Passion fruit(Passiflora edulis Sims)is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world.Here,we report an~1341.7Mb chromosome-scale genome assembly of passion fruit,w...Passion fruit(Passiflora edulis Sims)is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world.Here,we report an~1341.7Mb chromosome-scale genome assembly of passion fruit,with 98.91%(~1327.18Mb)of the assembly assigned to nine pseudochromosomes.The genome includes 23,171 protein-coding genes,and most of the assembled sequences are repetitive sequences,with long-terminal repeats(LTRs)being the most abundant.Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae.Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA,which may have contributed to its large genome size.An integrated analysis of genomic,transcriptomic,and metabolomic data showed that‘alpha-linolenic acid metabolism’,‘metabolic pathways’,and‘secondary metabolic pathways’were the main pathways involved in the synthesis of important volatile organic compounds(VOCs)in passion fruit,and this analysis identified some candidate genes,including GDP-fucose Transporter 1-like,Tetratricopeptide repeat protein 33,protein NETWORKED 4B isoform X1,and Golgin Subfamily A member 6-like protein 22.In addition,we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways.Gene family analysis showed that the ACX,ADH,ALDH,and HPL gene families,especially ACX13/14/15/20,ADH13/26/33,ALDH1/4/21,and HPL4/6,were the key genes for ester synthesis,while the TPS gene family,especially PeTPS2/3/4/24,was the key gene family for terpene synthesis.This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.展开更多
Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous su...Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.展开更多
Based on the data of GDP per capita and emissions of major pollutants in Binzhou City from 2013 to 2017,the changing trends of emissions of major pollutants with the increase of GDP per capita,as well as the coordinat...Based on the data of GDP per capita and emissions of major pollutants in Binzhou City from 2013 to 2017,the changing trends of emissions of major pollutants with the increase of GDP per capita,as well as the coordinated development level of ecological environment and social economy in Binzhou City were studied.The results showed that with the increase of GDP per capita,the changing curves of industrial wastewater and industrial soot in Binzhou City were inverted-U-shaped,and the emission of industrial wastewater reduced after peaking.However,the production of industrial solid waste and the emission of industrial waste gas did not show a downward trend with economic growth,and still increased year by year.The coordination degree of economic development and ecological environment protection in Binzhou City was moderately lagged.By the adjustment of industrial structure,environmental protection and control should be increased,and relevant regulations should be formulated to control pollutant emissions,thereby achieving sustainable development and coordinated development of regional ecology and environment.展开更多
Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild spec...Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild species remain unclear.In this study,we obtained near complete telomere-to-telomere genome assemblies and their haplotype forms for the cultivar AM560,the wild ancestors FLA4047 and W14,constructed a graphic pan-genome of 30 representatives with a size of 1.15 Gb,and built a clarified evolutionary tree of 486 accessions.A comparison of structural variations and single-nucleotide variations between the ancestors and cultivated cassavas reveals predominant expansions and contractions of numbers of genes and gene families,which are mainly driven by transposons.Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes.We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C4 photosynthesis in modern cassava.Coevolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1,MeFT2,and MeTFL2.Mutations in MeMATE1 and MeGTR occur in sweet cassava,and MeAHL19 has evolved to regulate the biosynthesis,transport,and endogenous remobilization of cyanogenic glucosides in cassava.These extensive genomic and gene resources provided here,along with the findings on the evolutionary mechanisms responsible for beneficial traits in modern cultivars,lay a strong foundation for future breeding improvements of cassava.展开更多
Background Both increasing native species diversity and reducing nutrient availability can increase the ability of native plant communities to resist alien plant invasions. Furthermore, native species diversity and nu...Background Both increasing native species diversity and reducing nutrient availability can increase the ability of native plant communities to resist alien plant invasions. Furthermore, native species diversity and nutrient availabil-ity may interact to influence alien plant invasions. So far, however, little is known about the interactive effect of spe-cies diversity and nutrient availability on reproduction of alien invasive plants. We constructed native plant communi-ties with one, four or eight species under low and high nutrient supply and then let them be invaded by the invasive alien plant Bidens pilosa.Results At both high and low nutrient supply, increasing native species richness significantly increased aboveground biomass of the native plant community and decreased aboveground biomass and biomass proportion of the invader B. pilosa. Reproductive biomass of B. pilosa decreased significantly with increasing native species richness under high nutrient supply, but this effect was not observed under low nutrient supply. Net biodiversity effect on seed mass of B. pilosa decreased significantly with increasing native species diversity under high nutrient supply, but not under low nutrient supply. This was mainly because the selection effect became dominant with increasing species richness under high nutrient supply.Conclusions Our study suggest that native species richness and nutrient supply can interact to influence repro-duction of invasive alien plant species and that measures to help maintain a high level of native species richness and to reduce nutrient supply could be useful for efficient invasive plant control.展开更多
Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family.This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance.Our study assembled the M.alba...Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family.This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance.Our study assembled the M.alba haplotype genome MC and MM by utilizing Nanopore ultralong reads,Pacbio Hifi long reads and parental second-generation data.Moreover,the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data.Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation.Finally,transcriptome data were generated to link genomic,methylation,and morphological patterns to reveal the reasons underlying the differences between M.alba and its parental lines in petal color,flower shape,and fragrance.We found that the AP1 and AP2 genes are crucial in M.alba petal formation,while the 4CL,PAL,and C4H genes control petal color.The data generated in this study serve as a foundation for future physiological and biochemical research on M.alba,facilitate the targeted improvement of M.alba varieties,and offer a theoretical basis for molecular research on Michelia L.展开更多
Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we in...Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we investigated the transcriptional differences of eight c DNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line,W14, using next generation sequencing system. A total of41302 assembled transcripts were obtained and from these,25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and3584 transcripts were found to be differentially expressed in leaf, stem and storage root(150 d after planting),respectively, between Arg7 and W14 and ascribed to 103,93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I(PSA) and photosystem II(PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes(PFK, PGK and PK, GAPDH)coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation(INVs), amylose synthesis(GBSS) and hydrolysis(RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation(ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed therelationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.展开更多
Recently,a novel extremely low-cost,effective,flexible,and high-throughput DNA sequencing library preparation and genotyping approach has been developed named Hyper-seq.This new technology has been adopted by more tha...Recently,a novel extremely low-cost,effective,flexible,and high-throughput DNA sequencing library preparation and genotyping approach has been developed named Hyper-seq.This new technology has been adopted by more than 15 research institutes and universities,which has significantly improved the efficiency of crop breeding.The collection and explanation of all DNA sequences froma species,known as pangenome,is the future and hotspot of genomics research.The effective and flexible identification of distinct genetic materials among individuals or populations from pangenome is crucial for exploring genetic and molecular biological processes.Single-nucleotide polymorphisms(SNPs)have become the preferred genetic component to examine humandiseases aswell as animal and plant resistance andmolecular breeding.1 Meanwhile,driven by next-generation sequencing(NGS)technology,the cost of DNA sequencing has been greatly decreased.Over the past decade,genomics-assisted breeding(GAB)has played an important role in utilizing the potential and characterization of modern genomic resources.展开更多
Cassava,a tropical food,feed and biofuel crop,has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition,which makes it highly suitable as a model plant for tropical...Cassava,a tropical food,feed and biofuel crop,has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition,which makes it highly suitable as a model plant for tropical crops.However,the understanding of the metabolism and genomics of this important crop is limited.The recent breakthroughs in the genomics of cassava,including whole-genome sequencing and transcriptome analysis,as well as advances in the biology of photosynthesis,starch biosynthesis,adaptation to drought and high temperature,and resistance to virus and bacterial diseases,are reviewed here.Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars.Finally,the current challenges and future potential of cassava as a model plant are discussed.展开更多
基金the Central Public-interest Scientific Institution Basal Research Fund for the Chinese Academy of Tropical Agricultural Sciences(No.1630092020003)Integrated Demonstration of Key Techniques for the Industrial Development of Featured Crops in Rocky Desertification Areas of Yunnan-Guangxi-Guizhou Provinces(SMH2019-2021)+1 种基金the Central Public-interest Scientific Institution Basal Research Fund for the Chinese Academy of Tropical Agricultural Sciences(No.1630052019022)the Foundation of the State Key Laboratory of Biobased Material and Green Papermaking(No.23190444).
文摘Passion fruit(Passiflora edulis Sims)is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world.Here,we report an~1341.7Mb chromosome-scale genome assembly of passion fruit,with 98.91%(~1327.18Mb)of the assembly assigned to nine pseudochromosomes.The genome includes 23,171 protein-coding genes,and most of the assembled sequences are repetitive sequences,with long-terminal repeats(LTRs)being the most abundant.Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae.Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA,which may have contributed to its large genome size.An integrated analysis of genomic,transcriptomic,and metabolomic data showed that‘alpha-linolenic acid metabolism’,‘metabolic pathways’,and‘secondary metabolic pathways’were the main pathways involved in the synthesis of important volatile organic compounds(VOCs)in passion fruit,and this analysis identified some candidate genes,including GDP-fucose Transporter 1-like,Tetratricopeptide repeat protein 33,protein NETWORKED 4B isoform X1,and Golgin Subfamily A member 6-like protein 22.In addition,we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways.Gene family analysis showed that the ACX,ADH,ALDH,and HPL gene families,especially ACX13/14/15/20,ADH13/26/33,ALDH1/4/21,and HPL4/6,were the key genes for ester synthesis,while the TPS gene family,especially PeTPS2/3/4/24,was the key gene family for terpene synthesis.This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.
基金supported by Guangxi Natural Science Foundation under Grant No.2019GXNSFBA18501.
文摘Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.
文摘Based on the data of GDP per capita and emissions of major pollutants in Binzhou City from 2013 to 2017,the changing trends of emissions of major pollutants with the increase of GDP per capita,as well as the coordinated development level of ecological environment and social economy in Binzhou City were studied.The results showed that with the increase of GDP per capita,the changing curves of industrial wastewater and industrial soot in Binzhou City were inverted-U-shaped,and the emission of industrial wastewater reduced after peaking.However,the production of industrial solid waste and the emission of industrial waste gas did not show a downward trend with economic growth,and still increased year by year.The coordination degree of economic development and ecological environment protection in Binzhou City was moderately lagged.By the adjustment of industrial structure,environmental protection and control should be increased,and relevant regulations should be formulated to control pollutant emissions,thereby achieving sustainable development and coordinated development of regional ecology and environment.
基金supported by grants from the National Key R&D Program of China(2018YFD1000501)the National Natural Science Foundation of China-CG joint foundation(3181101517)the startup funds for the double first-class disciplines of crop science in Hainan University(RZ2100003362).
文摘Cassava is a highly resilient tropical crop that produces large,starchy storage roots and high biomass.However,how did cassava’s remarkable environmental adaptability and key economic traits evolve from its wild species remain unclear.In this study,we obtained near complete telomere-to-telomere genome assemblies and their haplotype forms for the cultivar AM560,the wild ancestors FLA4047 and W14,constructed a graphic pan-genome of 30 representatives with a size of 1.15 Gb,and built a clarified evolutionary tree of 486 accessions.A comparison of structural variations and single-nucleotide variations between the ancestors and cultivated cassavas reveals predominant expansions and contractions of numbers of genes and gene families,which are mainly driven by transposons.Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes.We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C4 photosynthesis in modern cassava.Coevolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1,MeFT2,and MeTFL2.Mutations in MeMATE1 and MeGTR occur in sweet cassava,and MeAHL19 has evolved to regulate the biosynthesis,transport,and endogenous remobilization of cyanogenic glucosides in cassava.These extensive genomic and gene resources provided here,along with the findings on the evolutionary mechanisms responsible for beneficial traits in modern cultivars,lay a strong foundation for future breeding improvements of cassava.
基金supported by the National Natural Science Foundation of China(32001302)Startup Project for Doctor’s Scientifc Research of Binzhou University(2019Y35)the Innovation and Training Program of University Students of Shandong Province in 2021(S202110449140).
文摘Background Both increasing native species diversity and reducing nutrient availability can increase the ability of native plant communities to resist alien plant invasions. Furthermore, native species diversity and nutrient availabil-ity may interact to influence alien plant invasions. So far, however, little is known about the interactive effect of spe-cies diversity and nutrient availability on reproduction of alien invasive plants. We constructed native plant communi-ties with one, four or eight species under low and high nutrient supply and then let them be invaded by the invasive alien plant Bidens pilosa.Results At both high and low nutrient supply, increasing native species richness significantly increased aboveground biomass of the native plant community and decreased aboveground biomass and biomass proportion of the invader B. pilosa. Reproductive biomass of B. pilosa decreased significantly with increasing native species richness under high nutrient supply, but this effect was not observed under low nutrient supply. Net biodiversity effect on seed mass of B. pilosa decreased significantly with increasing native species diversity under high nutrient supply, but not under low nutrient supply. This was mainly because the selection effect became dominant with increasing species richness under high nutrient supply.Conclusions Our study suggest that native species richness and nutrient supply can interact to influence repro-duction of invasive alien plant species and that measures to help maintain a high level of native species richness and to reduce nutrient supply could be useful for efficient invasive plant control.
基金supported by a project on Hainan Provincial Project of Science and Technology(ZDYF2022XDNY149)Developing Bioinformatics Platform in Hainan Yazhou Bay Seed Lab(B21HJ0001)+1 种基金Supported by the PhD Scientific Research and Innovation Foundation of Sanya Yazhou Bay Science and Technology City(HSPHDSRF-2023-12-007)Hainan University Startup Fund(KYQD(ZR)-20101).
文摘Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family.This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance.Our study assembled the M.alba haplotype genome MC and MM by utilizing Nanopore ultralong reads,Pacbio Hifi long reads and parental second-generation data.Moreover,the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data.Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation.Finally,transcriptome data were generated to link genomic,methylation,and morphological patterns to reveal the reasons underlying the differences between M.alba and its parental lines in petal color,flower shape,and fragrance.We found that the AP1 and AP2 genes are crucial in M.alba petal formation,while the 4CL,PAL,and C4H genes control petal color.The data generated in this study serve as a foundation for future physiological and biochemical research on M.alba,facilitate the targeted improvement of M.alba varieties,and offer a theoretical basis for molecular research on Michelia L.
基金supported by the National Natural Science Foundation of China (31261140363, 31171230)the National Basic Research and Development Program (2010CB126601)+1 种基金China Agriculture Research System (CARS-12wwq)the Hainan Province Innovative Research Team Foundation (2016CXTD013)
文摘Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we investigated the transcriptional differences of eight c DNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line,W14, using next generation sequencing system. A total of41302 assembled transcripts were obtained and from these,25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and3584 transcripts were found to be differentially expressed in leaf, stem and storage root(150 d after planting),respectively, between Arg7 and W14 and ascribed to 103,93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I(PSA) and photosystem II(PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes(PFK, PGK and PK, GAPDH)coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation(INVs), amylose synthesis(GBSS) and hydrolysis(RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation(ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed therelationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.
基金This Hyper-seq technology(no.2020/06979)related research(nos.102543 and 202010102817.5)achievements have been authorized as three invention patents in Republic of South Africa,Luxembourg,and China in 2021.
文摘Recently,a novel extremely low-cost,effective,flexible,and high-throughput DNA sequencing library preparation and genotyping approach has been developed named Hyper-seq.This new technology has been adopted by more than 15 research institutes and universities,which has significantly improved the efficiency of crop breeding.The collection and explanation of all DNA sequences froma species,known as pangenome,is the future and hotspot of genomics research.The effective and flexible identification of distinct genetic materials among individuals or populations from pangenome is crucial for exploring genetic and molecular biological processes.Single-nucleotide polymorphisms(SNPs)have become the preferred genetic component to examine humandiseases aswell as animal and plant resistance andmolecular breeding.1 Meanwhile,driven by next-generation sequencing(NGS)technology,the cost of DNA sequencing has been greatly decreased.Over the past decade,genomics-assisted breeding(GAB)has played an important role in utilizing the potential and characterization of modern genomic resources.
基金This work was funded by the National Basic Research Program of China(2010CB126601)the National Natural Science Foundation of China(31261140363 and 31171230)+2 种基金the China Agriculture Research System(CARS-12)the National International Science and Technology Cooperation Plan(2011DFB31690)the National High Technology Research and Development Program of China(2012AA101204-2).
文摘Cassava,a tropical food,feed and biofuel crop,has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition,which makes it highly suitable as a model plant for tropical crops.However,the understanding of the metabolism and genomics of this important crop is limited.The recent breakthroughs in the genomics of cassava,including whole-genome sequencing and transcriptome analysis,as well as advances in the biology of photosynthesis,starch biosynthesis,adaptation to drought and high temperature,and resistance to virus and bacterial diseases,are reviewed here.Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars.Finally,the current challenges and future potential of cassava as a model plant are discussed.
