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
Common bean(Phaseolus vulgaris L.)is a vital source of protein and essential nutrients for human consumption and plays a key role in sustainable agriculture due to its nitrogen-fixing ability(Nadeem et al.,2021).Kidne...Common bean(Phaseolus vulgaris L.)is a vital source of protein and essential nutrients for human consumption and plays a key role in sustainable agriculture due to its nitrogen-fixing ability(Nadeem et al.,2021).Kidney beans,a subcategory of dry common beans,are highly valued for their rich protein,dietary fiber,low fat content,and various trace elements(Garcia-Cordero et al.,2021).Despite the release of several de novo genome assemblies(Goodstein et al.,2012;Schmutz et al.,2014;Vlasova et al.,2016;Cortinovis et al.,2024),existing common bean genomes remain incomplete,particularly in complex regions such as centromeres and telomeres,limiting a comprehensive understanding of the genomic landscape.展开更多
The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain...The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain unclear.Here,we construct a telomere-to-telomere gap-free genome assembly(T2TLarcro_1.0)spanning 716.87 Mb,with a contig N50 of 31.75 Mb.Compared to the current reference genome(L_crocea_2.0),T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes.This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes(e.g.,OPNVA,nNOS,RDH13)potentially involved in evolution of golden-yellow coloration.Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin(VA opsin)in skin tissues of the large yellow croaker,suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration.Integrating genomics and transcriptomics results,we uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change(golden-yellow to silvery-white)in L.crocea.Collectively,our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of goldenyellow coloration in L.crocea.This high-quality genome assembly also serves as an improved resource for biological evolution,genetic improvement,and selective breeding of L.crocea.展开更多
Northern wild rice(NWR;Zizania palustris L.),an annual aquatic plant in the Poaceae family,has high economic importance due to its nutrient-rich grains.However,the existing NWR genome assembly for this species has sev...Northern wild rice(NWR;Zizania palustris L.),an annual aquatic plant in the Poaceae family,has high economic importance due to its nutrient-rich grains.However,the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation.A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research.The assembled genome exhibited a total contig length of 1.41 Gb and a contig N50 of 109.22 Mb.Overall,a 73.60%repetitive sequence content was identified and 47,804 genes predicted.Phylogenetic analysis indicated that Z.palustris was most closely related to Zizania latifolia,with an estimated divergence time of 4.57–8.15 Mya.Meanwhile,Z.palustris underwent a recent,species-specific long terminal repeat(LTR)expansion,associated with its larger genome size.We identified two genomic blocks in the Z.palustris and Z.latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster.The centromeric satellite repeats in Z.palustris identified in this study primarily comprised a 145 bp repetitive unit.The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR.Among the genes missing in the previous NWR genome,we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome.The present updated NWR genome provides a valuable resource for crop genetic improvement,functional gene discovery,and research on critical biological processes.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
Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum infection.However,the underlying molecular mechanisms of this resistance are not yet known.Here,we perform th...Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum infection.However,the underlying molecular mechanisms of this resistance are not yet known.Here,we perform the first de novo genome assembly of M.fortis,comprehensive gene annotation analysis,and evolution analysis.Furthermore,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between M.fortis and mice at different time points after infection.We observe that the time and type of immune response in M.fortis are different from those in mice.M.fortis activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of schistosomes.In contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate schistosomes.Infected mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other functions.Our findings offer new insights into the intrinsic resistance mechanism of M.fortis against schistosome infection.The genome sequence also provides the basis for future studies of other important traits in M.fortis.展开更多
The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms.Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genoty...The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms.Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in maize.Here we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome mapping.We assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for Mo17.Based on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten chromosomes.Comparative analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred lines.As a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in maize.Combining our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.展开更多
Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bi...Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.展开更多
Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genom...Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.展开更多
Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions inclu...Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).展开更多
Dear Editor,Salix(willows)and Populus(poplars),the dominant genera of the Salicaceae family,are commercially important trees used for wood production and for creating artificial plantations aimed at stemming desertifi...Dear Editor,Salix(willows)and Populus(poplars),the dominant genera of the Salicaceae family,are commercially important trees used for wood production and for creating artificial plantations aimed at stemming desertification and high-yield bioenergy production(Teraminami et al.,2013).The willow Salix cheilophila,a dominant species in Xizang,has become a major focus of research due to its key role in the greening efforts of the Mu Us Desert.S.cheilophila is ecologically adaptable and has a widespread distribution from high to low altitudes,making it an ideal subject for investigating the evolutionary signatures driving environmental adaptation.展开更多
Dear Editor,Eggplant(Solanum melongena)belongs to the genus Solanum(Solanaceae),which ranks third in global production among Solanaceae crops.Although four cultivated eggplant genomes(Hirakawa et al.,2014;Barchi et al...Dear Editor,Eggplant(Solanum melongena)belongs to the genus Solanum(Solanaceae),which ranks third in global production among Solanaceae crops.Although four cultivated eggplant genomes(Hirakawa et al.,2014;Barchi et al.,2019,2021;Wei et al.,2020;Li et al.,2021)and two wild eggplant genomes(Song et al.,2019;Zhang et al.,2023)had been published by 2024,numerous gaps and unassembled regions remained,including telomeres and centromeres.展开更多
Dear Editor,Root rot,a severe soil-borne disease,affects economically significant crops like tomato,bean,and cotton.It significantly reduces the global yield and quality of sweet potato(Ipomoea batatas(L.)Lam.).Isolat...Dear Editor,Root rot,a severe soil-borne disease,affects economically significant crops like tomato,bean,and cotton.It significantly reduces the global yield and quality of sweet potato(Ipomoea batatas(L.)Lam.).Isolation of sweet potato root rot pathogens has been limited to a few pathogens in specific regions:Fusarium solani in China(Wang et al.,2014)and F.oxysporum and F.solani in the United States and South Korea(Scruggs and Quesada-Ocampo,2016;Kim et al.,2022),which pose risks to humans and animals.展开更多
Ficus carica L.,an ancient crop of considerable economic value,exhibits distinctive biological traits,including flowerless fruit(syconium)development,psoralen biosynthesis,and drought tolerance.In this study,we pre-se...Ficus carica L.,an ancient crop of considerable economic value,exhibits distinctive biological traits,including flowerless fruit(syconium)development,psoralen biosynthesis,and drought tolerance.In this study,we pre-sent a chromosome-levelgenome assembly(323.03 Mb,N50=23.82 Mb)of F.carica,revealing an evolutionary divergence from the closely related genus Broussonetia approximately 50 million years ago.Comparative genomic analyses revealed a contraction in the s-domain receptor-like kinase gene family,which is associ-ated with unisexual fruit formation,and identified conserved MADS-box transcription factor genes(FcAGL6,FcAP2,and FcSEP1/2)that regulate syconium development through spatiotemporal expression patterns.Me-tabolomic profiling demonstrated tissue-specific accumulation of bioactive compounds,with roots serving as the primary reservoir for psoralen.We also identified key genes-FcANS and FcCHS10,involved in antho-cyanin biosynthesis,andFcMS,involved in psoralen biosynthesis-and validated their functions using a newly established transient transformation system.Transcriptomic analysis under drought stress identified the NAC transcription factor FcJA2 as a central regulator of stress tolerance that enhances reactive oxygen spe-cies scavenging and osmotic regulation by activating FcPP2C5 and FcP5CS.Overexpression of FcJA2 signif-icantly improved drought resistance.Further analyses demonstrated that FcJA2-mediated drought-response modules are conserved across the Moraceae.These findings provide valuable insights into the genetic mech-anisms underlying fruit development,specialized metabolite biosynthesis,and stress tolerance in F.carica,offering potential applications for crop improvement and advancing our understanding of genome evolution and environmental adaptability in the Moraceae family.展开更多
Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et...Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et al.,2020).The rich starch and crude protein in its inflated tuber(commonly known as the greater yam)make this plant an essential crop in the tropical and subtropical regions of Southeast Asia,Africa,and Latin America(Sharif et al.,2020).Moreover,D.alata,D.cayenensis and D.rotundata represent the three major food crops among 11 cultivated yam species,whereas the other eight are often referred to as"minor yams"(Lebot et al.,2023).The global production of yam tubers reached 75 million tons in 2021(Food and Agriculture Organization Statistical Database,2022),indicating their importance in the food supply.A high-quality reference genome serves as an essential resource for the molecular breeding of crops to improve their quality and resistance to pathogens.With the recent publication of a chromosome-level genome,efforts have been made to identify the genes/loci associated with quality traits and resistance to pathogens in greater yam(Bredeson et al.展开更多
Dear Editor,This study reports a 379.33-Mb telomere-to-telomere genome assembly of the japonica rice variety Zhonghua 11,generated using PacBio HiFi and Oxford Nanopore Technologies sequencing data.The high quality of...Dear Editor,This study reports a 379.33-Mb telomere-to-telomere genome assembly of the japonica rice variety Zhonghua 11,generated using PacBio HiFi and Oxford Nanopore Technologies sequencing data.The high quality of this assembly will serve as a valuable resource for the rice research community.展开更多
Dear Editor,High-yield,high-quality,and stress-tolerant forage crops are crucial for the sustainable development of grass-based livestock husbandry.Medicago species are among the most important legume forage crops wor...Dear Editor,High-yield,high-quality,and stress-tolerant forage crops are crucial for the sustainable development of grass-based livestock husbandry.Medicago species are among the most important legume forage crops worldwide.Alfalfa(Medicago sativa subsp.sativa,M.sativa ssp.sativa),a crop known as the“Queen of the Forages”,has high biomass productivity,high nutritional value,and good adaptability.展开更多
The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reporte...The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reported.Schizopygopsis younghusbandi,a highly specialized Schizothoracine species and economically important fish inhabiting the Yarlung Tsangpo River,is threatened by overfishing and biological invasion.Herein,we generated a chromosome-level genome of S.younghusbandi and whole-genome resequencing data for 59 individuals from six locations of the river.The results showed that the divergence time between S.younghusbandi and other primitive Schizothoracine species was~4.2 Mya,coinciding with the major phase of the Neogene Tibetan uplift.The expanded gene families enriched in DNA integration and replication,ion binding and transport,energy storage,and metabolism likely contribute to the adaption of this species.The S.younghusbandi may have diverged from other highly specialized Schizothoracine species in the Zanda basin during the Pliocene epoch,which underwent major population reduction possibly due to the drastic climate change during the last glacial period.Population analysis indicated that the ancient population might have originated upstream before gradually adapting to evolve into the populations inhabiting the mid-stream and downstream regions of the Yarlung Tsangpo River.In conclusion,the chromosome-level genome and population diversity of S.younghusbandi provide valuable genetic resources for the evolution,ecology,and conservation studies of endemic fishes on the Tibetan Plateau.展开更多
High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China ove...High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China over the past decade.Here,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried out.The PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye assemblers.The combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing process.The assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly index.Furthermore,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,respectively.Based on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a reference.The de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.展开更多
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 Natural Science Foundation of China(32241045,32241046,32241038)the Major Special Science and Technology Projects in Shanxi Province(202101140601027)+3 种基金Shanxi Provincial Agricultural Key Technologies Breakthrough Project(NYGG01)Doctoral Research Starting Project at Shanxi Agricultural University(2024BQ77)the National Key Research and Development Program of China(2023YFD1202705/2023YFD120270503,2023YFD1202703/2023YFD1202703-4)Shanxi HouJi Laboratory Self-proposed Research Project(202304010930003/202304010930003-03).
文摘Common bean(Phaseolus vulgaris L.)is a vital source of protein and essential nutrients for human consumption and plays a key role in sustainable agriculture due to its nitrogen-fixing ability(Nadeem et al.,2021).Kidney beans,a subcategory of dry common beans,are highly valued for their rich protein,dietary fiber,low fat content,and various trace elements(Garcia-Cordero et al.,2021).Despite the release of several de novo genome assemblies(Goodstein et al.,2012;Schmutz et al.,2014;Vlasova et al.,2016;Cortinovis et al.,2024),existing common bean genomes remain incomplete,particularly in complex regions such as centromeres and telomeres,limiting a comprehensive understanding of the genomic landscape.
基金supported by the National Key Research and Development Program of China(2023YFD2401901)the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes(2024J004)。
文摘The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain unclear.Here,we construct a telomere-to-telomere gap-free genome assembly(T2TLarcro_1.0)spanning 716.87 Mb,with a contig N50 of 31.75 Mb.Compared to the current reference genome(L_crocea_2.0),T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes.This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes(e.g.,OPNVA,nNOS,RDH13)potentially involved in evolution of golden-yellow coloration.Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin(VA opsin)in skin tissues of the large yellow croaker,suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration.Integrating genomics and transcriptomics results,we uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change(golden-yellow to silvery-white)in L.crocea.Collectively,our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of goldenyellow coloration in L.crocea.This high-quality genome assembly also serves as an improved resource for biological evolution,genetic improvement,and selective breeding of L.crocea.
基金supported by the Youth Innovation Program of the Chinese Academy of Agricultural Sciences(Y2023QC34)the Natural Science Foundation of Shandong province(ZR2023MC034)+2 种基金the Technological Innovation Project of ECS-CAAS(ECS-KY-N-2024008)the Agricultural Science and Technology Innovation Program(ASTIP-TRIC05-2025)the Central Public-interest Scientific Institution Basal Research Fund(1610232024005,1610232023003).
文摘Northern wild rice(NWR;Zizania palustris L.),an annual aquatic plant in the Poaceae family,has high economic importance due to its nutrient-rich grains.However,the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation.A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research.The assembled genome exhibited a total contig length of 1.41 Gb and a contig N50 of 109.22 Mb.Overall,a 73.60%repetitive sequence content was identified and 47,804 genes predicted.Phylogenetic analysis indicated that Z.palustris was most closely related to Zizania latifolia,with an estimated divergence time of 4.57–8.15 Mya.Meanwhile,Z.palustris underwent a recent,species-specific long terminal repeat(LTR)expansion,associated with its larger genome size.We identified two genomic blocks in the Z.palustris and Z.latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster.The centromeric satellite repeats in Z.palustris identified in this study primarily comprised a 145 bp repetitive unit.The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR.Among the genes missing in the previous NWR genome,we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome.The present updated NWR genome provides a valuable resource for crop genetic improvement,functional gene discovery,and research on critical biological processes.
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This work was supported by the Key Project in the National Science&Technology Pillar Program from the Ministry of Science and Technology(2015BAI09B04)the National Natural Science Foundation of China(31872256,31472188)+2 种基金the National Key Research and Development Program of China(2017YFD0501306)the Science and Technology Service Network Initiative of Chinese Academy of Sciences(KFJ-STS-QYZD-126,ZDBS-SSW-DQC-02)CAS Youth Innovation Promotion Association,and SA-SIBS Scholarship Program.
文摘Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum infection.However,the underlying molecular mechanisms of this resistance are not yet known.Here,we perform the first de novo genome assembly of M.fortis,comprehensive gene annotation analysis,and evolution analysis.Furthermore,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between M.fortis and mice at different time points after infection.We observe that the time and type of immune response in M.fortis are different from those in mice.M.fortis activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of schistosomes.In contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate schistosomes.Infected mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other functions.Our findings offer new insights into the intrinsic resistance mechanism of M.fortis against schistosome infection.The genome sequence also provides the basis for future studies of other important traits in M.fortis.
基金supported by the National Natural Science Foundation of China(31871637,32072073,and 32001500)the Project of Transgenic New Variety Cultivation(2016ZX08003003)。
文摘The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms.Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in maize.Here we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome mapping.We assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for Mo17.Based on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten chromosomes.Comparative analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred lines.As a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in maize.Combining our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.
基金supported by the Chinese Academy of Agricultural Sciences Innovation Project(Grant No.CAASASTIP-2013CNRRI)Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute(Grant No.CPSIBRF-CNRRI-202102)。
文摘Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.
基金the China Agriculture Research System(CARS-02-77)the Shaanxi Province Research and Development Project(2021LLRH-07)the Yangling Seed Industry Innovation Center Project(YLZY-YM-01).
文摘Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.
基金supported by the Provincial Technology Innovation Program of Shandong,Ningbo Science and Technology Innovation Project 2021Z132Weifang Seed Innovation Group.
文摘Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).
基金supported by STI 2030—Major Projects(no.2023ZD 0405602)the National Natural Science Foundation of China(32100256 to B.G.)+2 种基金the Third Xinjiang Scientific Expedition Program(2021xjkk0500)the National High-Level Young Talent Programs(2022000005 and 2022000243 to B.G.)the RUDN University Scientific Projects Grant System(no.040416-2-000).
文摘Dear Editor,Salix(willows)and Populus(poplars),the dominant genera of the Salicaceae family,are commercially important trees used for wood production and for creating artificial plantations aimed at stemming desertification and high-yield bioenergy production(Teraminami et al.,2013).The willow Salix cheilophila,a dominant species in Xizang,has become a major focus of research due to its key role in the greening efforts of the Mu Us Desert.S.cheilophila is ecologically adaptable and has a widespread distribution from high to low altitudes,making it an ideal subject for investigating the evolutionary signatures driving environmental adaptation.
基金supported by the Youth Project of the National Natural Science Foundation of China(grant no.32002055)the New Variety Breeding Project of the Major Science and Technology Projects of Zhejiang(grant no.2021C02065-1-3).
文摘Dear Editor,Eggplant(Solanum melongena)belongs to the genus Solanum(Solanaceae),which ranks third in global production among Solanaceae crops.Although four cultivated eggplant genomes(Hirakawa et al.,2014;Barchi et al.,2019,2021;Wei et al.,2020;Li et al.,2021)and two wild eggplant genomes(Song et al.,2019;Zhang et al.,2023)had been published by 2024,numerous gaps and unassembled regions remained,including telomeres and centromeres.
基金supported by the National Natural Science Foundation of China(grant no.32472157)the National Key R&D Program of China(2023YFD1200700 and 2023YFD1200703)+2 种基金the Beijing Food Crops Innovation Consortium Program(BAIC02-2025)the Earmarked Fund for CARS-10-Sweetpotatothe 2115 Talent Development Program of China Agricultural University.
文摘Dear Editor,Root rot,a severe soil-borne disease,affects economically significant crops like tomato,bean,and cotton.It significantly reduces the global yield and quality of sweet potato(Ipomoea batatas(L.)Lam.).Isolation of sweet potato root rot pathogens has been limited to a few pathogens in specific regions:Fusarium solani in China(Wang et al.,2014)and F.oxysporum and F.solani in the United States and South Korea(Scruggs and Quesada-Ocampo,2016;Kim et al.,2022),which pose risks to humans and animals.
文摘Ficus carica L.,an ancient crop of considerable economic value,exhibits distinctive biological traits,including flowerless fruit(syconium)development,psoralen biosynthesis,and drought tolerance.In this study,we pre-sent a chromosome-levelgenome assembly(323.03 Mb,N50=23.82 Mb)of F.carica,revealing an evolutionary divergence from the closely related genus Broussonetia approximately 50 million years ago.Comparative genomic analyses revealed a contraction in the s-domain receptor-like kinase gene family,which is associ-ated with unisexual fruit formation,and identified conserved MADS-box transcription factor genes(FcAGL6,FcAP2,and FcSEP1/2)that regulate syconium development through spatiotemporal expression patterns.Me-tabolomic profiling demonstrated tissue-specific accumulation of bioactive compounds,with roots serving as the primary reservoir for psoralen.We also identified key genes-FcANS and FcCHS10,involved in antho-cyanin biosynthesis,andFcMS,involved in psoralen biosynthesis-and validated their functions using a newly established transient transformation system.Transcriptomic analysis under drought stress identified the NAC transcription factor FcJA2 as a central regulator of stress tolerance that enhances reactive oxygen spe-cies scavenging and osmotic regulation by activating FcPP2C5 and FcP5CS.Overexpression of FcJA2 signif-icantly improved drought resistance.Further analyses demonstrated that FcJA2-mediated drought-response modules are conserved across the Moraceae.These findings provide valuable insights into the genetic mech-anisms underlying fruit development,specialized metabolite biosynthesis,and stress tolerance in F.carica,offering potential applications for crop improvement and advancing our understanding of genome evolution and environmental adaptability in the Moraceae family.
基金supported by the National Natural Science Foundation of China(32172089 and 32270241)the Jiangsu Key Laboratory for the Research and Utilization of Plant Resources(JSPKLB202207)+1 种基金the National Administration of Traditional Chinese Medicine High-level Key Discipline Construction Project(grant no.zyyzdxk-2023293)Fundamental Research Funds for the Central Universities from Nanjing Agricultural University.Z.-Q.S.is supported by the Outstanding Young Teacher of the"QingLan Project"of Jiangsu Province.
文摘Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et al.,2020).The rich starch and crude protein in its inflated tuber(commonly known as the greater yam)make this plant an essential crop in the tropical and subtropical regions of Southeast Asia,Africa,and Latin America(Sharif et al.,2020).Moreover,D.alata,D.cayenensis and D.rotundata represent the three major food crops among 11 cultivated yam species,whereas the other eight are often referred to as"minor yams"(Lebot et al.,2023).The global production of yam tubers reached 75 million tons in 2021(Food and Agriculture Organization Statistical Database,2022),indicating their importance in the food supply.A high-quality reference genome serves as an essential resource for the molecular breeding of crops to improve their quality and resistance to pathogens.With the recent publication of a chromosome-level genome,efforts have been made to identify the genes/loci associated with quality traits and resistance to pathogens in greater yam(Bredeson et al.
基金supported by a grant from the Natural Science Foundation of China(32230077),the Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-CSIAF-202303)the National Key R&D Program of China(2021YFF1000200).
文摘Dear Editor,This study reports a 379.33-Mb telomere-to-telomere genome assembly of the japonica rice variety Zhonghua 11,generated using PacBio HiFi and Oxford Nanopore Technologies sequencing data.The high quality of this assembly will serve as a valuable resource for the rice research community.
基金supported by Biological Breeding-National Science and Technology Major Project(2023ZD04073)the National Natural Science Foundation of China(32341022,32325035)+3 种基金Fundamental Research Funds for Central Nonprofit Scientific Institution(1610392024008)Hainan Seed Industry Laboratory(B23CJ0208)Hohhot Key R&D Project(2023-JBGS-S-1)Inner Mongolia Center of Pratacultural Technology Innovation(CCPTZX2023B01)。
文摘Dear Editor,High-yield,high-quality,and stress-tolerant forage crops are crucial for the sustainable development of grass-based livestock husbandry.Medicago species are among the most important legume forage crops worldwide.Alfalfa(Medicago sativa subsp.sativa,M.sativa ssp.sativa),a crop known as the“Queen of the Forages”,has high biomass productivity,high nutritional value,and good adaptability.
基金supported by the National Natural Science Foundation of China[grant numbers 32160864,32072980]the National Natural Science Foundation of China(NSFC)Joint Fund Priority Support Program[grant number U23A20249]+1 种基金the National Talent Research Grant for 2023[grant number 5330500953]the Special Fund for Youth Team of the Southwest University[grant number SWUXJPY202302].
文摘The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reported.Schizopygopsis younghusbandi,a highly specialized Schizothoracine species and economically important fish inhabiting the Yarlung Tsangpo River,is threatened by overfishing and biological invasion.Herein,we generated a chromosome-level genome of S.younghusbandi and whole-genome resequencing data for 59 individuals from six locations of the river.The results showed that the divergence time between S.younghusbandi and other primitive Schizothoracine species was~4.2 Mya,coinciding with the major phase of the Neogene Tibetan uplift.The expanded gene families enriched in DNA integration and replication,ion binding and transport,energy storage,and metabolism likely contribute to the adaption of this species.The S.younghusbandi may have diverged from other highly specialized Schizothoracine species in the Zanda basin during the Pliocene epoch,which underwent major population reduction possibly due to the drastic climate change during the last glacial period.Population analysis indicated that the ancient population might have originated upstream before gradually adapting to evolve into the populations inhabiting the mid-stream and downstream regions of the Yarlung Tsangpo River.In conclusion,the chromosome-level genome and population diversity of S.younghusbandi provide valuable genetic resources for the evolution,ecology,and conservation studies of endemic fishes on the Tibetan Plateau.
基金the Agricultural Science and Technology Innovation Program,the Elite Young Scientists Program of CAAS,the Science Technology and Innovation Committee of Shenzhen Municipality(KQJSCX20180323140312935,AGIS-ZDKY202004)the Dapeng New District Special Fund for Industrial Development(KY20150113)。
文摘High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China over the past decade.Here,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried out.The PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye assemblers.The combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing process.The assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly index.Furthermore,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,respectively.Based on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a reference.The de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.
