Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid...Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.展开更多
Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria in bioleaching reactors. It plays the essential role in maintaining the high acidity and oxidation of reduced inorganic sulfur compounds during...Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria in bioleaching reactors. It plays the essential role in maintaining the high acidity and oxidation of reduced inorganic sulfur compounds during bioleaching process. In this report, the complete genome sequence of A. caldus SM-1 is presented. The genome is composed of one chromosome （2,932,225 bp） and four plasmids （pLAtcl, pLAtc2, pLAtc3, pLAtcm） and it is rich in repetitive sequences （accounting for 11% of the total genome）, which are often associated with transposable genetic elements. In particular, twelve copies of ISAtfe and thirty-seven copies of ISAtcl have been identified, suggesting that they are active transposons in the genome. A. caldus SM-1 encodes all enzymes for the central metabolism and the assimilation of carbon compounds, among which 29 proteins/enzymes were identifiable with proteomic tools. The SM-1 fixes CO2 via the classical Calvin-Bassham--Benson （CBB） cycle, and can operate complete Embden-Meyerhof pathway （EMP）, pentose phosphate pathway （PPP）, and gluconeogenesis. It has an incomplete tricarboxylic acid cycle （TCA）. Four putative transporters involved in carbohydrate uptake were identified. Taken together, the results suggested that SM-1 was able to assimilate carbohydrates and this was subsequently confirmed experimentally because addition of 1% glucose or sucrose in basic salt medium significantly increased the growth of SM-1. It was concluded that the complete genome of SM-1 provided fundamental data for further investigation of its physiology and genetics, in addition to the carbon metabolism revealed in this study.展开更多
Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strai...Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel ＇quasicore＇ with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.展开更多
The Lateral Organ Boundaries Domain(LBD)genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species.However,members of the LBD gene family have yet to be i...The Lateral Organ Boundaries Domain(LBD)genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species.However,members of the LBD gene family have yet to be identified in Brassica rapa var.rapa.In the present study,fifty-nine LBD genes were identified and distributed on 10 chromosomes.The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa;the theoretical pi for these proteins varies from 4.83 to 9.68.There were 17 paralogous gene pairs in the BrrLBD family,suggesting that the amplification of the BrrLBD gene family involved largescale gene duplication events.Members of the BrrLBD family were divided into 7 subclades(class I a to e,class II a and b).Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs.The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR(qRT-PCR).Most BrrLBD genes in the same subclade had similar gene expression profiles.However,the expression patterns of 7 genes differed from their duplicates,indicating that although the gene function of most BrrLBD genes has been conserved,some BrrLBD genes may have undergone evolutionary change.展开更多
Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are ...Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.展开更多
Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats(CRISPR) and CRISPR associated(Cas) nucleases, was developed. Previous technologies for genome ...Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats(CRISPR) and CRISPR associated(Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.展开更多
Slow speed of the Next-Generation sequencing data analysis, compared to the latest high throughput sequencers such as HiSeq X system, using the current industry standard genome analysis pipeline, has been the major fa...Slow speed of the Next-Generation sequencing data analysis, compared to the latest high throughput sequencers such as HiSeq X system, using the current industry standard genome analysis pipeline, has been the major factor of data backlog which limits the real-time use of genomic data for precision medicine. This study demonstrates the DRAGEN Bio-IT Processor as a potential candidate to remove the “Big Data Bottleneck”. DRAGENTM accomplished the variant calling, for ~40× coverage WGS data in as low as ~30 minutes using a single command, achieving the over 50-fold data analysis speed while maintaining the similar or better variant calling accuracy than the standard GATK Best Practices workflow. This systematic comparison provides the faster and efficient NGS data analysis alternative to NGS-based healthcare industries and research institutes to meet the requirement for precision medicine based healthcare.展开更多
Oligopeptide transporters(OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses reveal...Oligopeptide transporters(OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses revealed two well-supported clades in the OPT family, containing 15 BrrOPTs and 13 BrrYSLs.The exon/intron structure of OPT clade are conserved but the yellow stripe-like(YSL) clade was different.The exon/intron of the YSL clade possesses structural differences, whereas the YSL class motifs structure are conserved. The OPT genes are distributed unevenly among the chromosomes of the turnip genome.Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication. For the expression profiles at different developmental stages, a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family. Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution.Furthermore. BrrOPT8.1, BrrYSL1.2, BrrYSL1.3, BrrYSL6 and BrrYSL9 responded to Fe(Ⅱ) treatments and BrrYSL7 responded to calcium treatments, BrrYSL6 responded to multiple treatments in root, suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies. Our data provide important information for further functional dissection of BrrOPTs, especially in transporting metal ions and nutrient deficiency stress adaptation.展开更多
In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an ave...In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.展开更多
DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 coun...DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions worldwide.With continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.展开更多
Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae（M. pneumoniae）. However, these mutations alone do not fully explain the high resistance rates in As...Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae（M. pneumoniae）. However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. Methods The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina Hi Seq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone（CCCP）. Results A total of 56 single nucleotide polymorphisms（SNPs） were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene mac B encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations（MIC） of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains. Conclusion Our study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23 S r RNA gene.展开更多
Triterpenoid saponins(TSs)are common plant defense phytochemicals with potential pharmaceutical properties.Platycodon grandiflorus(Campanulaceae)has been traditionally used to treat bronchitis and asthma in East Asia....Triterpenoid saponins(TSs)are common plant defense phytochemicals with potential pharmaceutical properties.Platycodon grandiflorus(Campanulaceae)has been traditionally used to treat bronchitis and asthma in East Asia.The oleanane-type TSs,platycosides,are a major component of the P.grandiflorus root extract.Recent studies show that platycosides exhibit anti-inflammatory,antiobesity,anticancer,antiviral,and antiallergy properties.However,the evolutionary history of platycoside biosynthesis genes remains unknown.In this study,we sequenced the genome of P.grandiflorus and investigated the genes involved in platycoside biosynthesis.The draft genome of P.grandiflorus is 680.1 Mb long and contains 40,017 protein-coding genes.Genomic analysis revealed that the CYP716 family genes play a major role in platycoside oxidation.The CYP716 gene family of P.grandiflorus was much larger than that of other Asterid species.Orthologous gene annotation also revealed the expansion ofβ-amyrin synthases(bASs)in P.grandiflorus,which was confirmed by tissue-specific gene expression.In these expanded gene families,we identified key genes showing preferential expression in roots and association with platycoside biosynthesis.In addition,wholegenome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in P.grandiflorus,suggesting that epigenetic modification of these two gene families affects platycoside biosynthesis.Thus whole-genome,transcriptome,and methylome data of P.grandiflorus provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.展开更多
With over 10 million points of genetic variation from person to person, every individual’s genome is unique and provides a highly reliable form of identification. This is because the genetic code is specific to each ...With over 10 million points of genetic variation from person to person, every individual’s genome is unique and provides a highly reliable form of identification. This is because the genetic code is specific to each individual and does not change over time. Genetic information has been used to identify individuals in a variety of contexts, such as criminal investigations, paternity tests, and medical research. In this study, each individual’s genetic makeup has been formatted to create a secure, unique code that incorporates various elements, such as species, gender, and the genetic identification code itself. The combinations of markers required for this code have been derived from common single nucleotide polymorphisms (SNPs), points of variation found in the human genome. The final output is in the form of a 24 numerical code with each number having three possible combinations. The custom code can then be utilized to create various modes of identification on the decentralized blockchain network as well as personalized services and products that offer users a novel way to uniquely identify themselves in ways that were not possible before.展开更多
Nested in the environment of the nucleus of the cell, the 23 sets of chromosomes that comprise the human genome function as one integrated whole system, orchestrating the expression of thousands of genes underlying th...Nested in the environment of the nucleus of the cell, the 23 sets of chromosomes that comprise the human genome function as one integrated whole system, orchestrating the expression of thousands of genes underlying the biological characteristics of the cell, individual and the species. The extraction of meaningful information from this complex data set depends crucially upon the lens through which the data are examined. We present a biophysical perspective on genomic information encoded in single nucleotide polymorphisms (SNPs), and introduce metrics for modeling information encoded in the genome. Information, like energy, is considered to be a conserved physical property of the universe. The information structured in SNPs describes the adaptation of a human population to a given environment. The maintained order measured by the information content is associated with entropies, energies, and other state variables for a dynamic system in homeostasis. “Genodynamics” characterizes the state variables for genomic populations that are stable under stochastic environmental stresses. The determination of allelic energies allows the parameterization of specific environmental influences upon individual alleles across populations. The environment drives population-based genome variation. From this vantage point, the genome is modeled as a complex, dynamic information system defined by patterns of SNP alleles and SNP haplotypes.展开更多
The human genome is a complex, dynamic information system that encodes principles of life and living systems. These principles are incorporated in the structure of human genome sequence variation and are foundational ...The human genome is a complex, dynamic information system that encodes principles of life and living systems. These principles are incorporated in the structure of human genome sequence variation and are foundational for the continuity of life and human survival. Using first principles of thermodynamics and statistical physics, we have developed analogous “genodynamic tools” for population genomic studies. Characterizing genomic information through the lens of physics has allowed us to develop energy measures for modeling genome-environment interactions. In developing biophysical parameters for genome-environment homeostasis, we found that stable genomic free energy trades off low genomic energy (genomic conservation and increased order) and high genomic entropy (genomic variation) with an environmental potential that drives the variation. In our approach, we assert that common variants are dynamic sites in the genome of a population and that the stability of whole genome adaptation is reflected in the frequencies of maintained diversity in common variants for the population in its environment. In this paper, we address the relativity of whole genome adaptation towards homeostasis. By this we mean that adaptive forces are directly reflected in the frequency distribution of alleles and/or haplotypes of the population relative to its environment, with adaptive forces driving the genome towards homeostasis. The use of genomic energy units as a biophysical metric in DNA sequence variation analyses provides new insights into the foundations of population biology and diversity. Using our biophysical tools, population differences directly reflect the adaptive influences of the environment on populations.展开更多
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaptation that optimizes population survival in differing environments. This p...As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaptation that optimizes population survival in differing environments. This paper mathematically models environmentally induced adaptive forces that quantify changes in the distribution of SNP frequencies between populations. We make direct connections between biophysical methods (e.g. minimizing genomic free energy) and concepts in population genetics. Our unbiased computer program scanned a large set of SNPs in the major histocompatibility complex region and flagged an altitude dependency on a SNP associated with response to oxygen deprivation. The statistical power of our double-blind approach is demonstrated in the flagging of mathematical functional correlations of SNP information-based potentials in multiple populations with specific environmental parameters. Furthermore, our approach provides insights for new discoveries on the biology of common variants. This paper demonstrates the power of biophysical modeling of population diversity for better understanding genome-environment interactions in biological phenomenon.展开更多
Posttraumatic stress disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event. Multiple environmental and genetic factors can contribute to PTSD susceptibility. Since it is rare to...Posttraumatic stress disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event. Multiple environmental and genetic factors can contribute to PTSD susceptibility. Since it is rare to find members of the same family afflicted by the same catastrophic event, it is not practical to determine PTSD susceptibility genes by a gene linkage analysis. A natural disaster, such as the 2004 Tsunami, provided us with a rare chance for a genetic analysis of PTSD. To identify SNPs associated with PTSD susceptibility, we conducted a genome-association study (GWAS) in Thai-Tsunami survivors. Initial phase of the study with 396 chronic PTSD patients and 457 controls, we identified top ninety SNPs (P -4), which were further assessed in the second phase with 395 chronic PTSD patients and 798 controls. Two SNPs (rs267950 and rs954406), were identified in the second phase, and subjected to fine mapping using a data set from both phases. SNP rs267943 showed the strongest association with PTSD susceptibility and was in complete linkage disequilibrium with SNP rs267950 with P = 6.15 × 10-8, OR = 1.46 and 95% CI = 1.19 - 1.79, reaching genome-wide significance. SNP rs267943 is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and, when linked to a synthetic promoter, could regulate transcription. To our knowledge, this is the first GWAS for PTSD susceptibility in an Asian population which could provide an important insight into the genetic contribution of PTSD and may lead to new treatment strategies for PTSD.展开更多
A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition....A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.展开更多
In the event of the ever-increasing growth of the beauty industry and the burgeoning market for facial masks,high-performance and high-safety mask products have emerged.Among these,light-cured collagen peptide-based h...In the event of the ever-increasing growth of the beauty industry and the burgeoning market for facial masks,high-performance and high-safety mask products have emerged.Among these,light-cured collagen peptide-based hydrogels,which are non-toxic,photocurable natural materials,exhibit significant potential for use in facial masks.We developed a novel collagen peptide-lithium chloride hydrogel-based facial mask.Light-cured collagen peptide hydrogel is a non-toxic,light-activated natural material that holds considerable promise for application in facial masks.Nonetheless,there is a significant lack of effective methodologies for real-time assessment of skin quality currently available in the market.To address this deficiency,we have developed an innovative collagen peptide-lithium chloride hydrogel mask,which is characterized by exceptional transparency(98%within the visible spectrum of 400-800 nm),commendable tensile properties(tensile strength of 428.6±2.1 kPa,with a tensile strength increase of 123.9%),substantial water retention capacity(61%),and favorable antimicrobial efficacy(89%).The incorporation of lithium chloride enhances ionic conduction at the interface between the human body and hydrogel,thereby enabling quantitative evaluation of skin quality through impedance analysis.Our collagen peptide-lithium chloride hydrogel facial mask demonstrated effectiveness in distinguishing various skin types,including D+(severely dry),D(mildly to moderately dry),N(moderate),O(mildly to moderately oily),and O+(severely oily).This study presents significant opportunities for the advancement of hydrogel masks and provides a new application platform for polymer hydrogels.展开更多
基金supported by the National Natural Science Foundation of China(No.32072947)the China Agriculture Research System(No.CARS-47)。
文摘Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.
基金supported by the National Science Foundation of China(No.30870039)the National Basic Research Program of China(973 Program,No.2010CB630903)
文摘Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria in bioleaching reactors. It plays the essential role in maintaining the high acidity and oxidation of reduced inorganic sulfur compounds during bioleaching process. In this report, the complete genome sequence of A. caldus SM-1 is presented. The genome is composed of one chromosome （2,932,225 bp） and four plasmids （pLAtcl, pLAtc2, pLAtc3, pLAtcm） and it is rich in repetitive sequences （accounting for 11% of the total genome）, which are often associated with transposable genetic elements. In particular, twelve copies of ISAtfe and thirty-seven copies of ISAtcl have been identified, suggesting that they are active transposons in the genome. A. caldus SM-1 encodes all enzymes for the central metabolism and the assimilation of carbon compounds, among which 29 proteins/enzymes were identifiable with proteomic tools. The SM-1 fixes CO2 via the classical Calvin-Bassham--Benson （CBB） cycle, and can operate complete Embden-Meyerhof pathway （EMP）, pentose phosphate pathway （PPP）, and gluconeogenesis. It has an incomplete tricarboxylic acid cycle （TCA）. Four putative transporters involved in carbohydrate uptake were identified. Taken together, the results suggested that SM-1 was able to assimilate carbohydrates and this was subsequently confirmed experimentally because addition of 1% glucose or sucrose in basic salt medium significantly increased the growth of SM-1. It was concluded that the complete genome of SM-1 provided fundamental data for further investigation of its physiology and genetics, in addition to the carbon metabolism revealed in this study.
基金This paper is dedicated to the late Professor JS Chiao, who initiated the research in China for rifamycin production employing A. mediterranei more than 30 years ago and who continued the endeavor to resolve the mechanism of the ＇nitrate stimulating effect＇ up to the last breath of his life. This work was supported by the National Natural Science Foundation of China （30830002）, the National High Technology Research and Development Program of China （2007AA021301, 2007AA021503）, and the Research Unit Fund of Li Ka Shing Institute of Health Sciences （7103506）.
文摘Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel ＇quasicore＇ with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.
基金This study was supported by the Major Program of National Natural Science Foundation of China,China(31590820 and 31590823)the National Natural Science Foundation of China,China(41771123 and 31400244)the Natural Science Foundation of Yunnan Province(2017FB050).
文摘The Lateral Organ Boundaries Domain(LBD)genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species.However,members of the LBD gene family have yet to be identified in Brassica rapa var.rapa.In the present study,fifty-nine LBD genes were identified and distributed on 10 chromosomes.The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa;the theoretical pi for these proteins varies from 4.83 to 9.68.There were 17 paralogous gene pairs in the BrrLBD family,suggesting that the amplification of the BrrLBD gene family involved largescale gene duplication events.Members of the BrrLBD family were divided into 7 subclades(class I a to e,class II a and b).Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs.The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR(qRT-PCR).Most BrrLBD genes in the same subclade had similar gene expression profiles.However,the expression patterns of 7 genes differed from their duplicates,indicating that although the gene function of most BrrLBD genes has been conserved,some BrrLBD genes may have undergone evolutionary change.
基金supported by USDA/NIFA/SCRI under grant number 59-5306-2-333 and by the California Walnut Board.
文摘Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.
基金Supported by The Grants from the Ministry of EducationCulture+7 种基金SportsScience and Technology of Japanthe Ministry of HealthLabour and Welfare of Japanthe National Institute of Biomedical Innovationthe Asahi Glass Foundationthe Ichiro Kanehara Foundationthe Program for Cultivating Global Leaders in Heavy Ion Therapeutics and Engineering
文摘Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats(CRISPR) and CRISPR associated(Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.
文摘Slow speed of the Next-Generation sequencing data analysis, compared to the latest high throughput sequencers such as HiSeq X system, using the current industry standard genome analysis pipeline, has been the major factor of data backlog which limits the real-time use of genomic data for precision medicine. This study demonstrates the DRAGEN Bio-IT Processor as a potential candidate to remove the “Big Data Bottleneck”. DRAGENTM accomplished the variant calling, for ~40× coverage WGS data in as low as ~30 minutes using a single command, achieving the over 50-fold data analysis speed while maintaining the similar or better variant calling accuracy than the standard GATK Best Practices workflow. This systematic comparison provides the faster and efficient NGS data analysis alternative to NGS-based healthcare industries and research institutes to meet the requirement for precision medicine based healthcare.
基金supported financially by the Major Projects of National Natural Science Foundation of China(No. 31590823)the National Natural Science Foundation of China (No. 31601999)
文摘Oligopeptide transporters(OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses revealed two well-supported clades in the OPT family, containing 15 BrrOPTs and 13 BrrYSLs.The exon/intron structure of OPT clade are conserved but the yellow stripe-like(YSL) clade was different.The exon/intron of the YSL clade possesses structural differences, whereas the YSL class motifs structure are conserved. The OPT genes are distributed unevenly among the chromosomes of the turnip genome.Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication. For the expression profiles at different developmental stages, a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family. Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution.Furthermore. BrrOPT8.1, BrrYSL1.2, BrrYSL1.3, BrrYSL6 and BrrYSL9 responded to Fe(Ⅱ) treatments and BrrYSL7 responded to calcium treatments, BrrYSL6 responded to multiple treatments in root, suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies. Our data provide important information for further functional dissection of BrrOPTs, especially in transporting metal ions and nutrient deficiency stress adaptation.
基金Supported by the Knowledge Innovation Program of Chinese Academy of Sciences (No. KSCX2-YW-G-073)
文摘In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB38030200,XDB38050300,XDA19090116,XDA19050302)National Key R&D Program of China(2020YFC0848900,2020YFC0847000)。
文摘DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions worldwide.With continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.
基金supported by the grants from National Nature Science Foundation of China(81601778 and 81672062)the Beijing Natural Science Foundation(7152025)Beijing Talents Fund(2015000021469G192)
文摘Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae（M. pneumoniae）. However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. Methods The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina Hi Seq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone（CCCP）. Results A total of 56 single nucleotide polymorphisms（SNPs） were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene mac B encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations（MIC） of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains. Conclusion Our study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23 S r RNA gene.
基金supported by the Research Program for Agricultural Science and Technology Development(Grant No.PJ013485)the Cooperative Research Program for National Agricultural Genome Program(Grant Nos.PJ010351,PJ01035104,and PJ01349002).
文摘Triterpenoid saponins(TSs)are common plant defense phytochemicals with potential pharmaceutical properties.Platycodon grandiflorus(Campanulaceae)has been traditionally used to treat bronchitis and asthma in East Asia.The oleanane-type TSs,platycosides,are a major component of the P.grandiflorus root extract.Recent studies show that platycosides exhibit anti-inflammatory,antiobesity,anticancer,antiviral,and antiallergy properties.However,the evolutionary history of platycoside biosynthesis genes remains unknown.In this study,we sequenced the genome of P.grandiflorus and investigated the genes involved in platycoside biosynthesis.The draft genome of P.grandiflorus is 680.1 Mb long and contains 40,017 protein-coding genes.Genomic analysis revealed that the CYP716 family genes play a major role in platycoside oxidation.The CYP716 gene family of P.grandiflorus was much larger than that of other Asterid species.Orthologous gene annotation also revealed the expansion ofβ-amyrin synthases(bASs)in P.grandiflorus,which was confirmed by tissue-specific gene expression.In these expanded gene families,we identified key genes showing preferential expression in roots and association with platycoside biosynthesis.In addition,wholegenome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in P.grandiflorus,suggesting that epigenetic modification of these two gene families affects platycoside biosynthesis.Thus whole-genome,transcriptome,and methylome data of P.grandiflorus provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.
文摘With over 10 million points of genetic variation from person to person, every individual’s genome is unique and provides a highly reliable form of identification. This is because the genetic code is specific to each individual and does not change over time. Genetic information has been used to identify individuals in a variety of contexts, such as criminal investigations, paternity tests, and medical research. In this study, each individual’s genetic makeup has been formatted to create a secure, unique code that incorporates various elements, such as species, gender, and the genetic identification code itself. The combinations of markers required for this code have been derived from common single nucleotide polymorphisms (SNPs), points of variation found in the human genome. The final output is in the form of a 24 numerical code with each number having three possible combinations. The custom code can then be utilized to create various modes of identification on the decentralized blockchain network as well as personalized services and products that offer users a novel way to uniquely identify themselves in ways that were not possible before.
文摘Nested in the environment of the nucleus of the cell, the 23 sets of chromosomes that comprise the human genome function as one integrated whole system, orchestrating the expression of thousands of genes underlying the biological characteristics of the cell, individual and the species. The extraction of meaningful information from this complex data set depends crucially upon the lens through which the data are examined. We present a biophysical perspective on genomic information encoded in single nucleotide polymorphisms (SNPs), and introduce metrics for modeling information encoded in the genome. Information, like energy, is considered to be a conserved physical property of the universe. The information structured in SNPs describes the adaptation of a human population to a given environment. The maintained order measured by the information content is associated with entropies, energies, and other state variables for a dynamic system in homeostasis. “Genodynamics” characterizes the state variables for genomic populations that are stable under stochastic environmental stresses. The determination of allelic energies allows the parameterization of specific environmental influences upon individual alleles across populations. The environment drives population-based genome variation. From this vantage point, the genome is modeled as a complex, dynamic information system defined by patterns of SNP alleles and SNP haplotypes.
文摘The human genome is a complex, dynamic information system that encodes principles of life and living systems. These principles are incorporated in the structure of human genome sequence variation and are foundational for the continuity of life and human survival. Using first principles of thermodynamics and statistical physics, we have developed analogous “genodynamic tools” for population genomic studies. Characterizing genomic information through the lens of physics has allowed us to develop energy measures for modeling genome-environment interactions. In developing biophysical parameters for genome-environment homeostasis, we found that stable genomic free energy trades off low genomic energy (genomic conservation and increased order) and high genomic entropy (genomic variation) with an environmental potential that drives the variation. In our approach, we assert that common variants are dynamic sites in the genome of a population and that the stability of whole genome adaptation is reflected in the frequencies of maintained diversity in common variants for the population in its environment. In this paper, we address the relativity of whole genome adaptation towards homeostasis. By this we mean that adaptive forces are directly reflected in the frequency distribution of alleles and/or haplotypes of the population relative to its environment, with adaptive forces driving the genome towards homeostasis. The use of genomic energy units as a biophysical metric in DNA sequence variation analyses provides new insights into the foundations of population biology and diversity. Using our biophysical tools, population differences directly reflect the adaptive influences of the environment on populations.
文摘As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaptation that optimizes population survival in differing environments. This paper mathematically models environmentally induced adaptive forces that quantify changes in the distribution of SNP frequencies between populations. We make direct connections between biophysical methods (e.g. minimizing genomic free energy) and concepts in population genetics. Our unbiased computer program scanned a large set of SNPs in the major histocompatibility complex region and flagged an altitude dependency on a SNP associated with response to oxygen deprivation. The statistical power of our double-blind approach is demonstrated in the flagging of mathematical functional correlations of SNP information-based potentials in multiple populations with specific environmental parameters. Furthermore, our approach provides insights for new discoveries on the biology of common variants. This paper demonstrates the power of biophysical modeling of population diversity for better understanding genome-environment interactions in biological phenomenon.
文摘Posttraumatic stress disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event. Multiple environmental and genetic factors can contribute to PTSD susceptibility. Since it is rare to find members of the same family afflicted by the same catastrophic event, it is not practical to determine PTSD susceptibility genes by a gene linkage analysis. A natural disaster, such as the 2004 Tsunami, provided us with a rare chance for a genetic analysis of PTSD. To identify SNPs associated with PTSD susceptibility, we conducted a genome-association study (GWAS) in Thai-Tsunami survivors. Initial phase of the study with 396 chronic PTSD patients and 457 controls, we identified top ninety SNPs (P -4), which were further assessed in the second phase with 395 chronic PTSD patients and 798 controls. Two SNPs (rs267950 and rs954406), were identified in the second phase, and subjected to fine mapping using a data set from both phases. SNP rs267943 showed the strongest association with PTSD susceptibility and was in complete linkage disequilibrium with SNP rs267950 with P = 6.15 × 10-8, OR = 1.46 and 95% CI = 1.19 - 1.79, reaching genome-wide significance. SNP rs267943 is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and, when linked to a synthetic promoter, could regulate transcription. To our knowledge, this is the first GWAS for PTSD susceptibility in an Asian population which could provide an important insight into the genetic contribution of PTSD and may lead to new treatment strategies for PTSD.
基金supported by the National Natural Science Foundation of China(31822048)Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB17)。
文摘A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.
基金financially supported by the National Natural Science Foundation of China(Nos.52275290 and 51905222)Natural Science Foundation of Jiangsu Province(No.BK20211068)+2 种基金Research Project of State Key Laboratory of Mechanical System and Vibration(No.MSV202419)Major Program of the National Natural Science Foundation of China for Basic Theory and Key Technology of Tri-Co Robots(No.92248301)the Opening Project of the Key Laboratory of Bionic Engineering(Ministry of Education),Jilin University(No.KF2023006)。
文摘In the event of the ever-increasing growth of the beauty industry and the burgeoning market for facial masks,high-performance and high-safety mask products have emerged.Among these,light-cured collagen peptide-based hydrogels,which are non-toxic,photocurable natural materials,exhibit significant potential for use in facial masks.We developed a novel collagen peptide-lithium chloride hydrogel-based facial mask.Light-cured collagen peptide hydrogel is a non-toxic,light-activated natural material that holds considerable promise for application in facial masks.Nonetheless,there is a significant lack of effective methodologies for real-time assessment of skin quality currently available in the market.To address this deficiency,we have developed an innovative collagen peptide-lithium chloride hydrogel mask,which is characterized by exceptional transparency(98%within the visible spectrum of 400-800 nm),commendable tensile properties(tensile strength of 428.6±2.1 kPa,with a tensile strength increase of 123.9%),substantial water retention capacity(61%),and favorable antimicrobial efficacy(89%).The incorporation of lithium chloride enhances ionic conduction at the interface between the human body and hydrogel,thereby enabling quantitative evaluation of skin quality through impedance analysis.Our collagen peptide-lithium chloride hydrogel facial mask demonstrated effectiveness in distinguishing various skin types,including D+(severely dry),D(mildly to moderately dry),N(moderate),O(mildly to moderately oily),and O+(severely oily).This study presents significant opportunities for the advancement of hydrogel masks and provides a new application platform for polymer hydrogels.
