Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase...Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.展开更多
A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomi...A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental pressures.Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.展开更多
The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells.In this Review,we summarize CRISPR-base...The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells.In this Review,we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications.展开更多
The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In th...The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。展开更多
Mitochondrial genomes(mitogenomes)in frogs are essential for reconstructing the phylogenetic relationships and shedding light on the molecular evolution in these animals.However,there are only seven complete Rhacophor...Mitochondrial genomes(mitogenomes)in frogs are essential for reconstructing the phylogenetic relationships and shedding light on the molecular evolution in these animals.However,there are only seven complete Rhacophoridae genomes that have been reported to date.In this paper,two complete mitogenomes of the Chinese whipping frog(Zhangixalus chenfui)and Emei tree frog(Z.omeimontis)were described,each of which was 20520 and 19782 bp in size,and had A+T contents of 64.26%and 63.83%.The two mitogenomes each included two non-coding control region(D-loop,CR),two ribosomal RNA genes(rRNAs),13 protein-coding genes(PCGs),and 22 transfer RNA genes(tRNAs),and it was found that the mitogenome of Z.chenfui also includes three tandem tRNAMet gene sequences.A typical clover-leaf structure was found for all tRNAs except for tRNASer1(AGN),which showed a reduced DHU arm.The putative D-loop region contains multiple types of tandem repeats regions.Both of these two mitogenomes showed similar pattern of gene rearrangement(tRNA-Ser-ND6-tRNA-Glu-CytbCR1-ND5-CR2-tRNA-Thr-tRNA-Leu-tRNA-Pro).Additionally,three consecutive tRNAMet genes were found for the first time in Z.chenfui,a species in the Rhacophoridae family.For all phylogenetic analyses,which were based on 13 protein-coding genes from 91 Ranoidea mitogenomes,the same phylogenetic trees were observed using either maximum likelihood or Bayesian approaches.These results suggest that the phylogenetic hypotheses for the Ranoidea(including Rhacophoridae,Mantellidae,Ranidae and Dicroglossidae)derived from these mitogenomic data could provide substantiation for the relationships of(Dicroglossidae(Ranidae,(Mantellidae,Rhacophoridae))),and support the presence of a monophyletic group in four families.Moreover,Z.omeimontis and Z.dennysi were found to cluster on the same branch,indicating that they were more closely related as a group.This group may in turn form sister groups with Z.arboreus and Z.schlegelii.However,Z.chenfui is located on the base of other species in the genera.Increased mitogenome sampling should be conducted to provide a more satisfactory resolution to the phylogeny of the Rhacophorus,Rhacophoridae,and Mantellidae.展开更多
Environmentally heterogeneous mountains provide opportunities for rapid diversification and speciation.The family Prunellidae(accentors)is a group of birds comprising primarily mountain specialists that have recently ...Environmentally heterogeneous mountains provide opportunities for rapid diversification and speciation.The family Prunellidae(accentors)is a group of birds comprising primarily mountain specialists that have recently radiated across the Palearctic region.This rapid diversification poses challenges to resolving their phylogeny.Herein we sequenced the complete mitogenomes and estimated the phylogeny using all 12(including 28 individuals)currently recognized species of Prunellidae.We reconstructed the mitochondrial genome phylogeny using 13 protein-coding genes of 12 species and 2 Eurasian Tree Sparrows(Passer montanus).Phylogenetic relationships were estimated using a suite of analyses:maximum likelihood,maximum parsimony and the coalescent-based SVDquartets.Divergence times were estimated by implementing a Bayesian relaxed clock model in BEAST2.Based on the BEAST time-calibrated tree,we implemented an ancestral area reconstruction using RASP v.4.3.Our phylogenies based on the maximum likelihood,maximum parsimony and SVDquartets approaches support a clade of large-sized accentors(subgenus Laiscopus)to be sister to all other accentors with small size(subgenus Prunella).In addition,the trees also support the sister relationship of P.immaculata and P.rubeculoides+P.atrogularis with 100%bootstrap support,but the relationships among the remaining eight species in the Prunella clade are poorly resolved.These species cluster in different positions in the three phylogenetic trees and the nodes are often poorly supported.The five nodes separating the seven species diverged simultaneously within less than half million years(i.e.,between 2.71 and 3.15 million years ago),suggesting that the recent radiation is likely responsible for rampant incomplete lineage sorting and gene tree conflicts.Ancestral area reconstruction indicates a central Palearctic region origin for Prunellidae.Our study highlights that whole mitochondrial genome phylogeny can resolve major lineages within Prunellidae but is not sufficient to fully resolve the relationship among the species in the Prunella clade that almost simultaneously diversify during a short time period.Our results emphasize the challenge to reconstruct reliable phylogenetic relationship in a group of recently radiated species.展开更多
Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic va...Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid species.Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation.Whereas,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still scarce.To close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing reads.Systematic analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton mitogenomes.The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression level.Interestingly,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton species.Finally,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.展开更多
Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serv...Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serve as pollinators.However,higher-level chalcidoid relationships remain controversial.Here,we performed mitochondrial phylogenomic analyses for major clades(18out of 25 families)of Chalcidoidea based on 139 mitochondrial genomes.The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences.Our phylogenetic results supported the monophyly of 16families and polyphyly of Aphelinidae and Pteromalidae.Our preferred topology recovered the relationship(Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+remaining Chalcidoidea))).The monophyly of Agaonidae and Sycophaginae was rejected,while the gall-associated((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae))relationship was supported in most results.A six-gene inversion may be a synapomorphy for most families,whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes.Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea.We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea.Ancestral state reconstruction analyses supported the hypothesis that gallinducers were mainly derived from parasitoids of gallinducers,while other gall-inducers were derived from phytophagous groups.Taken together,these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.展开更多
Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mit...Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates + Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.展开更多
Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal's entire genome sequence or specific region(s) of interest is increasingly important f...Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal's entire genome sequence or specific region(s) of interest is increasingly important for agricultura researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing (NGS) technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models (e.g. nutrition). Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.展开更多
Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequen...Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures. The parameters estimated in the RIFS model reflect information on species classification.展开更多
Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared w...Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.展开更多
Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespre...Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.展开更多
For structural comparisons of paired prokaryotic genomes,an important topic in synthetic and evolutionary biology,the locations of shared orthologous genes(henceforth orthologs)are observed as binned data.This and oth...For structural comparisons of paired prokaryotic genomes,an important topic in synthetic and evolutionary biology,the locations of shared orthologous genes(henceforth orthologs)are observed as binned data.This and other data,e.g.,wind directions recorded at monitoring sites and intensive care unit arrival times on the 24-hour clock,are counted in binned circular arcs,thus modeling them by discrete circular distributions(DCDs)is required.We propose a novel method to construct a DCD from a base continuous circular distribution(CCD).The probability mass function is defined to take the normalized values of the probability density function at some pre-fixed equidistant points on the circle.Five families of constructed DCDs which have normalizing constants in closed form are presented.Simulation studies show that DCDs outperform the corresponding CCDs in modeling grouped(discrete)circular data,and minimum chi-square estimation outperforms maximum likelihood estimation for parameters.We apply the constructed DCDs,invariant wrapped Poisson and wrapped discrete skew Laplace to compare the structures of paired bacterial genomes.Specifically,discrete four-parameter wrapped Cauchy(nonnegative trigonometric sums)distribution models multi-modal shared orthologs in Clostridium(Sulfolobus)better than the others considered,in terms of AIC and Freedman’s goodness-of-fit test.The result that different DCDs fit the shared orthologs is consistent with the fact they belong to two kingdoms.Nevertheless,these prokaryotes have a common favored site around 70°on the unit circle;this finding is important for building synthetic prokaryotic genomes in synthetic biology.These DCDs can also be applied to other binned circular data.展开更多
Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system (T4SS) is one ...Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system (T4SS) is one of the secretion systems and it usually consists of 12 genes: VirB1, VirB2 ...VirB11, and VirD4[2]. The structure and molecular mechanisms of these genes have been well analyzed in Gram-negative strains[3] and Gram-positive strains were once believed to be lack of T4SS. However, some recent studies revealed that one or more virB/D genes also exist in some kinds of Gram-positive bacteria and play similar role, and form a T4SS-like system[3]. The VirBl-like, VirB4, VirB6, and VirD4 genes were identified in the chromosome of Gram-positive bacterium Streptococcus suis in our previous studies and their role as important mobile elements for horizontal transfer to recipients in an 89 K pathogenicity island (PAl) was demonstrated[45]. However, their structure and molecular mechanisms in other strains, especially in Gram-positive strains, are remained unclear.展开更多
INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For...INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For example, a statistical data from ahospital in Shanghai showed that 80% of HCCpatients were positive for HBsAg ( personalcommunication).展开更多
Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the geno...Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study(GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a-log10 P value for surrounding SNPs higher than the Bonferroni threshold(α/n, α < 0.001) when a mixed linear model(MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium(LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of π and Tajima's D were significantly(P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing(180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.展开更多
Herbgenomics is an emerging field of traditional Chinese medicine(TCM)research and development.By combining TCM research with genomics,herbgenomics can help to establish the scientific validity of TCM and bring it int...Herbgenomics is an emerging field of traditional Chinese medicine(TCM)research and development.By combining TCM research with genomics,herbgenomics can help to establish the scientific validity of TCM and bring it into wider usage within the field of medicine.Salvia Linn.(S.Linn.)is a large genus of Labiatae that includes important medicinal plants.In this herbgenomics study,the complete chloroplast(cp)genomes of two Salvia spp.—namely,S.przewalskii and S.bulleyana,which are used as a surrogate for S.miltiorrhiza—were sequenced and compared with those of two other reported Salvia spp.—namely,S.miltiorrhiza and S.japonica.The genome organization,gene number,type,and repeat sequences were compared.The annotation results showed that both Salvia plants contain 114 unique genes,including 80 protein-coding,30 transfer RNA(tRNA),and four ribosomal RNA(rRNA)genes.Repeat sequence analysis revealed 21 forward and 22 palindromic sequences in both Salvia cp genomes,and 17 and 21 tandem repeats in S.przewalskii and S.bulleyana,respectively.A synteny comparison of the Salvia spp.cp genomes showed a high degree of sequence similarity in the coding regions and a relatively high divergence of the intergenic spacers.Pairwise alignment and single-nucleotide polymorphism(SNP)analyses found some candidate fragments to identify Salvia spp.,such as the intergenic region of the trnV–ndhC,trnQ–rps16,atpI–atpH,psbA–ycf3,ycf1,rpoC2,ndhF,matK,rpoB,rpoA,and accD genes.All of the results—including the repeat sequences and SNP sites,the inverted repeat(IR)region border,and the phylogenetic analysis—showed that S.przewalskii and S.bulleyana are extremely similar from a genetic standpoint.The cp genome sequences of the two Salvia spp.reported here will pave the way for breeding,species identification,phylogenetic evolution,and cp genetic engineering studies of Salvia medicinal plants.展开更多
Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes ar...Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies.In the present study,the chloroplast genomes of Corchorus capsularis and C.olitorius were assembled,with sizes of respectively 161,088 and 161,766 bp.Both genomes contained 112 unique genes(78 protein-coding,four rRNA,and 30 tRNA genes).Four regionswith high variation between the two species were located in single-copy rather than inverted-repeat regions.A total of 66 simple sequence repeats(SSRs)were identified in the C.capsularis chloroplast genome and 56 in that of C.olitorius.Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites,of which one marker(cpInDel 205)could discriminate the two jute species.Comparison of the C.capsularis and C.olitorius chloroplast genomeswith those of other species in theMalvaceae revealed breakpoints in the accD locus,which is involved in fatty acid synthesis,in C.capsularis and C.olitorius.This finding suggests that genes from the chloroplast genomemight have been transferred to the nuclear genome in some Corchorus species.This hypothesis was supported by synteny analysis of the accD region among the nuclear,chloroplast,and mitochondrial genomes.To our knowledge,this is the first report of the assembled chloroplast genome sequences of C.capsularis and C.olitorius.C.capsularis and C.olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera.These results will expand our understanding of the systematics of species in the Malvaceae.展开更多
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ...Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.展开更多
基金Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)under contract No.2021CXGC011306MNR Key Laboratory of Eco-Environmental Science and Technology,China under contract No.MEEST-2021-05+2 种基金Natural Science Foundation of Shandong Province under contract No.ZR2020MD002Doctoral Science Research Foundation of Yantai University under contract Nos SM15B01,SM19B70 and SM19B28Double-Hundred Action of Yantai City under contract No.2320004-SM20RC02。
文摘Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.
基金supported by the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2022QNLM030004)Hainan Science and Technology Department(ZDKJ2019011)+2 种基金Open Project Fund of Key Laboratory of Sustainable Development of Polar Fisheries,Ministry of Agriculture and Rural Affairs of PRC(2022OPF02)State Key R&D Project(2021YFF0502500)Qingdao Postdoctoral Applied Research Project(JZ2223j06100)。
文摘A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental pressures.Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.
文摘The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells.In this Review,we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications.
文摘The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。
基金This work was supported by the National Natural Science Foundation of China(No.32270457)the Natural Science Foundation Province of Science and Technology Department of Sichuan Probince(No.2023NSFSC0206)+1 种基金the Research Project of Ecological Security and Protection Key Laboratory of Sichuan Province(No.ESP2003)the Research Project of Education Office Project of Sichuan Province(No.18ZA0261).
文摘Mitochondrial genomes(mitogenomes)in frogs are essential for reconstructing the phylogenetic relationships and shedding light on the molecular evolution in these animals.However,there are only seven complete Rhacophoridae genomes that have been reported to date.In this paper,two complete mitogenomes of the Chinese whipping frog(Zhangixalus chenfui)and Emei tree frog(Z.omeimontis)were described,each of which was 20520 and 19782 bp in size,and had A+T contents of 64.26%and 63.83%.The two mitogenomes each included two non-coding control region(D-loop,CR),two ribosomal RNA genes(rRNAs),13 protein-coding genes(PCGs),and 22 transfer RNA genes(tRNAs),and it was found that the mitogenome of Z.chenfui also includes three tandem tRNAMet gene sequences.A typical clover-leaf structure was found for all tRNAs except for tRNASer1(AGN),which showed a reduced DHU arm.The putative D-loop region contains multiple types of tandem repeats regions.Both of these two mitogenomes showed similar pattern of gene rearrangement(tRNA-Ser-ND6-tRNA-Glu-CytbCR1-ND5-CR2-tRNA-Thr-tRNA-Leu-tRNA-Pro).Additionally,three consecutive tRNAMet genes were found for the first time in Z.chenfui,a species in the Rhacophoridae family.For all phylogenetic analyses,which were based on 13 protein-coding genes from 91 Ranoidea mitogenomes,the same phylogenetic trees were observed using either maximum likelihood or Bayesian approaches.These results suggest that the phylogenetic hypotheses for the Ranoidea(including Rhacophoridae,Mantellidae,Ranidae and Dicroglossidae)derived from these mitogenomic data could provide substantiation for the relationships of(Dicroglossidae(Ranidae,(Mantellidae,Rhacophoridae))),and support the presence of a monophyletic group in four families.Moreover,Z.omeimontis and Z.dennysi were found to cluster on the same branch,indicating that they were more closely related as a group.This group may in turn form sister groups with Z.arboreus and Z.schlegelii.However,Z.chenfui is located on the base of other species in the genera.Increased mitogenome sampling should be conducted to provide a more satisfactory resolution to the phylogeny of the Rhacophorus,Rhacophoridae,and Mantellidae.
基金funded by the National Natural Science Foundation of China(NSFC32020103005)the Third Xinjiang Scientific Expedition and Research(XIKK)(2022xjkk0205)Second Tibetan Plateau Scientific Expedition and Research(2019QZKK0501)。
文摘Environmentally heterogeneous mountains provide opportunities for rapid diversification and speciation.The family Prunellidae(accentors)is a group of birds comprising primarily mountain specialists that have recently radiated across the Palearctic region.This rapid diversification poses challenges to resolving their phylogeny.Herein we sequenced the complete mitogenomes and estimated the phylogeny using all 12(including 28 individuals)currently recognized species of Prunellidae.We reconstructed the mitochondrial genome phylogeny using 13 protein-coding genes of 12 species and 2 Eurasian Tree Sparrows(Passer montanus).Phylogenetic relationships were estimated using a suite of analyses:maximum likelihood,maximum parsimony and the coalescent-based SVDquartets.Divergence times were estimated by implementing a Bayesian relaxed clock model in BEAST2.Based on the BEAST time-calibrated tree,we implemented an ancestral area reconstruction using RASP v.4.3.Our phylogenies based on the maximum likelihood,maximum parsimony and SVDquartets approaches support a clade of large-sized accentors(subgenus Laiscopus)to be sister to all other accentors with small size(subgenus Prunella).In addition,the trees also support the sister relationship of P.immaculata and P.rubeculoides+P.atrogularis with 100%bootstrap support,but the relationships among the remaining eight species in the Prunella clade are poorly resolved.These species cluster in different positions in the three phylogenetic trees and the nodes are often poorly supported.The five nodes separating the seven species diverged simultaneously within less than half million years(i.e.,between 2.71 and 3.15 million years ago),suggesting that the recent radiation is likely responsible for rampant incomplete lineage sorting and gene tree conflicts.Ancestral area reconstruction indicates a central Palearctic region origin for Prunellidae.Our study highlights that whole mitochondrial genome phylogeny can resolve major lineages within Prunellidae but is not sufficient to fully resolve the relationship among the species in the Prunella clade that almost simultaneously diversify during a short time period.Our results emphasize the challenge to reconstruct reliable phylogenetic relationship in a group of recently radiated species.
基金the Zhejiang Natural Science Foundation Outstanding Youth Grant(LR20C020002)the Zhejiang Provincial Natural Science Foundation of China(LZ23C020002)+4 种基金the National Natural Science Foundation of China(32200231)the National Key Research and Development Program of China(2022YFD1401600)the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002)Key Research Project of Zhejiang Lab(2021PE0AC04)the U.S.National Science Foundation(MCB 2148206).
文摘Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid species.Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation.Whereas,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still scarce.To close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing reads.Systematic analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton mitogenomes.The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression level.Interestingly,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton species.Finally,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.
基金supported by the Key International Joint Research Program of the National Natural Science Foundation of China(31920103005)General Program of the National Natural Science Foundation of China(32070467)+3 种基金Provincial Key R&D Program of Zhejiang,China(2021C02045)Key Project of Laboratory of Lingnan Modern Agriculture(NT2021003)Fundamental Research Funds for the Central UniversitiesSpecial Research Fund for Distinguished Scholars of Zhejiang Province,China(2018R51004)。
文摘Chalcidoidea is one of the most biologically diverse groups among Hymenoptera.Members are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serve as pollinators.However,higher-level chalcidoid relationships remain controversial.Here,we performed mitochondrial phylogenomic analyses for major clades(18out of 25 families)of Chalcidoidea based on 139 mitochondrial genomes.The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences.Our phylogenetic results supported the monophyly of 16families and polyphyly of Aphelinidae and Pteromalidae.Our preferred topology recovered the relationship(Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+remaining Chalcidoidea))).The monophyly of Agaonidae and Sycophaginae was rejected,while the gall-associated((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae))relationship was supported in most results.A six-gene inversion may be a synapomorphy for most families,whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes.Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea.We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea.Ancestral state reconstruction analyses supported the hypothesis that gallinducers were mainly derived from parasitoids of gallinducers,while other gall-inducers were derived from phytophagous groups.Taken together,these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.
基金supported by the Innovative Research Team in University of Sichuan Bureau of Education (No.14TD0002)the Scientific Research Fund of Sichuan Provincial Education Department (No.11ZA077)
文摘Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates + Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.
基金supported by the National Institutes of Health Grant #U54 DA021519
文摘Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal's entire genome sequence or specific region(s) of interest is increasingly important for agricultura researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing (NGS) technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models (e.g. nutrition). Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.
文摘Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures. The parameters estimated in the RIFS model reflect information on species classification.
基金the Special Funds for Major National Basic Research Projects,国家自然科学基金,北京市创新工程项目
文摘Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.
基金funded by Kunyu Mountain National Nature Reserve Administration。
文摘Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.
基金supported by JSPS KAKENHI Grant Number 18K13459 and Grace S.Shieh was supported in part by MOST 106-2118-M-001-017 and MOST 107-2118-M-001-009-MY2.
文摘For structural comparisons of paired prokaryotic genomes,an important topic in synthetic and evolutionary biology,the locations of shared orthologous genes(henceforth orthologs)are observed as binned data.This and other data,e.g.,wind directions recorded at monitoring sites and intensive care unit arrival times on the 24-hour clock,are counted in binned circular arcs,thus modeling them by discrete circular distributions(DCDs)is required.We propose a novel method to construct a DCD from a base continuous circular distribution(CCD).The probability mass function is defined to take the normalized values of the probability density function at some pre-fixed equidistant points on the circle.Five families of constructed DCDs which have normalizing constants in closed form are presented.Simulation studies show that DCDs outperform the corresponding CCDs in modeling grouped(discrete)circular data,and minimum chi-square estimation outperforms maximum likelihood estimation for parameters.We apply the constructed DCDs,invariant wrapped Poisson and wrapped discrete skew Laplace to compare the structures of paired bacterial genomes.Specifically,discrete four-parameter wrapped Cauchy(nonnegative trigonometric sums)distribution models multi-modal shared orthologs in Clostridium(Sulfolobus)better than the others considered,in terms of AIC and Freedman’s goodness-of-fit test.The result that different DCDs fit the shared orthologs is consistent with the fact they belong to two kingdoms.Nevertheless,these prokaryotes have a common favored site around 70°on the unit circle;this finding is important for building synthetic prokaryotic genomes in synthetic biology.These DCDs can also be applied to other binned circular data.
基金supported by the National Natural Science Foundation of China (No. 81201322)the Priority Project on Infectious Disease Control and Prevention 2011ZX10004-001 and 2013ZX10003006-002 by the Chinese Ministry of Science and Technology and the Chinese Ministry of Healththe Foundation of State Key Laboratory for Infectious Disease Prevention and Control (Grand No. 2011SKLID303)
文摘Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system (T4SS) is one of the secretion systems and it usually consists of 12 genes: VirB1, VirB2 ...VirB11, and VirD4[2]. The structure and molecular mechanisms of these genes have been well analyzed in Gram-negative strains[3] and Gram-positive strains were once believed to be lack of T4SS. However, some recent studies revealed that one or more virB/D genes also exist in some kinds of Gram-positive bacteria and play similar role, and form a T4SS-like system[3]. The VirBl-like, VirB4, VirB6, and VirD4 genes were identified in the chromosome of Gram-positive bacterium Streptococcus suis in our previous studies and their role as important mobile elements for horizontal transfer to recipients in an 89 K pathogenicity island (PAl) was demonstrated[45]. However, their structure and molecular mechanisms in other strains, especially in Gram-positive strains, are remained unclear.
基金This work was supported by Projects of Tackling Key Problems in ScienceTechnology from the State Science+2 种基金Technology Ministry (TJ99-LA01) Shanghai ScienceTechnology Commission (994919033 )
文摘INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For example, a statistical data from ahospital in Shanghai showed that 80% of HCCpatients were positive for HBsAg ( personalcommunication).
基金supported by the Chinese National "863" Program from the China Ministry of Science and Technology (Grant No. 2012AA10A306-3)the National Science Foundation of China (Grant No. 31171562) to CXthe Core Research Budget of the Non-profit Governmental Research Institution from the Chinese Government to the Institute of Crop Science, Chinese Academy of Agricultural Sciences (Grant No. 2012001)
文摘Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study(GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a-log10 P value for surrounding SNPs higher than the Bonferroni threshold(α/n, α < 0.001) when a mixed linear model(MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium(LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of π and Tajima's D were significantly(P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing(180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
基金This work is supported by the National Nature Science Foundation of China(QFSL2018004,2017YFC1702100,and 81741060)the Fundamental Research Funds for the Central Public Welfare Research Institutes(ZXKT17004).
文摘Herbgenomics is an emerging field of traditional Chinese medicine(TCM)research and development.By combining TCM research with genomics,herbgenomics can help to establish the scientific validity of TCM and bring it into wider usage within the field of medicine.Salvia Linn.(S.Linn.)is a large genus of Labiatae that includes important medicinal plants.In this herbgenomics study,the complete chloroplast(cp)genomes of two Salvia spp.—namely,S.przewalskii and S.bulleyana,which are used as a surrogate for S.miltiorrhiza—were sequenced and compared with those of two other reported Salvia spp.—namely,S.miltiorrhiza and S.japonica.The genome organization,gene number,type,and repeat sequences were compared.The annotation results showed that both Salvia plants contain 114 unique genes,including 80 protein-coding,30 transfer RNA(tRNA),and four ribosomal RNA(rRNA)genes.Repeat sequence analysis revealed 21 forward and 22 palindromic sequences in both Salvia cp genomes,and 17 and 21 tandem repeats in S.przewalskii and S.bulleyana,respectively.A synteny comparison of the Salvia spp.cp genomes showed a high degree of sequence similarity in the coding regions and a relatively high divergence of the intergenic spacers.Pairwise alignment and single-nucleotide polymorphism(SNP)analyses found some candidate fragments to identify Salvia spp.,such as the intergenic region of the trnV–ndhC,trnQ–rps16,atpI–atpH,psbA–ycf3,ycf1,rpoC2,ndhF,matK,rpoB,rpoA,and accD genes.All of the results—including the repeat sequences and SNP sites,the inverted repeat(IR)region border,and the phylogenetic analysis—showed that S.przewalskii and S.bulleyana are extremely similar from a genetic standpoint.The cp genome sequences of the two Salvia spp.reported here will pave the way for breeding,species identification,phylogenetic evolution,and cp genetic engineering studies of Salvia medicinal plants.
基金supported by the National Natural Science Foundation of China(31771369)the China Agriculture Research System for Crops of Bast and Leaf Fiber,China(nycytx-19-E06)。
文摘Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies.In the present study,the chloroplast genomes of Corchorus capsularis and C.olitorius were assembled,with sizes of respectively 161,088 and 161,766 bp.Both genomes contained 112 unique genes(78 protein-coding,four rRNA,and 30 tRNA genes).Four regionswith high variation between the two species were located in single-copy rather than inverted-repeat regions.A total of 66 simple sequence repeats(SSRs)were identified in the C.capsularis chloroplast genome and 56 in that of C.olitorius.Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites,of which one marker(cpInDel 205)could discriminate the two jute species.Comparison of the C.capsularis and C.olitorius chloroplast genomeswith those of other species in theMalvaceae revealed breakpoints in the accD locus,which is involved in fatty acid synthesis,in C.capsularis and C.olitorius.This finding suggests that genes from the chloroplast genomemight have been transferred to the nuclear genome in some Corchorus species.This hypothesis was supported by synteny analysis of the accD region among the nuclear,chloroplast,and mitochondrial genomes.To our knowledge,this is the first report of the assembled chloroplast genome sequences of C.capsularis and C.olitorius.C.capsularis and C.olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera.These results will expand our understanding of the systematics of species in the Malvaceae.
基金supported by the National key research and development plan(2016TFC1202700,2016YFC1200900)Beijing Municipal Science&Technology Commission project(grant numbers D151100002115003)Guangzhou Municipal Science&Technology Commission project(grant numbers 2015B2150820)
文摘Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.