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
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 genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four...The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.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
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 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
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
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
As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutiona...The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutionary evidence hinders true classification of O.cubicus.To clarify its evolutionary position within Tetraodontiformes,a chromosome-level genome assembly was generated,representing the most contiguous and complete genome to date for this lineage.Notably,O.cubicus possessed the largest genome within the order Tetraodontiformes,primarily due to extensive transposable element expansion.Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups(Ostraciidae-Molidae,Tetraodontidae,and Balistidae-Monacanthidae).Comparative genomic evidence indicated that O.cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa.Although overall genomic architecture was largely conserved,certain genetic and environmental changes may have contributed to its phenotypic adaptations,including climate cooling during the Miocene-Pliocene Transition,recent DNA and long interspersed nuclear element(LINE)transposon bursts,lineage-specific chromosomal rearrangements,and gene family expansion.Many positively selected genes and rapidly evolving genes were associated with skeletal development,including bmp7,egf7,and bmpr2.Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation,such as postn,scpp1,and components of the TGF-βsignaling pathway.A derived amino acid substitution in eda,coupled with protein structural modeling,suggested potential molecular convergence in dermal plate formation among teleosts.These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O.cubicus,offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.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
Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descen...Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship,migration patterns,and population dynamics.Within forensic science,forensic investigative genetic genealogy(FIGG)has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources,opening useful investigative avenues.In this review,we synthesize current knowledge,underscore recent advancements,and discuss the growing role of FIGG in forensic genomics.FIGG has been pivotal in revitalizing dormant inquiries and offering genetic leads in numerous cold cases.Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases.Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics,anthropology,and ancient DNA studies.As the field progresses,FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline,shaping the future of forensic investigations.展开更多
Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly oc...Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly occurs in plants belonging to the Papilionoideae and Caesalpinioideae subfamilies(Tederso0 et al.,2018;van Velzen et al.,2019).Nodulation mechanisms in Fabaceae are well studied(Yang et al.,2022),and genomic comparisons of nodulating and non-nodulating host species can provide valuable insights into the evolutionary and genetic basis of this key process.展开更多
Precise chromosome engineering has traditionally relied on the Cre-Lox recombination system-an approach in which the enzyme Cre functions like molecular scissors,cutting and rejoining DNA at specific“Lox”sites to ad...Precise chromosome engineering has traditionally relied on the Cre-Lox recombination system-an approach in which the enzyme Cre functions like molecular scissors,cutting and rejoining DNA at specific“Lox”sites to add,remove,or flip genomic DNA segments inside living cells.展开更多
BACKGROUND The evolutionary mutational changes of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)since its emergence in Chhattisgarh,India in 2020 have warranted the need for the characterization of every ...BACKGROUND The evolutionary mutational changes of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)since its emergence in Chhattisgarh,India in 2020 have warranted the need for the characterization of every lineage/sublineage that has evolved until February 2024.AIM To unravel the evolutionary pathway of SARS-CoV-2 in Chhattisgarh from 2020 to February 2024.METHODS A total of 635 coronavirus disease 2019 cases obtained between 2020 and February 2024 were investigated by whole genome sequencing.RESULTS Whole genome sequencing analysis identified the evolution of SARS-CoV-2 into seventeen lineages from 2020 to 2024.SARS-CoV-2 initially emerged in Chhattisgarh in its Alpha(B.1.1.7)variant in 2020.Thereafter,it continuously underwent periodical mutational changes in the spike gene to further differentiate into various lineages/sublineages,viz.,Kappa,Delta,BA.1,and BA.2 in 2021;the Omicron lineage(BA.5,BA.2.12.1,BA.2.75,BQ.1,and XBB)in 2022;the new Omicron lineage(XBB.1.5,XBB.1.16,XBB.1.9.1,and XBB.2.3)in 2023;and finally to JN.1 in January and February 2024.The predominant lineages over these 4 years were BA.1.1.7(Alpha)in 2020,B.1.617.2(Delta)in the period between 2021 and mid-2022,B.1.1.529(Omicron)in late 2022 to 2023,and Omicron-JN.1 in early 2024.The presently circulating JN.1 lineage was observed harboring exclusive predominant mutations of E4554K,A570V,P621A,and P1143 L with 99%CONCLUSION SARS-CoV-2 from 2020 to 2024 has evolved into 17 lineages/sublineages in Chhattisgarh.The presently circulating JN.1 harbored 40 mutations,especially E554K,A570V,P621S,and P1143 L,capacitating the virus with features of host cell entry,stability,replication,rapid transmissibility,and crucial immune evasion.Therefore,earlier immunity from either vaccination or prior infection may not protect against the current lineage and increases the possibility of future outbreaks.Thus,the periodical genomic surveillance of SARS-CoV-2 is essential for the genomic blueprint of the circulating virus,which may help in updating the vaccine strain and various basic research for developing appropriate therapeutics and diagnostics.展开更多
Prunus spinulosa(2n=4x=32)is an evergreen species of significantmedicinal usage and ecological value.However,the lacking of a high-quality genome of P.spinulosa has obstructed further exploration of its ecological stu...Prunus spinulosa(2n=4x=32)is an evergreen species of significantmedicinal usage and ecological value.However,the lacking of a high-quality genome of P.spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus.In this study,we present the first haplotype-resolved genome assembly of Prunus s.l.subgenus Laurocerasus,the tetraploid genome of P.spinulosa was phased into 32 pseudochromosomes with 4 haplotypes,the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb,and N50 fluctuatedfrom 31.35 Mb to 33.25 Mb,the protein-coding genes vary from 21,272 to 22,668.Different evaluation methods showed that the P.spinulosa genome assembly has high quality of completeness,continuity and accuracy.Being the firstcomplete genome of P.spinulosa,it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.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
The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannot...The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.展开更多
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).
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.
文摘The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.
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 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 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(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.
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
基金supported by the Basic and Applied Basic Research Foundation of Guangdong Province(2020A1515110882)National Science Fund for Distinguished Young Scholars(32225049)。
文摘The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutionary evidence hinders true classification of O.cubicus.To clarify its evolutionary position within Tetraodontiformes,a chromosome-level genome assembly was generated,representing the most contiguous and complete genome to date for this lineage.Notably,O.cubicus possessed the largest genome within the order Tetraodontiformes,primarily due to extensive transposable element expansion.Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups(Ostraciidae-Molidae,Tetraodontidae,and Balistidae-Monacanthidae).Comparative genomic evidence indicated that O.cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa.Although overall genomic architecture was largely conserved,certain genetic and environmental changes may have contributed to its phenotypic adaptations,including climate cooling during the Miocene-Pliocene Transition,recent DNA and long interspersed nuclear element(LINE)transposon bursts,lineage-specific chromosomal rearrangements,and gene family expansion.Many positively selected genes and rapidly evolving genes were associated with skeletal development,including bmp7,egf7,and bmpr2.Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation,such as postn,scpp1,and components of the TGF-βsignaling pathway.A derived amino acid substitution in eda,coupled with protein structural modeling,suggested potential molecular convergence in dermal plate formation among teleosts.These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O.cubicus,offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.
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(82202078)the Major Project of the National Social Science Foundation of China(23&ZD203)+3 种基金the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(2022FGKFKT05)the Center for Archaeological Science of Sichuan University(23SASA01)the 1‧3‧5 Project for Disciplines of Excellence,West China Hospital,Sichuan University(ZYJC20002)the Sichuan Science and Technology Program(2024NSFSC1518).
文摘Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship,migration patterns,and population dynamics.Within forensic science,forensic investigative genetic genealogy(FIGG)has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources,opening useful investigative avenues.In this review,we synthesize current knowledge,underscore recent advancements,and discuss the growing role of FIGG in forensic genomics.FIGG has been pivotal in revitalizing dormant inquiries and offering genetic leads in numerous cold cases.Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases.Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics,anthropology,and ancient DNA studies.As the field progresses,FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline,shaping the future of forensic investigations.
基金supported by the National Natural Science Foundation of China(No.32160142)Guangxi Natural Science Foundation(No.2023GXNSFDA026034)+3 种基金State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources(SKLCUSAb202302)to H.W.,the National Natural Science Foundation of China(No.32460062)to Y.L.,and 1+9 Leading the Charge with Open Competition'project of Sichuan Academy of Agricultural Sciences(1+9KJGG010)Fruit tree breeding project in Sichuan Province(2021YFYZ0023)to H.X.
文摘Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly occurs in plants belonging to the Papilionoideae and Caesalpinioideae subfamilies(Tederso0 et al.,2018;van Velzen et al.,2019).Nodulation mechanisms in Fabaceae are well studied(Yang et al.,2022),and genomic comparisons of nodulating and non-nodulating host species can provide valuable insights into the evolutionary and genetic basis of this key process.
文摘Precise chromosome engineering has traditionally relied on the Cre-Lox recombination system-an approach in which the enzyme Cre functions like molecular scissors,cutting and rejoining DNA at specific“Lox”sites to add,remove,or flip genomic DNA segments inside living cells.
文摘BACKGROUND The evolutionary mutational changes of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)since its emergence in Chhattisgarh,India in 2020 have warranted the need for the characterization of every lineage/sublineage that has evolved until February 2024.AIM To unravel the evolutionary pathway of SARS-CoV-2 in Chhattisgarh from 2020 to February 2024.METHODS A total of 635 coronavirus disease 2019 cases obtained between 2020 and February 2024 were investigated by whole genome sequencing.RESULTS Whole genome sequencing analysis identified the evolution of SARS-CoV-2 into seventeen lineages from 2020 to 2024.SARS-CoV-2 initially emerged in Chhattisgarh in its Alpha(B.1.1.7)variant in 2020.Thereafter,it continuously underwent periodical mutational changes in the spike gene to further differentiate into various lineages/sublineages,viz.,Kappa,Delta,BA.1,and BA.2 in 2021;the Omicron lineage(BA.5,BA.2.12.1,BA.2.75,BQ.1,and XBB)in 2022;the new Omicron lineage(XBB.1.5,XBB.1.16,XBB.1.9.1,and XBB.2.3)in 2023;and finally to JN.1 in January and February 2024.The predominant lineages over these 4 years were BA.1.1.7(Alpha)in 2020,B.1.617.2(Delta)in the period between 2021 and mid-2022,B.1.1.529(Omicron)in late 2022 to 2023,and Omicron-JN.1 in early 2024.The presently circulating JN.1 lineage was observed harboring exclusive predominant mutations of E4554K,A570V,P621A,and P1143 L with 99%CONCLUSION SARS-CoV-2 from 2020 to 2024 has evolved into 17 lineages/sublineages in Chhattisgarh.The presently circulating JN.1 harbored 40 mutations,especially E554K,A570V,P621S,and P1143 L,capacitating the virus with features of host cell entry,stability,replication,rapid transmissibility,and crucial immune evasion.Therefore,earlier immunity from either vaccination or prior infection may not protect against the current lineage and increases the possibility of future outbreaks.Thus,the periodical genomic surveillance of SARS-CoV-2 is essential for the genomic blueprint of the circulating virus,which may help in updating the vaccine strain and various basic research for developing appropriate therapeutics and diagnostics.
基金supported by the National Natural Science Foundation of China(Grant No.32570239)Key Technology Research and Development Program of Zhejiang Province(Grant No.2023C03138).
文摘Prunus spinulosa(2n=4x=32)is an evergreen species of significantmedicinal usage and ecological value.However,the lacking of a high-quality genome of P.spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus.In this study,we present the first haplotype-resolved genome assembly of Prunus s.l.subgenus Laurocerasus,the tetraploid genome of P.spinulosa was phased into 32 pseudochromosomes with 4 haplotypes,the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb,and N50 fluctuatedfrom 31.35 Mb to 33.25 Mb,the protein-coding genes vary from 21,272 to 22,668.Different evaluation methods showed that the P.spinulosa genome assembly has high quality of completeness,continuity and accuracy.Being the firstcomplete genome of P.spinulosa,it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.
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the Natural Science Foundation of Shandong Province(ZR2020QC022)the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900)+2 种基金the Major Program for Basic Research Project of Yunnan Province(202401BC070001)Yunnan Revitalization Talent Support Program:Yunling Scholar Project to Tingshuang Yithe open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.
