Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin...Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.展开更多
Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated th...Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.展开更多
Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its impor...Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.展开更多
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac...Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(...Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.展开更多
Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to h...Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).展开更多
Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a...Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.展开更多
Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phe...Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.展开更多
ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resist...ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resistance to the Cry1 F toxin from Bt in Spodoptera frugiperda.Here we generated a SfABCC2 knockout strain of S.frugiperda using the CRISPR/Cas9 system to provide further functional evidence of the role of this gene in susceptibility and resistance to Cry1 F.Results from bioassays showed that the SfABCC2 knockout S.frugiperda strain displayed 118-fold resistance to Cry1 F compared with the parental DH19 strain,but no resistance to Vip3 A toxin from Bt.These results provide the first reverse genetic evidence for SfABCC2 as a functional receptor for Cry1 F.展开更多
With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies....With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://github.com/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.展开更多
The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative...The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.展开更多
The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In ...The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In this study,A total of 217 MYB genes,including 901R-MYBs,124 R2R3-MYBs,and 3 R1R2R3-MYBs have been identified from the potato genome.The 1R-MYB and R2R3-MYB family members could be divided into 20 and 35 subgroups respectively.Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization,further supporting the results of phylogenetic analysis.Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB,as the anthocyanins could be accumulated in different tissues,showing colorful phenotypes.Five pairs of colored and colorless tissues,stigma,petal,stem,leaf,and tuber flesh,were applied to the transcriptomic analysis.A total of 70 MYB genes were found to be differentially expressed between colored and colorless tissues,and these differentially expressed genes were suspected to regulate the biosynthesis of anthocyanin of different tissues.Co-expression analysis identified numerous potential interactive regulators of anthocyanins biosynthesis,involving 39 MYBs,24 bHLHs,2 WD-repeats,and 29 biosynthesis genes.Genome-wide association study(GWAS)of tuber flesh color revealed amajor signal at the end of Chromosome 10,which was co-localized with reported I gene(StMYB88),controlling tuber peel color.Analyses of DEGs(Differentially Expression Genes)revealed that both StMYB88 and StMYB89 were closely related to regulating anthocyanin biosynthesis of tuber flesh.This work offers a comprehensive overview of the MYB family in potato and will lay a foundation for the functional validation of these genes in the tissue-specific regulation of anthocyanin biosynthesis.展开更多
Transfer DNA(T-DNA)of Agrobacterium tumefaciens integration in the plant genome may lead to rearrangements of host plant chromosomal fragments,including inversions.However,there is very little information concerning t...Transfer DNA(T-DNA)of Agrobacterium tumefaciens integration in the plant genome may lead to rearrangements of host plant chromosomal fragments,including inversions.However,there is very little information concerning the inversion.The present study re-ports a transgenic rice line selected from a T-DNA tagged population,which displays a semi-dwarf phenotype.Molecular analysis of this mutant indicated an insertion of two tandem copies of T-DNA into a locus on the rice genome in a head to tail mode.This insertion of T-DNA resulted in the inversion of a 4.9 Mb chromosomal segment.Results of sequence analysis suggest that the chromosomal inversion resulted from the insertion of T-DNA with the help of sequence microhomology between insertion region of T-DNA and target sequence of the host plant.展开更多
Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea p...Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea plant genomes have been published,they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species.Here,we present a phased chromosome-scale assembly for an elite oolong tea cultivar,"Huangdan",that is well known for its high levels of aroma.Based on the two sets of haplotype genome data,we identi fi ed numerous genetic variations and a substantial proportion of allelic imbalance related to important traits,including aroma-and stress-related alleles.Comparative genomics revealed extensive structural variations as well as expansion of some gene families,such as terpene synthases(TPSs),that likely contribute to the high-aroma characteristics of the backbone parent,underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea.Our results uncovered the genetic basis of special features of this oolong tea cultivar,providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.展开更多
1.Introduction Rice is a staple food for 3.2 billion people.The food security threat that shook many Asian countries in 2008 still looms,because farmers are facing the challenge of producing more rice with fewer resou...1.Introduction Rice is a staple food for 3.2 billion people.The food security threat that shook many Asian countries in 2008 still looms,because farmers are facing the challenge of producing more rice with fewer resources of water,land,and inputs.展开更多
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of ...CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of CRISPR systems.The on-target efficiency has been improved in several advanced versions of CRISPR systems,whereas the off-target detection still remains a key challenge.Here,we outline the different versions of CRISPR systems and off-target detection strategies,discuss the merits and limitations of off-target detection methods,and provide potential implications for further gene editing research.展开更多
Rice is a staple food for more than half of the human population.It has been estimated that by 2030,40%more rice needs to be produced in order to meet the growing demand（Khush,2005）.One of the strategies to improve ...Rice is a staple food for more than half of the human population.It has been estimated that by 2030,40%more rice needs to be produced in order to meet the growing demand（Khush,2005）.One of the strategies to improve rice productivity is to enlarge rice growth areas, such as the northward expansion of the growth region in Heilongjiang Province, the northernmost region of China （Li et al., 2015）. However, the northward cultivation is accompanied with daylength extension and temperature decrease, which are unfavor- able for rice, a tropical short-day plant, to complete flowering and seed setting. Thus, the need for early-maturing rice cultivars with extremely low photoperiod sensitivity is urgent.展开更多
A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequenc...A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.展开更多
基金supported by Central Public-interest Scientific Institution Basal Research Fund(CATAS-Nos.1630152023007,1630152023011,1630152023012,1630152023013)the National Natural Science Foundation of China(Grant No.32071805).
文摘Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.
基金funded by the National Key Research and Development Program of China(Grant No.2022YFF1003100)Modern Citrus Industry Technology System of China(Grant No.CARS-26).
文摘Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.
基金supported by the Yunnan Seed Laboratory,China(202205AR070001-15)the National Natural Science Foundation of China,China(Grant No.32160697)。
文摘Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.
基金supported by the National Key Research and Development Program of China(2023YFF1000100 and 2023YFA0914601)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01).
文摘Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by grants from the National Natural Science Foundation of China(32170238,32400191)Guangdong Basic and Applied Basic Research Foundation(2023A1515111029)+2 种基金the Science,Technology and Innovation Commission of Shenzhen Municipality(RCYX20200714114538196)the Chinese Academy of Agricultural Sciences Elite Youth Program(grant 110243160001007)the Guangdong Pearl River Talent Program(2021QN02N792)。
文摘Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.
基金financially supported by the National Key R&D Program of China(2024YFD1200800)the Guangdong Basic and Applied Basic Research Foundation,China(2024A1515030094)。
文摘Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.
基金funded by the National Key Research and Development Program of China(Grant No.2019YFD1001900)the HZAU-AGIS Cooperation Fund(Grant No.SZYJY2022006).
文摘Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.
基金supported by the Key Project for Breeding Genetic Modified Organisms of China(2016ZX08012004003)。
文摘ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resistance to the Cry1 F toxin from Bt in Spodoptera frugiperda.Here we generated a SfABCC2 knockout strain of S.frugiperda using the CRISPR/Cas9 system to provide further functional evidence of the role of this gene in susceptibility and resistance to Cry1 F.Results from bioassays showed that the SfABCC2 knockout S.frugiperda strain displayed 118-fold resistance to Cry1 F compared with the parental DH19 strain,but no resistance to Vip3 A toxin from Bt.These results provide the first reverse genetic evidence for SfABCC2 as a functional receptor for Cry1 F.
基金supported by the National Key Research and Development Project Program of China(2022YFC3400300,2019YFE0109600)the China Postdoctoral Science Foundation(2021M701584).
文摘With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://github.com/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.
基金funded by the National Key Research and Development Program of China(2016YFD0100301)the National Natural Science Foundation of China(31671602)the Agricultural Science and Technology Innovation Program and the Cooperation and Innovation Mission(CAASZDXT2018001)
文摘The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.
基金the National Natural Science Foundation of China(Grant No.31601756)the National Science Fund of Yunnan for Distinguished Young Scholars(Grant No.202001AV070003)。
文摘The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In this study,A total of 217 MYB genes,including 901R-MYBs,124 R2R3-MYBs,and 3 R1R2R3-MYBs have been identified from the potato genome.The 1R-MYB and R2R3-MYB family members could be divided into 20 and 35 subgroups respectively.Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization,further supporting the results of phylogenetic analysis.Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB,as the anthocyanins could be accumulated in different tissues,showing colorful phenotypes.Five pairs of colored and colorless tissues,stigma,petal,stem,leaf,and tuber flesh,were applied to the transcriptomic analysis.A total of 70 MYB genes were found to be differentially expressed between colored and colorless tissues,and these differentially expressed genes were suspected to regulate the biosynthesis of anthocyanin of different tissues.Co-expression analysis identified numerous potential interactive regulators of anthocyanins biosynthesis,involving 39 MYBs,24 bHLHs,2 WD-repeats,and 29 biosynthesis genes.Genome-wide association study(GWAS)of tuber flesh color revealed amajor signal at the end of Chromosome 10,which was co-localized with reported I gene(StMYB88),controlling tuber peel color.Analyses of DEGs(Differentially Expression Genes)revealed that both StMYB88 and StMYB89 were closely related to regulating anthocyanin biosynthesis of tuber flesh.This work offers a comprehensive overview of the MYB family in potato and will lay a foundation for the functional validation of these genes in the tissue-specific regulation of anthocyanin biosynthesis.
基金supported by the National High Technology Development Program of China(No.2008AA10Z104)China Postdoctoral Science Foundation(No.20060600519)
文摘Transfer DNA(T-DNA)of Agrobacterium tumefaciens integration in the plant genome may lead to rearrangements of host plant chromosomal fragments,including inversions.However,there is very little information concerning the inversion.The present study re-ports a transgenic rice line selected from a T-DNA tagged population,which displays a semi-dwarf phenotype.Molecular analysis of this mutant indicated an insertion of two tandem copies of T-DNA into a locus on the rice genome in a head to tail mode.This insertion of T-DNA resulted in the inversion of a 4.9 Mb chromosomal segment.Results of sequence analysis suggest that the chromosomal inversion resulted from the insertion of T-DNA with the help of sequence microhomology between insertion region of T-DNA and target sequence of the host plant.
基金This research was funded by the Fujian Province"2011 Collaborative Innovation Center",the Chinese Oolong Tea Industry Innovation Center special project(J 2015-75)the National Natural Science Foundation of China(31701874)+3 种基金the Major Special Project of Scientific and Technological Innovation on Anxi Tea(AX2021001)the Earmarked Fund for the China Agriculture Research System(CARS-19)the Scientific Research Foundation of the Graduate School of Fujian Agriculture and Forestry University(324-1122yb060)the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University(2018B02).
文摘Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea plant genomes have been published,they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species.Here,we present a phased chromosome-scale assembly for an elite oolong tea cultivar,"Huangdan",that is well known for its high levels of aroma.Based on the two sets of haplotype genome data,we identi fi ed numerous genetic variations and a substantial proportion of allelic imbalance related to important traits,including aroma-and stress-related alleles.Comparative genomics revealed extensive structural variations as well as expansion of some gene families,such as terpene synthases(TPSs),that likely contribute to the high-aroma characteristics of the backbone parent,underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea.Our results uncovered the genetic basis of special features of this oolong tea cultivar,providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.
文摘1.Introduction Rice is a staple food for 3.2 billion people.The food security threat that shook many Asian countries in 2008 still looms,because farmers are facing the challenge of producing more rice with fewer resources of water,land,and inputs.
基金supported by the grants 81771230(W.C.),31922048(E.Z.)and 31522037(H.Y.)from the National Natural Science Foundation of China.
文摘CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of CRISPR systems.The on-target efficiency has been improved in several advanced versions of CRISPR systems,whereas the off-target detection still remains a key challenge.Here,we outline the different versions of CRISPR systems and off-target detection strategies,discuss the merits and limitations of off-target detection methods,and provide potential implications for further gene editing research.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences (No.XDA08040101)the Hundred Talents Program of Chinese Academy of Sciences to Q.Y. Bu+1 种基金the Natural Science Foundation of Heilongjiang (No.ZD2015005)Excellent Academic Leaders of Harbin (No.RC2014XK002003)
文摘Rice is a staple food for more than half of the human population.It has been estimated that by 2030,40%more rice needs to be produced in order to meet the growing demand（Khush,2005）.One of the strategies to improve rice productivity is to enlarge rice growth areas, such as the northward expansion of the growth region in Heilongjiang Province, the northernmost region of China （Li et al., 2015）. However, the northward cultivation is accompanied with daylength extension and temperature decrease, which are unfavor- able for rice, a tropical short-day plant, to complete flowering and seed setting. Thus, the need for early-maturing rice cultivars with extremely low photoperiod sensitivity is urgent.
基金This work was supported by funds from the National Natural Science Foundation of China(31972474,31471157)the Open Fund of State Key Laboratory of Tea Plant Biology and Utilization(SKLTOF20150103).
文摘A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.
