring risks such as canker disease.Introgression of desired traits from wild relatives is an important method for improving kiwifruit cultivars.Actinidia eriantha(Ae)is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits.Here,we assembled a chromosome-scale high-quality genome of a Ae sample which was directly collected from its wild populations.Our analysis revealed that 41.3%of the genome consists of repetitive elements,comparable to the percentage in Ac and Ae cultivar“White”genomes.The genomic structural variation,including the presence/absence-variation(PAV)of genes,is distinct between Ae and Ac,despite both sharing the same two kiwifruit-specific whole genome duplication(WGD)events.This suggests that a post-WGD divergence mechanism occurred during their evolution.We further investigated genes involved in ascorbic acid biosynthesis and disease-resistance of Ae,and we found introgressive genome could contribute to the complex relationship between Ae and other representative kiwifruit taxa.Collectively,the Ae genome offers valuable genetic resource to accelerate kiwifruit breeding applications.展开更多
基金the Natural Science Foundation of Hunan Province(2019JJ50475)Key Scientific Research Projects of Hunan Education Department(18A448)Foundation of Hunan Double First-rate Discipline Construction Pr ojects of Bioengineering and Key Lab oratory of Resea rch and Utilizati on of Ethnomedicinal Plant Resources of Hunan Province,and the National Science Foundation(81874334).
文摘Akebia trifoliata subsp.australis is a well-known medicinal and potential woody oil plant in China.The limited genetic information available for A.trifoliata subsp.australis has hindered its exploitation.Here,a high-quality chromosomelevel genome sequence of A.trifoliata subsp.australis is reported.The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb.The genome includes 25,598 protein-coding genes,and 71.18%(485.55 Mb)of the assembled sequences were identi fi ed as repetitive sequences.An ongoing massive burst of long terminal repeat(LTR)insertions,which occurred~1.0 million years ago,has contributed a large proportion of LTRs in the genome of A.trifoliata subsp.australis.Phylogenetic analysis shows that A.trifoliata subsp.australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera,which supports the well-established hypothesis of a close relationship between basal eudicot species.The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and fi-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A.trifoliata subsp.australis.Furthermore,the acyl-ACP desaturase gene family,including 12 stearoyl-acyl-carrier protein desaturase(SAD)genes,has expanded exclusively.A combined transcriptome and fatty-acid analysis of seeds at fi ve developmental stages revealed that homologs of SADs,acyl-lipid desaturase omega fatty acid desaturases(FADs),and oleosins were highly expressed,consistent with the rapid increase in the content of fatty acids,especially unsaturated fatty acids.The genomic sequences of A.trifoliata subsp.australis will be a valuable resource for comparative genomic analyses and molecular breeding.
基金supported by the Provincial Technology Innovation Program of Shandongan award from the Natural Science Foundation of Shandong Province(ZR2021ZD30)+2 种基金the Director’s Award from the Peking University Institute of Advanced Agricultural Sciences,the National Top Young Talents Program of Chinathe Boya Postdoctoral Program of Peking University,the National Key R&D Program of China(2019YFD1000200)the Youth Innovation Promotion Association CAS(2018376).
文摘Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value,especially because of the high content of vitamin C in its fruit.In this study,we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var.‘Donghong’(DH)and Actinidia latifolia‘Kuoye’(KY),with total lengths of 608327852 and 640561626 bp for 29 chromosomes,respectively.With a burst of structural variants involving inversion,translocations,and duplications within 8.39 million years,the metabolite content of DH and KY exhibited differences in saccharides,lignans,and vitamins.A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha,both of which have ultra-high vitamin C content.With each assembly phased into two complete haplotypes,we identified allelic variations between two sets of haplotypes,leading to protein sequence variations in 26494 and 27773 gene loci and allele-specific expression of 4687 and 12238 homozygous gene pairs.Synchronized metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents;free fatty acids and flavonols accumulated in the early stages,but sugar substances and amino acids accumulated in the late stages.The AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in fruit.Compared with wild varieties and other Actinidia species,AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content,providing a possible explanation on why red-flesh kiwifruits are sweeter.Collectively,these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.
基金This study was supported by the National Key Research and Development Program of China(Grant No.2018YFD1000105)the National Natural Science Foundation of China(31870198 and 31770374).
文摘The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis(Ac)which may bring risks such as canker disease.Introgression of desired traits from wild relatives is an important method for improving kiwifruit cultivars.Actinidia eriantha(Ae)is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits.Here,we assembled a chromosome-scale high-quality genome of a Ae sample which was directly collected from its wild populations.Our analysis revealed that 41.3%of the genome consists of repetitive elements,comparable to the percentage in Ac and Ae cultivar“White”genomes.The genomic structural variation,including the presence/absence-variation(PAV)of genes,is distinct between Ae and Ac,despite both sharing the same two kiwifruit-specific whole genome duplication(WGD)events.This suggests that a post-WGD divergence mechanism occurred during their evolution.We further investigated genes involved in ascorbic acid biosynthesis and disease-resistance of Ae,and we found introgressive genome could contribute to the complex relationship between Ae and other representative kiwifruit taxa.Collectively,the Ae genome offers valuable genetic resource to accelerate kiwifruit breeding applications.
