Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study ...Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.展开更多
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
Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta ...Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.展开更多
The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we d...The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.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 genomes of three groups of grass carp, namely the Xiangjiang River grass carp group (Xiangjiang group), a one-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-1 group), and a...The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group (Xiangjiang group), a one-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-1 group), and a two-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-2 group), were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.展开更多
The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four...The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.展开更多
MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus (NC-003 378.1) from the NCB...MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus (NC-003 378.1) from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.展开更多
[Objective] Genomic in situ hybridization (GISH) was used to study the relationship between the two CCDD genomes of Oryza alta and Oryza latifolia. [Method] Total DNA of Oryza officinalis (C-genome) was used as a prob...[Objective] Genomic in situ hybridization (GISH) was used to study the relationship between the two CCDD genomes of Oryza alta and Oryza latifolia. [Method] Total DNA of Oryza officinalis (C-genome) was used as a probe for genomic in situ hybridization on metaphase chromosomes from Oryza alta and Oryza latifolia, respectively. [Result] Under certain post-hybridization washing stringencies, C- and D-genome could be distinguished in CCDD genome type; there were huge differences in some CC chromosomes of Oryza alta, Oryza latifolia, and Oryza officinalis. The genome of Oryza latifolia was more original. [Conclusion] Comparative analysis of the Oryza species with identical genome type may facilitate to elucidate the possible approaches to plant genome evolution and species evolution.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
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
Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cyt...Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.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
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
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
Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analy-sis of EV...Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analy-sis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, long-length EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.展开更多
The genomes of the barley, Arabidopsis and pea powdery mildew are significantly larger than those of related fungi. This is due to an extraordinary expansion of retro-trasposons that are evident as repetitive elements...The genomes of the barley, Arabidopsis and pea powdery mildew are significantly larger than those of related fungi. This is due to an extraordinary expansion of retro-trasposons that are evident as repetitive elements in the sequence. The protein coding genes are fewer than expected due to an overall reduction in the size of gene families, a reduction in the number of paralogs and because of the loss of certain metabolic pathways. Many of these changes have also been observed in the genomes of other taxonomically unrelated obligate biotrophic pathogens. The only group of genes that bucks the trend of gene loss, are those encoding small secreted proteins that bear the hall marks of effectors.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
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
基金funded by the Jiangxi Provincial Natural Science Foundation,Grant Number 20232BAB216119.
文摘Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.
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 Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)(No.2021CXGC011306)the MNR Key Laboratory of Eco-Environmental Science and Technology,China(No.MEEST-2021-05)+2 种基金the Natural Science Foundation of Shandong Province(No.ZR2020MD002)the Doctoral Science Research Foundation of Yantai University(Nos.SM15B01,SM19B70,SM19B28)the“Double-Hundred Action”of Yantai City(No.2320004-SM20RC02)。
文摘Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.
基金supported by the National Natural Science Foundation of China(Grant No.32102364)the General Program of Shandong Natural Science Foundation(Grant No.ZR2022MC064)+3 种基金the Shanxi Province Postdoctoral Research Activity Fund(Grant No.K462101001)the Doctoral Research Initiation Fund of Shanxi Datong University(Grant No.2023-B-15)the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.2023CYJSTX07)the Shanxi Province Excellent Doctoral Work Award Project(Grant No.606-02010609)。
文摘The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.
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.
基金This work was supported by National Natural Sciences Foundation of China (No. 39830300 )the Ministry of Education (No. 20065-14)
文摘The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group (Xiangjiang group), a one-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-1 group), and a two-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-2 group), were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.
文摘The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.
基金Supported by the Eleventh Five-year Development Planning Project for Instructional Science in Hubei Province (2006B131)~~
文摘MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus (NC-003 378.1) from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.
文摘[Objective] Genomic in situ hybridization (GISH) was used to study the relationship between the two CCDD genomes of Oryza alta and Oryza latifolia. [Method] Total DNA of Oryza officinalis (C-genome) was used as a probe for genomic in situ hybridization on metaphase chromosomes from Oryza alta and Oryza latifolia, respectively. [Result] Under certain post-hybridization washing stringencies, C- and D-genome could be distinguished in CCDD genome type; there were huge differences in some CC chromosomes of Oryza alta, Oryza latifolia, and Oryza officinalis. The genome of Oryza latifolia was more original. [Conclusion] Comparative analysis of the Oryza species with identical genome type may facilitate to elucidate the possible approaches to plant genome evolution and species evolution.
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 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National Natural Science Foundation of China(31530053)
文摘Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.
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.
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 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Foundation item:The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analy-sis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, long-length EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.
文摘The genomes of the barley, Arabidopsis and pea powdery mildew are significantly larger than those of related fungi. This is due to an extraordinary expansion of retro-trasposons that are evident as repetitive elements in the sequence. The protein coding genes are fewer than expected due to an overall reduction in the size of gene families, a reduction in the number of paralogs and because of the loss of certain metabolic pathways. Many of these changes have also been observed in the genomes of other taxonomically unrelated obligate biotrophic pathogens. The only group of genes that bucks the trend of gene loss, are those encoding small secreted proteins that bear the hall marks of effectors.
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.
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.