The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of trans...The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s).展开更多
Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.frag...Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.展开更多
Bone defects caused by trauma,tumour resection,infection and congenital deformities,together with articular cartilage defects and cartilage–subchondral bone complex defects caused by trauma and degenerative diseases,...Bone defects caused by trauma,tumour resection,infection and congenital deformities,together with articular cartilage defects and cartilage–subchondral bone complex defects caused by trauma and degenerative diseases,remain great challenges for clinicians.Novel strategies utilising cell sheet technology to enhance bone and cartilage regeneration are being developed.The cell sheet technology has shown great clinical potential in regenerative medicine due to its effective preservation of cell–cell connections and extracellular matrix and its scaffold-free nature.This review will first introduce several widely used cell sheet preparation systems,including traditional approaches and recent improvements,as well as their advantages and shortcomings.Recent advances in utilising cell sheet technology to regenerate bone or cartilage defects and bone–cartilage complex defects will be reviewed.The key challenges and future research directions for the application of cell sheet technology in bone and cartilage regeneration will also be discussed.展开更多
文摘The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s).
基金This work was supported by research grants provided by the National Natural Science Foundation(31870695 and 31601785)the Project of Key Research and Development Plan(Modern Agriculture)in Jiangsu(BE2017375)+1 种基金the Selection and Breeding of Excellent Tree Species and Effective Cultivation Techniques(CX(16)1005)the Project of Osmanthus National Germplasm Bank,and the Top-notch Academic Programs Project of Jiangsu Higher Education Institutions.
文摘Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.
基金supported by the National Key Research and Development Program of China (2016YFC1102900)the National Natural Science Foundation of China (No.81620108006, No.81430012, and No.31700848)
文摘Bone defects caused by trauma,tumour resection,infection and congenital deformities,together with articular cartilage defects and cartilage–subchondral bone complex defects caused by trauma and degenerative diseases,remain great challenges for clinicians.Novel strategies utilising cell sheet technology to enhance bone and cartilage regeneration are being developed.The cell sheet technology has shown great clinical potential in regenerative medicine due to its effective preservation of cell–cell connections and extracellular matrix and its scaffold-free nature.This review will first introduce several widely used cell sheet preparation systems,including traditional approaches and recent improvements,as well as their advantages and shortcomings.Recent advances in utilising cell sheet technology to regenerate bone or cartilage defects and bone–cartilage complex defects will be reviewed.The key challenges and future research directions for the application of cell sheet technology in bone and cartilage regeneration will also be discussed.
