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
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
Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’spe...Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.展开更多
Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural...Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.展开更多
The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysac...The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.展开更多
Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studyin...Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.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
Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(...Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.展开更多
Oxalate content in spinach is a key trait of interest due to its relevance to human health.Understanding the genetic basis of it can facilitate the development of spinach varieties with reduced oxalate levels.In pursu...Oxalate content in spinach is a key trait of interest due to its relevance to human health.Understanding the genetic basis of it can facilitate the development of spinach varieties with reduced oxalate levels.In pursuit of understanding the genetic determinants,a diverse panel comprising 288 spinach accessions underwent thorough phenotyping of oxalate content and were subjected to whole-genome resequencing,resulting in a comprehensive dataset encompassing 14386 single-nucleotide polymorphisms(SNPs).Leveraging this dataset,we conducted a genome-wide association study(GWAS)to identify noteworthy SNPs associated with oxalate content.Furthermore,we employed genomic prediction(GP)via cross-prediction,utilizing five GP models,to assess genomic estimated breeding values(GEBVs)for oxalate content.The observed normal distribution and the wide range of oxalate content,exceeding 600.0 mg$100 g^(-1),underscore the complex and quantitative nature of this trait,likely influenced by multiple genes.Additionally,our analysis revealed distinct stratification,delineating the population into four discernible subpopulations.Furthermore,GWAS analysis employing five models in GAPIT 3 and TASSEL 5 unveiled nine significant SNPs(four SNPs on chromosome 1 and five on chromosome 5)associated with oxalate content.These loci exhibited associations with six candidate genes,which might have potential contribution to oxalate content regulation.Remarkably,our GP models exhibited notable predictive abilities,yielding average accuracies of up to 0.51 for GEBV estimation.The integration of GWAS and GP approaches offers a holistic comprehension of the genetic underpinnings of oxalate content in spinach.These findings offered a promising avenue for the development of spinach cultivars and hybrids optimized for oxalate levels,promoting consumer health.展开更多
Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fun...Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.展开更多
Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid b...Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.展开更多
Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut ...Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources.To address this issue,we used GMATA to screen simple sequence repeat(SSR)markers throughout the Chinese chestnut genome.A total of 312,302 molecular markers were obtained with a density of 434.38 Mb-1.Subsequently,all SSR markers were examined for polymorphism using the Hip STR program and 138,208 polymorphic loci were ultimately obtained.To verify the capability of the developed SSR for identification,we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains.The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees,showing that the developed markers have good potential for identification.We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species.The molecular markers amplified 94%of the interspecies with a polymorphic information content(PIC)value of 0.859.Cluster analysis revealed that the resources can be well differentiated using these developed markers,and these markers can be widely used to identify interspecific boundaries.The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity,which can provide references for genetic diversity research,variety identification,kinship analysis,the selection of good products,and the construction of core germplasm resources of chestnut and even chestnut plants.Also these markers provide a solid foundation for the molecular design of hybrids,improved breeding and development of germplasm resources.展开更多
Inoculated fermentation enables rapid fermentation of aquatic products.No studies have been conducted on the lipid profiles of inoculated fermented golden pompano(Trachinotus ovatus).In this study,a lipase-producing B...Inoculated fermentation enables rapid fermentation of aquatic products.No studies have been conducted on the lipid profiles of inoculated fermented golden pompano(Trachinotus ovatus).In this study,a lipase-producing Bacillus subtilis with salt tolerance was screened from traditionally fermented golden pompano(TF)and used as a starter culture.Whole-genome sequencing analysis revealed it carries 4 clustered regularly interspaced short vpalindromic repeats structures and 2 genes encoding triacylglycerol lipase.Untargeted lipidomics identified lipid molecules(833)in 6 major classes from B.subtilis SCSMX-2 fermented golden pompano(IF).A total of 28 lipid molecules were upregulated in IF,including phosphatidylcholines(PCs),triacylglycerols(TAGs),and lysophosphatidylcholine.B.subtilis supplementation enhanced the production of polyenyl PCs and mediumand long-chain TAGs.The IF rich in linoleic,docosahexaenoic acids(DHA),and eicosapentaenoic acid were primarily distributed in the sn-2 position of DHA,PC and phosphatidylethanolamine.This research revealed the lipid profiles of IF,providing theoretical basis for the application of B.subtilis in the fermented fish industry.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
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
The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utilit...The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.展开更多
Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basi...Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basis of this somatic polymorphism is understood,the developmental and molecular mechanisms are largely unknown.To address this knowledge gap,we selected Monochoria elata(Pontederiaceae)as our study system due to its typical heterantherous floral structure.We constructed a chromosome-level genome assembly of M.elata,conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery.We focused on three key stamen characteristics—colour,spatial patterning,and filament elongation—selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species.Our analyses suggest that gene networks involving MelLEAFY3,MADS-box,and TCP genes regulate stamen identity,with anthocyanin influencing colour,and lignin contributing to filament elongation.Additionally,variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence.Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.展开更多
Enhancing the mechanical properties is crucial for polyimide films,but the mechanical properties(Young's modulus,tensile strength,and elongation at break)mutually constrain each other,complicating simultaneous enh...Enhancing the mechanical properties is crucial for polyimide films,but the mechanical properties(Young's modulus,tensile strength,and elongation at break)mutually constrain each other,complicating simultaneous enhancement via traditional trial-and-error methods.In this work,we proposed a materials genome approach to design and screen phenylethynyl-terminated polyimides for films with enhanced mechani-cal properties.We first established machine learning models to predict Young's modulus,tensile strength,and elongation at break to explore the chemical space containing thousands of candidate structures.The accuracies of the machine learning models were verified by molecular dynamics simulations on screened polyimides and experimental testing on three representative polyimide films.The performance advantages of the best-selected polyimides were analyzed by comparing well-known polyimides based on molecular dynamics simulations,and the structural rationale was revealed by"gene"analysis and feature importance evaluation.This work provides a cost-effective strategy for designing polyimide films withenhancedmechanical properties.展开更多
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(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
基金supported by the National Natural Science Foundation of China(No.42171063)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(No.Y4ZK111B01)+6 种基金the Special Fund for ScientificResearch of Shanghai Landscaping&City Appearance Administrative Bureau(G242414,G242416)the“Yunnan Revitalization Talent Support Program”in Yunnan Province(XDYC-QNRC-2022-0028)Yunnan Revitalization Talent Support Program“Innovation Team”Project(202405AS350019)the CAS“Light of West China”Programthe 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy Sciences(XTBG-1450303)the European Research Council(ERC)under the European Union's Horizon 2020 research and innovation program(No.833522)GhentUniversity(Methusalem funding,BOF.MET.2021.0005.01).
文摘Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.
文摘Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.
基金supported by the National Natural Science Foundation of China(32360058)the Central Government Guides Local Science and Technology Development Projects,China(2023ZYZX1224)Xinjiang University Excellent Doctoral Student Innovation Project(XJU2022BS051)。
文摘The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.
基金supported by the National Key Research and Development Program of China(2024YFF1001400)the Open Project of State Key Laboratory of Animal Biotech Breeding(2024SKLAB6-106)Fundamental Research Funds for Central University(7110100870).
文摘Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.
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 grants from the National Natural Science Foundation of China(32170238,32400191)Guangdong Basic and Applied Basic Research Foundation(2023A1515111029)+2 种基金the Science,Technology and Innovation Commission of Shenzhen Municipality(RCYX20200714114538196)the Chinese Academy of Agricultural Sciences Elite Youth Program(grant 110243160001007)the Guangdong Pearl River Talent Program(2021QN02N792)。
文摘Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.
基金supported by USDA-SCRI(Grant Nos.2017-51181-26830 and 2023-51181-41321)USDA-AMS SCMP(Grant No.16SCCMAR0001)+1 种基金Arkansas Department of Agriculture SCBGP(Grant No.AM22SCBGPAR1130-00)USDA NIFA Hatch project(Grant Nos.ARK0VG2018 and ARK02440).
文摘Oxalate content in spinach is a key trait of interest due to its relevance to human health.Understanding the genetic basis of it can facilitate the development of spinach varieties with reduced oxalate levels.In pursuit of understanding the genetic determinants,a diverse panel comprising 288 spinach accessions underwent thorough phenotyping of oxalate content and were subjected to whole-genome resequencing,resulting in a comprehensive dataset encompassing 14386 single-nucleotide polymorphisms(SNPs).Leveraging this dataset,we conducted a genome-wide association study(GWAS)to identify noteworthy SNPs associated with oxalate content.Furthermore,we employed genomic prediction(GP)via cross-prediction,utilizing five GP models,to assess genomic estimated breeding values(GEBVs)for oxalate content.The observed normal distribution and the wide range of oxalate content,exceeding 600.0 mg$100 g^(-1),underscore the complex and quantitative nature of this trait,likely influenced by multiple genes.Additionally,our analysis revealed distinct stratification,delineating the population into four discernible subpopulations.Furthermore,GWAS analysis employing five models in GAPIT 3 and TASSEL 5 unveiled nine significant SNPs(four SNPs on chromosome 1 and five on chromosome 5)associated with oxalate content.These loci exhibited associations with six candidate genes,which might have potential contribution to oxalate content regulation.Remarkably,our GP models exhibited notable predictive abilities,yielding average accuracies of up to 0.51 for GEBV estimation.The integration of GWAS and GP approaches offers a holistic comprehension of the genetic underpinnings of oxalate content in spinach.These findings offered a promising avenue for the development of spinach cultivars and hybrids optimized for oxalate levels,promoting consumer health.
基金supported by the National Science Foundation(NSF),Award Number 1557995(IS,AZZ)IS was partially supported by the U.S.Department of Agriculture's National Institute of Food and Agriculture(USDA-NIFA)Hatch project CA-D-PPA-2739-H.
文摘Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.
基金supported by the Italian Ministry of Agriculture,Food Sovereignty and Forests(project GOOD-MILK,D.M.9367185—09/12/2020,CUP C29C20000450001,Roma,Italy)the Regional Government of Sardinia(Progetto Strategico Sulcis,CUP J73C17000070007,Cagliari,Italy).
文摘Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.
基金supported by the National Key Research&Development Program of China(2024YFD2200602)the National Natural Science Foundation of China(32471917)。
文摘Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources.To address this issue,we used GMATA to screen simple sequence repeat(SSR)markers throughout the Chinese chestnut genome.A total of 312,302 molecular markers were obtained with a density of 434.38 Mb-1.Subsequently,all SSR markers were examined for polymorphism using the Hip STR program and 138,208 polymorphic loci were ultimately obtained.To verify the capability of the developed SSR for identification,we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains.The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees,showing that the developed markers have good potential for identification.We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species.The molecular markers amplified 94%of the interspecies with a polymorphic information content(PIC)value of 0.859.Cluster analysis revealed that the resources can be well differentiated using these developed markers,and these markers can be widely used to identify interspecific boundaries.The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity,which can provide references for genetic diversity research,variety identification,kinship analysis,the selection of good products,and the construction of core germplasm resources of chestnut and even chestnut plants.Also these markers provide a solid foundation for the molecular design of hybrids,improved breeding and development of germplasm resources.
基金supported by the National Natural Science Foundation of China(32372367)the earmarked fund for CARS(CARS-47)+1 种基金Natural Science Foundation of Hainan Provine(323CXTD391)the Special Scientific Research Funds for Central Non-profit Institutes and the Chinese Academy of Fishery Sciences(2020TD69)。
文摘Inoculated fermentation enables rapid fermentation of aquatic products.No studies have been conducted on the lipid profiles of inoculated fermented golden pompano(Trachinotus ovatus).In this study,a lipase-producing Bacillus subtilis with salt tolerance was screened from traditionally fermented golden pompano(TF)and used as a starter culture.Whole-genome sequencing analysis revealed it carries 4 clustered regularly interspaced short vpalindromic repeats structures and 2 genes encoding triacylglycerol lipase.Untargeted lipidomics identified lipid molecules(833)in 6 major classes from B.subtilis SCSMX-2 fermented golden pompano(IF).A total of 28 lipid molecules were upregulated in IF,including phosphatidylcholines(PCs),triacylglycerols(TAGs),and lysophosphatidylcholine.B.subtilis supplementation enhanced the production of polyenyl PCs and mediumand long-chain TAGs.The IF rich in linoleic,docosahexaenoic acids(DHA),and eicosapentaenoic acid were primarily distributed in the sn-2 position of DHA,PC and phosphatidylethanolamine.This research revealed the lipid profiles of IF,providing theoretical basis for the application of B.subtilis in the fermented fish industry.
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 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.
基金by the National Key Research and Development Program of China(2023YFC3303701-02 and 2024YFC3306701)the National Natural Science Foundation of China(T2425014 and 32270667)+3 种基金the Natural Science Foundation of Fujian Province of China(2023J06013)the Major Project of the National Social Science Foundation of China granted to Chuan-Chao Wang(21&ZD285)Open Research Fund of State Key Laboratory of Genetic Engineering at Fudan University(SKLGE-2310)Open Research Fund of Forensic Genetics Key Laboratory of the Ministry of Public Security(2023FGKFKT07).
文摘The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.
基金supported by grants from the National Natural Science Foundation of China(32100186)the Selfdetermined Project of the State Key Laboratory of Plant Diversity and Specialty Crops,Chinese Academy of Sciences,China(PDSC2023-5)+1 种基金the Special Research Assistant Project,Chinese Academy of Sciences(E2291M01)a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada.
文摘Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basis of this somatic polymorphism is understood,the developmental and molecular mechanisms are largely unknown.To address this knowledge gap,we selected Monochoria elata(Pontederiaceae)as our study system due to its typical heterantherous floral structure.We constructed a chromosome-level genome assembly of M.elata,conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery.We focused on three key stamen characteristics—colour,spatial patterning,and filament elongation—selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species.Our analyses suggest that gene networks involving MelLEAFY3,MADS-box,and TCP genes regulate stamen identity,with anthocyanin influencing colour,and lignin contributing to filament elongation.Additionally,variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence.Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.
基金supported by the National Key R&D Program of China(No.2022YFB3707302)the National Natural Science Foundation of China(Nos.52394271 , 52394270).
文摘Enhancing the mechanical properties is crucial for polyimide films,but the mechanical properties(Young's modulus,tensile strength,and elongation at break)mutually constrain each other,complicating simultaneous enhancement via traditional trial-and-error methods.In this work,we proposed a materials genome approach to design and screen phenylethynyl-terminated polyimides for films with enhanced mechani-cal properties.We first established machine learning models to predict Young's modulus,tensile strength,and elongation at break to explore the chemical space containing thousands of candidate structures.The accuracies of the machine learning models were verified by molecular dynamics simulations on screened polyimides and experimental testing on three representative polyimide films.The performance advantages of the best-selected polyimides were analyzed by comparing well-known polyimides based on molecular dynamics simulations,and the structural rationale was revealed by"gene"analysis and feature importance evaluation.This work provides a cost-effective strategy for designing polyimide films withenhancedmechanical properties.
