Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of geneti...Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.展开更多
The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the ...The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the wild populations of C.guichenoti have dramatically declined in recent decades.In this study,we generated a reference chromosomal-level genome assembly of C.guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies.The final genome assembly was 1.10 Gb in length(contig N50:28.64 Mb;scaffold N50:42.39 Mb)with 25 chromosomes.The completeness score of the C.guichenoti genome was 96.4%,and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes.A total of 24325 PCGs were annotated for the C.guichenoti genome.Comparative genomics analysis identified 986 expanded gene families in C.guichenoti,which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity.Furthermore,positively selected genes(PSGs)detected in C.guichenoti were mainly associated with DNA repair,ATP binding,mitochondrion,and lipid homeostasis.Based on the reference genome and resequencing data,the polymorphic microsatellite(SSR)loci were comprehensively analyzed for C.guichenoti,and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping.All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium(HWE)deviation showed high polymorphism,good amplification stability,and selective neutrality.The PID(sibs)curves revealed that the subset of four tetra-nucleotide SSR loci(cgui1,cgui5,cgui3,cgui13)was sufficient for accurate identification of C.guichenoti individuals(PIDsib<0.01).These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis.The chromosome-level genome assembly and findings laid solid foundations for molecular breeding,genomic research,and biological conservation of C.guichenoti.展开更多
Diamondback terrapins(Malaclemys terrapin centrata)exhibit strong environmental adaptability and live in both freshwater and saltwater.However,the genetic basis of this adaptability has not been the focus of research....Diamondback terrapins(Malaclemys terrapin centrata)exhibit strong environmental adaptability and live in both freshwater and saltwater.However,the genetic basis of this adaptability has not been the focus of research.In this study,we successfully constructed a~2.21-Gb chromosome-level genome assembly for M.t.centrata using highcoverage and high-depth genomic sequencing data generated on multiple platforms.The M.t.centrata genome contains 25 chromosomes and the scaffold N50 of~143.75 Mb,demonstrating high continuity and accuracy.In total,53.82% of the genome assembly was composed of repetitive sequences,and 22435 protein-coding genes were predicted.Our phylogenetic analysis indicated that M.t.centrata was closely related to the red-eared slider turtle(Trachemys scripta elegans),with divergence approximately~23.6 million years ago(Mya)during the early Neogene period of the Cenozoic era.The population size of M.t.centrata decreased significantly over the past~14 Mya during the Cenozoic era.Comparative genomic analysis indicated that 36 gene families related to ion transport were expanded and several genes(AQP3,solute carrier subfamily,and potassium channel genes)underwent specific amino acid site mutations in the M.t.centrata genome.Changes to these ion transport-related genes may have contributed to the remarkable salinity adaptability of diamondback terrapin.The results of this study not only provide a high-quality reference genome for M.t.centrata but also elucidate the possible genetic basis for salinity adaptation in this species.展开更多
Chiroptera(bats)presents a fascinating model due to its remarkable variation in chromosome numbers,which range from 14 to 62.This astonishing diversity makes bats an excellent subject for studying chromosome evolution...Chiroptera(bats)presents a fascinating model due to its remarkable variation in chromosome numbers,which range from 14 to 62.This astonishing diversity makes bats an excellent subject for studying chromosome evolution.The black-bearded tomb bat(Taphozous melanopogon)occupies a pivotal phylogenetic position within Chiroptera,emphasizing its crucial role in the systematic examination of bat chromosome evolution.In this study,we present the first chromosome-level genome of T.melanopogon within the family Emballonuridae.Together with previously published genomes,we construct a strongly supported phylogenetic tree of bats,which supports that Emballonuridae forms a basal group within Yangochiroptera.Furthermore,we reconstruct ancestral karyotypes at key nodes along the bat phylogeny and conduct a synteny analysis among the genomes of 12 bat species.Our findings identified evolutionary breakpoint regions(EBRs)that are of particular interest.Notably,some bat genomes exhibit an enrichment of genes related to host defense against microbial pathogens within EBRs.Remarkably,one species possesses multiple copies of someβ-defensin genes,while six other species have experienced the loss of someβ-defensin genes due to EBRs.Furthermore,some olfactory receptor genes are located in EBRs of 12 species,4 of which have a significant enrichment in sensory perception of smell.Together,our comparative genomic analysis underscores the potential link between chromosome rearrangements and the adaptation of bats to defend against microbial pathogens.展开更多
Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,w...Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,we report a high-quality reference genome of P.notoginseng,with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb,produced with third-generation PacBio sequencing technology.This is the first chromosome-level genome assembly for the genus Panax.Through genome evolution analysis,we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis.We performed a detailed transcriptional analysis of P.notoginseng and explored genelevel mechanisms that regulate the formation of characteristic tubercles.Next,we studied the biosynthesis and regulation of saponins at temporal and spatial levels.We combined multi-omics data to identify genes that encode key enzymes in the P.notoginseng terpenoid biosynthetic pathway.Finally,we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P.notoginseng.The genetic information obtained in this study provides a resource for further exploration of the growth characteristics,cultivation,breeding,and saponin biosynthesis of P.notoginseng.展开更多
Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can pr...Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can provide a molecular genetic basis for effective control of D.citri.Here,the DNBSEQ™,Oxford Nanopore Technologies,and Hi-C technologies are applied to generate a high-quality chromosome-level genome of D.citri.The genome size of D.citri was 523.78 Mb with a scaffold N50 of 47.05 Mb distributed on 13 chromosomes.A total of 250.64 Mb(47.85%)repeat sequences and 24048 protein-coding genes were predicted.Genome resequencing of female and male individuals indicated that the sex chromosome system of D.citri is XO.Phylogenetic analysis demonstrated that D.citri and Pachypsylla venusta,which separated from their most recent common ancestor about 336.62 million years ago,were the most closely related.Additionally,we identified genes potentially involved in detoxification metabolism,pathogen transmission,and honeydew secretion for further investigation.The high-quality genome provides an important reference for developing effective management strategies of D.citri.展开更多
Background Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia.Oncomelania hupensis (Gastropoda: Pomatiops...Background Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia.Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host ofS. japonicum. A complete genome sequence ofO. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with theS. japonicum parasite. Assembling a high-quality reference genome ofO. hupehensis will provide data for further research on the snail biology and controlling the spread ofS. japonicum.Methods The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.Results A total length of 1.46 Gb high-qualityO. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed thatO. hupensis was separated from a common ancestor ofPomacea canaliculata andBellamya purificata approximately 170 million years ago. Comparing the genome ofO. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.Conclusions Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level ofO. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies betweenS. japonicum and the snail host.展开更多
Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties.However,the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes.Th...Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties.However,the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes.Thymus quinquecostatus Celak.,which contains large amounts of bioactive monoterpenes suchas thymol and carvacrol,is an important wild medicinal and aromatic plant in China.Monoterpenoids are abundant in glandular secretory trichomes.Here,high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T.quinquecostatus genome at the chromosome level.The 13 chromosomes of T.quinquecostatus had a total length of 528.66 Mb,a contig N50 of 8.06 Mb,and a BUSCO score of 97.34%.We found that T.quinquecostatus had experienced two whole-genome duplications,with the most recent event occurring4.34 million years ago.Deep analyses of the genome,in conjunction with comparative genomic,phylogenetic,transcriptomic,and metabonomic studies,uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development.Genes encoding terpene synthase(TPS),cytochrome P450 monooxygenases(CYPs),short-chain dehydrogenase/reductase(SDR),R2R3-MYB,and homeodomain-leucine zipper(HD-ZIP)IV were among those present in the T.quinquecostatus genome.Notably,Tq02G002290.1(TqTPS1)was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product g-terpinene from geranyl diphosphate(GPP).Our study provides significant insight into the mechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme.This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.展开更多
The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of t...The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment.Here,we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology.A total of 324.14 Gb clean data were generated,and the chromosomelevel genome with 26 chromosomes(25+X)and scaffold N50 of 101.77 Mb was obtained for the kiang.The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species.Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya.The expanded gene families were mainly related to the hypoxia response,metabolism,and immunity.The kiang suffered a significant loss of olfaction-related genes,which might indicate decreased olfactory sensibility.Positively selected genes(PSGs)detected in the kiang were mainly associated with hypoxia response.Especially,there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway,which may play an important role in the high-altitude adaptation of the kiang.Moreover,structure variations in the kiang genome were also identified,which possibly contributed to the high-altitude adaptation of the kiang.Comparative analysis revealed a lot of speciesspecific insertions and deletions in the kiang genome,such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region,respectively,possibly affecting the expression and regulation of hypoxia-related downstream pathways.This study provided valuable genomic resources,and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.展开更多
Blister beetles(Coleoptera:Meloidae)produce a natural defensive toxin cantharidin(CTD),which has been used for various cancer treatments and other diseases.Currently,the lack of chromosome-level reference genomes in M...Blister beetles(Coleoptera:Meloidae)produce a natural defensive toxin cantharidin(CTD),which has been used for various cancer treatments and other diseases.Currently,the lack of chromosome-level reference genomes in Meloidae limits further understanding of the mechanism of CTD biosynthesis and environmental adaptation.In this study,the chromosome-level genome assembly of Mylabris phalerata was generated based on PacBio and Hi-C sequencing.This reference genome was about 136.68 Mb in size with contig N50 of 9.17 Mb and composed of 12 chromosomes.In comparison to six other Coleoptera insects,M.phalerata exhibited multiple expanded gene families enriched in juvenile hormone(JH)biosynthetic process pathway,farnesol dehydrogenase activity,and cytochrome P450,which may be related to CTD biosynthesis.Consistently,the transcriptomic analysis suggested the“terpenoid backbone biosynthesis”pathway and“the juvenile hormone”as putative core pathways of CTD biosynthesis and presented eight up-regulated differential expression genes in male adults as candidate genes.It is possible that the restricted feeding niche and lifestyle of M.phalerata were the cause of the gene family’s contraction of odorant binding proteins.The ABC transporters(ABCs)related to exporting bound toxins out of the cell and the resistance to the self-secreted toxins(e.g.CTD)were also contracted,possibly due to other self-protection strategies in M.phalerata.A foundation of understanding CTD biosynthesis and environmental adaptation of blister beetles will be established by our reference genome and discoveries.展开更多
Cistanche deserticola(C.deserticola)is a holoparasitic plant of the Orobanchaceae family that parasitizes the roots of Haloxylon ammodendron(H.ammodendron).The absence of a high-quality genome has impeded our understa...Cistanche deserticola(C.deserticola)is a holoparasitic plant of the Orobanchaceae family that parasitizes the roots of Haloxylon ammodendron(H.ammodendron).The absence of a high-quality genome has impeded our understanding of its parasitic mechanisms.Here,we present a chromosome-level genome assembly of C.deserticola(6.26 Gb)based on PacBio high fidelity(HiFi)and high-throughput chromosome conformation capture(Hi-C)sequencing,with a contig N50 of 81.25 Mb,92.2%Benchmarking Universal Single-Copy Ortholog(BUSCO)completeness,and 54640 protein-coding genes.Evolutionary analysis shows that C.deserticola diverged from related Orobanchaceae species approximately 38.23 million years ago.Among its key parasitic adaptations is the extensive loss of photosynthetic genes,which is compensated by the retention of transporters and carbon metabolic pathways for the utilization of host-derived nutrition.Bidirectional genetic exchanges include 34 H.ammodendron-derived horizontally transferred genes and 98 mobile mRNAs,as well as 14 C.deserticola-derived horizontally transferred genes and 77 mobile mRNAs targeting host defenses.Spatial transcriptomic data reveal haustorium-specific gene expression related to nutrient extraction and chemical defense,particularly the biosynthesis of phenylethanoid glycosides via dispersedduplication-driven gene expansion.This genomic resource illuminates the evolutionary trajectory of C.deserticola and provides a foundation for conservation strategies and the biotechnological development of C.deserticola.展开更多
Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the form...Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.展开更多
The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW g...The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies.Here,we assembled a chromosome-level genome of a male FAW(SFynMstLFR)and compared re-sequencing results of the populations from America,Africa,and China.Strain identification of 163 individuals collected from America,Africa and China showed that both C and R strains were found in the American pop-ulations,while only C strain was found in the Chinese and African populations.Moreover,population geno-mics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations.Taken toge-ther,FAWs invaded into China were most likely origi-nated from Africa.Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW,of which 283 genes are specific to FAW.Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles,and several detoxification genes such as AOX,UGT and GST spe-cially responded to the pesticides.These findings will be useful in developing effective strategies for manage-ment of FAW in China and other invaded areas.展开更多
Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and l...Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and low reproduction.Here,we report the most contiguous,high-quality chromosomelevel genomes of two extant giant panda subspecies to date,with the first genome assembly of the Qinling subspecies.Compared with the previously assembled giant panda genomes based on short reads,our two assembled genomes increased contiguity over 200-fold at the contig level.Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago.Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2(DACH2)gene and specific changes in the synaptotagmin 6(SYT6)gene,which may be responsible for the reduced fertility of the giant panda.Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D(IQCD)gene may at least partly explain the different reproduction rates of the two subspecies.Furthermore,several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements,which may contribute to the reduced inner organ sizes of the giant panda.展开更多
基金supported by the Natural Science Foundation of Guangxi Autonomous Region,China(2022GXNSFAA035558)the Technology Development Foundation of Guangxi Academy of Agricultural Sciences(2021ZX09)+2 种基金the China Agriculture Research System of MOF and MARA(CARS-10-B3 and CARS-10-C19)the Guangxi Innovation Team Construction Project(nycytxgxcxtd-11-03)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD),China。
文摘Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.
基金supported by the Postdoctoral Research and Development Fund of Sichuan University(2023SCU12111)the China Postdoctoral Science Foundation(2023M732476).
文摘The largemouth bronze gudgeon(Coreius guichenoti),an endemic fish species,is distributed in the upper Yangtze River drainage.Due to anthropogenetic factors such as water pollution,overfishing,and dam construction,the wild populations of C.guichenoti have dramatically declined in recent decades.In this study,we generated a reference chromosomal-level genome assembly of C.guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies.The final genome assembly was 1.10 Gb in length(contig N50:28.64 Mb;scaffold N50:42.39 Mb)with 25 chromosomes.The completeness score of the C.guichenoti genome was 96.4%,and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes.A total of 24325 PCGs were annotated for the C.guichenoti genome.Comparative genomics analysis identified 986 expanded gene families in C.guichenoti,which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity.Furthermore,positively selected genes(PSGs)detected in C.guichenoti were mainly associated with DNA repair,ATP binding,mitochondrion,and lipid homeostasis.Based on the reference genome and resequencing data,the polymorphic microsatellite(SSR)loci were comprehensively analyzed for C.guichenoti,and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping.All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium(HWE)deviation showed high polymorphism,good amplification stability,and selective neutrality.The PID(sibs)curves revealed that the subset of four tetra-nucleotide SSR loci(cgui1,cgui5,cgui3,cgui13)was sufficient for accurate identification of C.guichenoti individuals(PIDsib<0.01).These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis.The chromosome-level genome assembly and findings laid solid foundations for molecular breeding,genomic research,and biological conservation of C.guichenoti.
基金supported by the National Natural Science Foundation of China Regional Fund Project(32160135)the National Natural Science Foundation of China(32322018)+3 种基金the Fundamental Research Funds for the Central Universities(23GH02025)the Double First-Class Construction Special Fund(G2022KY05105)the Foundation of Shaanxi Academy of Sciences(2023K-10)the National Natural Science Foundation of China(32000383).
文摘Diamondback terrapins(Malaclemys terrapin centrata)exhibit strong environmental adaptability and live in both freshwater and saltwater.However,the genetic basis of this adaptability has not been the focus of research.In this study,we successfully constructed a~2.21-Gb chromosome-level genome assembly for M.t.centrata using highcoverage and high-depth genomic sequencing data generated on multiple platforms.The M.t.centrata genome contains 25 chromosomes and the scaffold N50 of~143.75 Mb,demonstrating high continuity and accuracy.In total,53.82% of the genome assembly was composed of repetitive sequences,and 22435 protein-coding genes were predicted.Our phylogenetic analysis indicated that M.t.centrata was closely related to the red-eared slider turtle(Trachemys scripta elegans),with divergence approximately~23.6 million years ago(Mya)during the early Neogene period of the Cenozoic era.The population size of M.t.centrata decreased significantly over the past~14 Mya during the Cenozoic era.Comparative genomic analysis indicated that 36 gene families related to ion transport were expanded and several genes(AQP3,solute carrier subfamily,and potassium channel genes)underwent specific amino acid site mutations in the M.t.centrata genome.Changes to these ion transport-related genes may have contributed to the remarkable salinity adaptability of diamondback terrapin.The results of this study not only provide a high-quality reference genome for M.t.centrata but also elucidate the possible genetic basis for salinity adaptation in this species.
基金supported by the National Key Research and Development Program of China(2021YFF0702004)the National Natural Science Foundation of China(32270436)+1 种基金Fundamental Research Funds for the Central Universities(2042022dx0003)the Natural Science Foundation of Hubei Province(2023AFA015).
文摘Chiroptera(bats)presents a fascinating model due to its remarkable variation in chromosome numbers,which range from 14 to 62.This astonishing diversity makes bats an excellent subject for studying chromosome evolution.The black-bearded tomb bat(Taphozous melanopogon)occupies a pivotal phylogenetic position within Chiroptera,emphasizing its crucial role in the systematic examination of bat chromosome evolution.In this study,we present the first chromosome-level genome of T.melanopogon within the family Emballonuridae.Together with previously published genomes,we construct a strongly supported phylogenetic tree of bats,which supports that Emballonuridae forms a basal group within Yangochiroptera.Furthermore,we reconstruct ancestral karyotypes at key nodes along the bat phylogeny and conduct a synteny analysis among the genomes of 12 bat species.Our findings identified evolutionary breakpoint regions(EBRs)that are of particular interest.Notably,some bat genomes exhibit an enrichment of genes related to host defense against microbial pathogens within EBRs.Remarkably,one species possesses multiple copies of someβ-defensin genes,while six other species have experienced the loss of someβ-defensin genes due to EBRs.Furthermore,some olfactory receptor genes are located in EBRs of 12 species,4 of which have a significant enrichment in sensory perception of smell.Together,our comparative genomic analysis underscores the potential link between chromosome rearrangements and the adaptation of bats to defend against microbial pathogens.
基金support from the National Natural Science Foundation of China(nos.81891010,81891013)the Key Project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(no.2060302-1806-03)+1 种基金the High-level Teachers in Beijing Municipal Universities in the Period of 13th Five-year Plan(no.CIT&TCD20170324)the National Program for Special Support of Eminent Professionals.
文摘Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,we report a high-quality reference genome of P.notoginseng,with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb,produced with third-generation PacBio sequencing technology.This is the first chromosome-level genome assembly for the genus Panax.Through genome evolution analysis,we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis.We performed a detailed transcriptional analysis of P.notoginseng and explored genelevel mechanisms that regulate the formation of characteristic tubercles.Next,we studied the biosynthesis and regulation of saponins at temporal and spatial levels.We combined multi-omics data to identify genes that encode key enzymes in the P.notoginseng terpenoid biosynthetic pathway.Finally,we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P.notoginseng.The genetic information obtained in this study provides a resource for further exploration of the growth characteristics,cultivation,breeding,and saponin biosynthesis of P.notoginseng.
文摘Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can provide a molecular genetic basis for effective control of D.citri.Here,the DNBSEQ™,Oxford Nanopore Technologies,and Hi-C technologies are applied to generate a high-quality chromosome-level genome of D.citri.The genome size of D.citri was 523.78 Mb with a scaffold N50 of 47.05 Mb distributed on 13 chromosomes.A total of 250.64 Mb(47.85%)repeat sequences and 24048 protein-coding genes were predicted.Genome resequencing of female and male individuals indicated that the sex chromosome system of D.citri is XO.Phylogenetic analysis demonstrated that D.citri and Pachypsylla venusta,which separated from their most recent common ancestor about 336.62 million years ago,were the most closely related.Additionally,we identified genes potentially involved in detoxification metabolism,pathogen transmission,and honeydew secretion for further investigation.The high-quality genome provides an important reference for developing effective management strategies of D.citri.
基金supported by National Key Research and Development Program of China(No.2021YFC2300800,2021YFC2300803).
文摘Background Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia.Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host ofS. japonicum. A complete genome sequence ofO. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with theS. japonicum parasite. Assembling a high-quality reference genome ofO. hupehensis will provide data for further research on the snail biology and controlling the spread ofS. japonicum.Methods The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.Results A total length of 1.46 Gb high-qualityO. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed thatO. hupensis was separated from a common ancestor ofPomacea canaliculata andBellamya purificata approximately 170 million years ago. Comparing the genome ofO. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.Conclusions Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level ofO. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies betweenS. japonicum and the snail host.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(grant XDA23080603).
文摘Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties.However,the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes.Thymus quinquecostatus Celak.,which contains large amounts of bioactive monoterpenes suchas thymol and carvacrol,is an important wild medicinal and aromatic plant in China.Monoterpenoids are abundant in glandular secretory trichomes.Here,high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T.quinquecostatus genome at the chromosome level.The 13 chromosomes of T.quinquecostatus had a total length of 528.66 Mb,a contig N50 of 8.06 Mb,and a BUSCO score of 97.34%.We found that T.quinquecostatus had experienced two whole-genome duplications,with the most recent event occurring4.34 million years ago.Deep analyses of the genome,in conjunction with comparative genomic,phylogenetic,transcriptomic,and metabonomic studies,uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development.Genes encoding terpene synthase(TPS),cytochrome P450 monooxygenases(CYPs),short-chain dehydrogenase/reductase(SDR),R2R3-MYB,and homeodomain-leucine zipper(HD-ZIP)IV were among those present in the T.quinquecostatus genome.Notably,Tq02G002290.1(TqTPS1)was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product g-terpinene from geranyl diphosphate(GPP).Our study provides significant insight into the mechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme.This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research Program(No.2019QZKK0501)the National Natural Science Foundation of China(No.32270454).
文摘The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment.Here,we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology.A total of 324.14 Gb clean data were generated,and the chromosomelevel genome with 26 chromosomes(25+X)and scaffold N50 of 101.77 Mb was obtained for the kiang.The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species.Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya.The expanded gene families were mainly related to the hypoxia response,metabolism,and immunity.The kiang suffered a significant loss of olfaction-related genes,which might indicate decreased olfactory sensibility.Positively selected genes(PSGs)detected in the kiang were mainly associated with hypoxia response.Especially,there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway,which may play an important role in the high-altitude adaptation of the kiang.Moreover,structure variations in the kiang genome were also identified,which possibly contributed to the high-altitude adaptation of the kiang.Comparative analysis revealed a lot of speciesspecific insertions and deletions in the kiang genome,such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region,respectively,possibly affecting the expression and regulation of hypoxia-related downstream pathways.This study provided valuable genomic resources,and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.
基金supported by the National Natural Science Foundation of China(grant number:31960117)the Miaozi Project in Science and Technology Innovation Program of Sichuan Province(grant number:2022006).
文摘Blister beetles(Coleoptera:Meloidae)produce a natural defensive toxin cantharidin(CTD),which has been used for various cancer treatments and other diseases.Currently,the lack of chromosome-level reference genomes in Meloidae limits further understanding of the mechanism of CTD biosynthesis and environmental adaptation.In this study,the chromosome-level genome assembly of Mylabris phalerata was generated based on PacBio and Hi-C sequencing.This reference genome was about 136.68 Mb in size with contig N50 of 9.17 Mb and composed of 12 chromosomes.In comparison to six other Coleoptera insects,M.phalerata exhibited multiple expanded gene families enriched in juvenile hormone(JH)biosynthetic process pathway,farnesol dehydrogenase activity,and cytochrome P450,which may be related to CTD biosynthesis.Consistently,the transcriptomic analysis suggested the“terpenoid backbone biosynthesis”pathway and“the juvenile hormone”as putative core pathways of CTD biosynthesis and presented eight up-regulated differential expression genes in male adults as candidate genes.It is possible that the restricted feeding niche and lifestyle of M.phalerata were the cause of the gene family’s contraction of odorant binding proteins.The ABC transporters(ABCs)related to exporting bound toxins out of the cell and the resistance to the self-secreted toxins(e.g.CTD)were also contracted,possibly due to other self-protection strategies in M.phalerata.A foundation of understanding CTD biosynthesis and environmental adaptation of blister beetles will be established by our reference genome and discoveries.
基金supported by the Science and Technology Innovation Plan of the Shanghai Science and Technology Commission(grant number:22YF1420500)the Fundamental Research Funds for the Central Universities(grant numbers:KLSB2022QN-01 and KLSB2024KF-06)+2 种基金Shanghai Jiao Tong University Scientific and Technological Innovation Funds(grant numbers:YG2022QN070 and 19X190020005)the National Natural Science Foundation of China(grant number:81872274)the Initiation Program for New Teachers of Shanghai Jiao Tong University(grant number:23X010502168).
文摘Cistanche deserticola(C.deserticola)is a holoparasitic plant of the Orobanchaceae family that parasitizes the roots of Haloxylon ammodendron(H.ammodendron).The absence of a high-quality genome has impeded our understanding of its parasitic mechanisms.Here,we present a chromosome-level genome assembly of C.deserticola(6.26 Gb)based on PacBio high fidelity(HiFi)and high-throughput chromosome conformation capture(Hi-C)sequencing,with a contig N50 of 81.25 Mb,92.2%Benchmarking Universal Single-Copy Ortholog(BUSCO)completeness,and 54640 protein-coding genes.Evolutionary analysis shows that C.deserticola diverged from related Orobanchaceae species approximately 38.23 million years ago.Among its key parasitic adaptations is the extensive loss of photosynthetic genes,which is compensated by the retention of transporters and carbon metabolic pathways for the utilization of host-derived nutrition.Bidirectional genetic exchanges include 34 H.ammodendron-derived horizontally transferred genes and 98 mobile mRNAs,as well as 14 C.deserticola-derived horizontally transferred genes and 77 mobile mRNAs targeting host defenses.Spatial transcriptomic data reveal haustorium-specific gene expression related to nutrient extraction and chemical defense,particularly the biosynthesis of phenylethanoid glycosides via dispersedduplication-driven gene expansion.This genomic resource illuminates the evolutionary trajectory of C.deserticola and provides a foundation for conservation strategies and the biotechnological development of C.deserticola.
基金supported by the Open Fund of State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry)(Grant No.TGB2021004)National Natural Science Foundation of China (Grant Nos.31770225,31570594)Program of Guangzhou Municipal Science and Technology Bureau(Grant No.202102021257)。
文摘Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.
基金This study was financially supported by the Yunnan Eco-friendly Food International Cooperation Research Center(YEFICRC)Project of Yunnan Provincial Key Programs(Grant No.2019ZG009)the National Key R&D Program of China(Grant No.2019YFD0300101)+3 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(Grant No.2017B030301011)the Key Research Program of the Chinese Academy of Sciences(KJZD-SW-L07)the Youth Innovation Promotion Association,CAS(No.2016080)Key-Area Research and Development Program of Guangdong Province(No.2020B020224002)。
文摘The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies.Here,we assembled a chromosome-level genome of a male FAW(SFynMstLFR)and compared re-sequencing results of the populations from America,Africa,and China.Strain identification of 163 individuals collected from America,Africa and China showed that both C and R strains were found in the American pop-ulations,while only C strain was found in the Chinese and African populations.Moreover,population geno-mics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations.Taken toge-ther,FAWs invaded into China were most likely origi-nated from Africa.Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW,of which 283 genes are specific to FAW.Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles,and several detoxification genes such as AOX,UGT and GST spe-cially responded to the pesticides.These findings will be useful in developing effective strategies for manage-ment of FAW in China and other invaded areas.
基金supported by the National Key Program(2016YFC0503200)from the Ministry of Science and Technology of Chinaa special grant for the giant panda from the State Forestry Administration of the People’s Republic of China+2 种基金the Fundamental Research Funds for the Central Universities of the People’s Republic of Chinathe Foundation of Key Laboratory of State Forestry and Grassland Administration(State Park Administration)on Conservation Biology of Rare Animals in the Giant Panda National Park(KLSFGAGP2020.002)the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)。
文摘Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and low reproduction.Here,we report the most contiguous,high-quality chromosomelevel genomes of two extant giant panda subspecies to date,with the first genome assembly of the Qinling subspecies.Compared with the previously assembled giant panda genomes based on short reads,our two assembled genomes increased contiguity over 200-fold at the contig level.Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago.Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2(DACH2)gene and specific changes in the synaptotagmin 6(SYT6)gene,which may be responsible for the reduced fertility of the giant panda.Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D(IQCD)gene may at least partly explain the different reproduction rates of the two subspecies.Furthermore,several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements,which may contribute to the reduced inner organ sizes of the giant panda.
