A preliminary feasibility study was set up for the HNBM standard system. By introducing the set theory and basic methods of the solid geometry and adopting the Verman three-dimensional structure ideology innovatively,...A preliminary feasibility study was set up for the HNBM standard system. By introducing the set theory and basic methods of the solid geometry and adopting the Verman three-dimensional structure ideology innovatively, the standards system of Hainan National Breeding and Multiplication (HNBM) was studied with the four-dimensional structure and integration by combining with the time dimension. The four-dimensional structure standards system will be useful for guiding the construction of the HNBM standards system, carrying on the division of labor and realizing the dynamic development of the standards system. The standards set of HNBM helps to computer programming and information management.展开更多
Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regi...Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.展开更多
Olive(Olea europaea L.)is internationally renowned for its high-end product,extra virgin olive oil.An incomplete genome of O.europaea was previously obtained using shotgun sequencing in 2016.To further explore the gen...Olive(Olea europaea L.)is internationally renowned for its high-end product,extra virgin olive oil.An incomplete genome of O.europaea was previously obtained using shotgun sequencing in 2016.To further explore the genetic and breeding utilization of olive,an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology.Seven different assembly strategies were used to assemble the fi nal genome of 1.30 Gb,with contig and scaffold N50 sizes of4.67 Mb and 42.60 Mb,respectively.This greatly increased the quality of the olive genome.We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C,and 53,518 protein-coding genes were predicted in the current assembly.Comparative genomics analyses,including gene family expansion and contraction,whole-genome replication,phylogenetic analysis,and positive selection,were performed.Based on the obtained high-quality olive genome,a total of nine gene families with 202 genes were identi fi ed in the oleuropein biosynthesis pathway,which is twice the number ofgenes identi fi ed from the previous data.This new accession of the olive genome is of suf fi cient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.展开更多
Cacao(Theobroma cacao)is a tropical tree that produces the essential raw material for chocolate.Because yields have been stagnant,land use has expanded to provide for increasing chocolate demand.Assembled genomes of k...Cacao(Theobroma cacao)is a tropical tree that produces the essential raw material for chocolate.Because yields have been stagnant,land use has expanded to provide for increasing chocolate demand.Assembled genomes of key parents could modernize breeding programs in the remote and under-resourced locations where cacao is grown.The MinION,a long read sequencer that runs off of a laptop computer,has the potential to facilitate the assembly of the complex genomes of high-yielding F1 hybrids.Here,we validate the MinION’s application to heterozygous crops by creating a de novo genome assembly of a key parent in breeding programs,the clone Pound 7.Our MinION-only assembly was 20%larger than the latest released cacao genome,with 10-fold greater contiguity,and the resolution of complex heterozygosity and repetitive elements.Polishing with Illumina short reads brought the predicted completeness of our assembly to similar levels to the previously released cacao genome assemblies.In contrast to previous cacao genome projects,our assembly required only a small scientific team and limited reagents.Our sequencing and assembly methods could easily be adopted by under-resourced breeding programs,speeding crop improvement in the developing world.展开更多
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,nu...Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,numerous research on cotton has navigated various aspects,from multi-genome assembly,genome editing,mechanism of fiber development,metabolite biosynthesis,and analysis to genetic breeding.Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers.Mature multiple genome editing systems,such as CRISPR/Cas9,Cas12(Cpf1)and cytidine base editing(CBE),have been widely used in the study of candidate genes affecting fiber development.Based on this,the cotton fiber cell development network has been preliminarily drawn.Among them,the MYB-b HLH-WDR(MBW)transcription factor complex and IAA and BR signaling pathway regulate the initiation;various plant hormones,including ethylene,mediated regulatory network and membrane protein overlap fine-regulate elongation.Multistage transcription factors targeting Ces A 4,7,and 8 specifically dominate the whole process of secondary cell wall thickening.And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development.Furthermore,research on the synthesis of cotton secondary metabolite gossypol,resistance to diseases and insect pests,plant architecture regulation,and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties.This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects,thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.展开更多
文摘A preliminary feasibility study was set up for the HNBM standard system. By introducing the set theory and basic methods of the solid geometry and adopting the Verman three-dimensional structure ideology innovatively, the standards system of Hainan National Breeding and Multiplication (HNBM) was studied with the four-dimensional structure and integration by combining with the time dimension. The four-dimensional structure standards system will be useful for guiding the construction of the HNBM standards system, carrying on the division of labor and realizing the dynamic development of the standards system. The standards set of HNBM helps to computer programming and information management.
基金supported by funds from the National Natural Science Foundation of China(31972474,90717110)Hubei Natural Science Fund for Distinguished Young Scholars(2020CFA062).
文摘Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.
基金The National Key R&D Program of China(2018YFD1000603-3)Fundamental Research Funds for the Central Non-profit Research Institution of Chinese Academy of Forestry(CAFYBB2018QB001)。
文摘Olive(Olea europaea L.)is internationally renowned for its high-end product,extra virgin olive oil.An incomplete genome of O.europaea was previously obtained using shotgun sequencing in 2016.To further explore the genetic and breeding utilization of olive,an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology.Seven different assembly strategies were used to assemble the fi nal genome of 1.30 Gb,with contig and scaffold N50 sizes of4.67 Mb and 42.60 Mb,respectively.This greatly increased the quality of the olive genome.We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C,and 53,518 protein-coding genes were predicted in the current assembly.Comparative genomics analyses,including gene family expansion and contraction,whole-genome replication,phylogenetic analysis,and positive selection,were performed.Based on the obtained high-quality olive genome,a total of nine gene families with 202 genes were identi fi ed in the oleuropein biosynthesis pathway,which is twice the number ofgenes identi fi ed from the previous data.This new accession of the olive genome is of suf fi cient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.
文摘Cacao(Theobroma cacao)is a tropical tree that produces the essential raw material for chocolate.Because yields have been stagnant,land use has expanded to provide for increasing chocolate demand.Assembled genomes of key parents could modernize breeding programs in the remote and under-resourced locations where cacao is grown.The MinION,a long read sequencer that runs off of a laptop computer,has the potential to facilitate the assembly of the complex genomes of high-yielding F1 hybrids.Here,we validate the MinION’s application to heterozygous crops by creating a de novo genome assembly of a key parent in breeding programs,the clone Pound 7.Our MinION-only assembly was 20%larger than the latest released cacao genome,with 10-fold greater contiguity,and the resolution of complex heterozygosity and repetitive elements.Polishing with Illumina short reads brought the predicted completeness of our assembly to similar levels to the previously released cacao genome assemblies.In contrast to previous cacao genome projects,our assembly required only a small scientific team and limited reagents.Our sequencing and assembly methods could easily be adopted by under-resourced breeding programs,speeding crop improvement in the developing world.
基金the National Natural Science Foundation of China(32200286)the China Postdoctoral Science Foundation(2022TQ0240,2022M722470)。
文摘Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,numerous research on cotton has navigated various aspects,from multi-genome assembly,genome editing,mechanism of fiber development,metabolite biosynthesis,and analysis to genetic breeding.Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers.Mature multiple genome editing systems,such as CRISPR/Cas9,Cas12(Cpf1)and cytidine base editing(CBE),have been widely used in the study of candidate genes affecting fiber development.Based on this,the cotton fiber cell development network has been preliminarily drawn.Among them,the MYB-b HLH-WDR(MBW)transcription factor complex and IAA and BR signaling pathway regulate the initiation;various plant hormones,including ethylene,mediated regulatory network and membrane protein overlap fine-regulate elongation.Multistage transcription factors targeting Ces A 4,7,and 8 specifically dominate the whole process of secondary cell wall thickening.And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development.Furthermore,research on the synthesis of cotton secondary metabolite gossypol,resistance to diseases and insect pests,plant architecture regulation,and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties.This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects,thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
