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
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
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
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,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,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
Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adapta...Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.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
Background:Arundo donax L.has great potential as an energy crop due to its high biomass yield and broad adaptability,while lack of a reference genome is a hindrance to genetic improvement efforts for this species.Meth...Background:Arundo donax L.has great potential as an energy crop due to its high biomass yield and broad adaptability,while lack of a reference genome is a hindrance to genetic improvement efforts for this species.Methods:Genome assembly of A.donax was conducted by utilizing PacBio SMRT sequencing and high-throughput chromosome conformation capture technology,with further analysis exploring the plant's ploidy,whole-genome duplication event,and evolutionary history through comparative genomics.Results:The genome assembly of A.donax consists of 1.30 Gb with a contig N50 size of 33.15 Mb.A total of 74403 gene models were identified,with over 90%of genes being functionally annotated.Karyotype and synteny analyses revealed that A.donax is an autoalloenneaploid(3n=9x=108)and has experienced significant gene family expansion and two whole-genome duplication events during its evolutionary history.Furthermore,utilizing the genome assembly,a variety of salinity stress-related genes were uncovered through the analysis of public RNA-seq data.Conclusions:This study presents the initial chromosome-scale genome assembly of A.donax,which will advance genetic comprehension and support the genetic enhancement of this important energy crop.展开更多
Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the...Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.展开更多
The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported...The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.展开更多
Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hinde...Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.展开更多
Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on t...Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin.Heinong 531(HN531)is an elite cultivar that was released in China in June 2021 with 22.34%seed oil,high resistance to soybean cyst nematode(SCN)race 3,and enhanced yield.However,the genetic basis for these desirable agronomic traits is unclear.In this study,we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN.The assembled genome spans 981.20 Mb,featuring a contig N50 of 19.47 Mb,and contains 58,151 predicted gene models.Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants(SVs)of>50 bp,of which 602 were HN531-specific.Furthermore,we identified a copy number variation at rhg1 that underlies resistance to SCN,and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content,adaptability,and yield.This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar,and is a valuable resource for breeders aiming to improve HN531 and related cultivars.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 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 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 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 Key R&D Program of China(Grant No.2018YFA0901800)the National Natural Science Foundation of China(Grant No.32072101)+1 种基金the Guangdong Basic and Applied Basic Research Foundation,China(Grant No.2019A1515111150)the Shenzhen Science and Technology Program,China(Grant No.KQTD20180411143628272)。
文摘Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.
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Jianghan University,Grant/Award Number:2023XKZ024National Forestry and Grassland Administration,Grant/Award Number:KJZXXP202314。
文摘Background:Arundo donax L.has great potential as an energy crop due to its high biomass yield and broad adaptability,while lack of a reference genome is a hindrance to genetic improvement efforts for this species.Methods:Genome assembly of A.donax was conducted by utilizing PacBio SMRT sequencing and high-throughput chromosome conformation capture technology,with further analysis exploring the plant's ploidy,whole-genome duplication event,and evolutionary history through comparative genomics.Results:The genome assembly of A.donax consists of 1.30 Gb with a contig N50 size of 33.15 Mb.A total of 74403 gene models were identified,with over 90%of genes being functionally annotated.Karyotype and synteny analyses revealed that A.donax is an autoalloenneaploid(3n=9x=108)and has experienced significant gene family expansion and two whole-genome duplication events during its evolutionary history.Furthermore,utilizing the genome assembly,a variety of salinity stress-related genes were uncovered through the analysis of public RNA-seq data.Conclusions:This study presents the initial chromosome-scale genome assembly of A.donax,which will advance genetic comprehension and support the genetic enhancement of this important energy crop.
基金the project “Genomics for Conservation of Indigenous Cattle Breeds and for Enhancing Milk Yield, Phase-I” [BT/ PR26466/AAQ/1/704/2017], funded by the Department of Biotechnology (DBT ), Indiathe project “Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows” [BT/PR32758/AAQ/1/760/2019], which was also funded by Department of Biotechnology (DBT ), India。
文摘Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
基金supported by the National Natural Science Foundation of China(32201873)the Key Research and Development Plan of Hubei Province(2023BBB050)。
文摘The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.
基金funded by the National Natural Science Foundation of China(Grant No.81903921)the Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)the Distinguished Young Scholars of Hubei University of Chinese Medicine(Grant No.2022ZZXJ002).
文摘Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.
基金supported by National Natural Science Foundation of China(32201759,32172002)Inner Mongolia Innovation Center of Biological Breeding Technology,National Key Research and Development Program of China(2021YFD1201600)+1 种基金Earmarked Fund for CARS(CARS-04-PS01)Agricultural Science and Technology Innovation Program(ASTIP).
文摘Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin.Heinong 531(HN531)is an elite cultivar that was released in China in June 2021 with 22.34%seed oil,high resistance to soybean cyst nematode(SCN)race 3,and enhanced yield.However,the genetic basis for these desirable agronomic traits is unclear.In this study,we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN.The assembled genome spans 981.20 Mb,featuring a contig N50 of 19.47 Mb,and contains 58,151 predicted gene models.Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants(SVs)of>50 bp,of which 602 were HN531-specific.Furthermore,we identified a copy number variation at rhg1 that underlies resistance to SCN,and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content,adaptability,and yield.This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar,and is a valuable resource for breeders aiming to improve HN531 and related cultivars.
