Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identif...Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.展开更多
Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge wit...Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge with complex installation,which necessitate custom coding,thereby impeding efficient data processing activities.To address this issue,Filterx,a user-friendly command line tool that written in C language,was developed that supports multi-condition filtering,based on frequency or occurrence.This tool enables users to complete the data processing tasks through a simple command line,greatly reducing both workload and data processing time.In addition,future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.展开更多
MicroRNAs(miRNAs)and short RNA fragments(18–25 nt)are crucial biomarkers in biological research and disease diagnostics.However,their accurate and rapid detection remains a challenge,largely due to their low abundanc...MicroRNAs(miRNAs)and short RNA fragments(18–25 nt)are crucial biomarkers in biological research and disease diagnostics.However,their accurate and rapid detection remains a challenge,largely due to their low abundance,short length,and sequence similarities.In this study,we report on a highly sensitive,one-step RNA O-circle amplification(ROA)assay for rapid and accurate miRNA detection.The ROA assay commences with the hybridization of a circular probe with the test RNA,followed by a linear rolling circle amplification(RCA)using dUTP.This amplification process is facilitated by U-nick reactions,which lead to an exponential amplification for readout.Under optimized conditions,assays can be completed within an hour,producing an amplification yield up to the microgram level,with a detection limit as low as 0.15 fmol(6 pM).Notably,the ROA assay requires only one step,and the results can be easily read visually,making it user-friendly.This ROA assay has proven effective in detecting various miRNAs and phage ssRNA.Overall,the ROA assay offers a user-friendly,rapid,and accurate solution for miRNA detection.展开更多
基金This work was supported by the National Key R&D Program of China(Grant No.2018YFD0502204)the Agricultural Science and Technology Innovation Program of China(Grant No.CAAS-ASTIP-2019-ISAPS)+1 种基金the Special Animal Genetic Resources Platform of National Scientific and Technical Infrastructure Center(Grant No.NSTIC TZDWZYK2019)the Sika deer Genome Project of China(Grant No.20140309016YY).
文摘Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
基金supported by grant CNTC-110202101039(JY-16)and YNTC-2022530000241008.
文摘Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge with complex installation,which necessitate custom coding,thereby impeding efficient data processing activities.To address this issue,Filterx,a user-friendly command line tool that written in C language,was developed that supports multi-condition filtering,based on frequency or occurrence.This tool enables users to complete the data processing tasks through a simple command line,greatly reducing both workload and data processing time.In addition,future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.
基金supported the National Key R&D Program of China(2019YFA0707003 and 2022YFC3400300 to J.R.)the Innovation Program of Chinese Academy of Agricultural Sciences.
文摘MicroRNAs(miRNAs)and short RNA fragments(18–25 nt)are crucial biomarkers in biological research and disease diagnostics.However,their accurate and rapid detection remains a challenge,largely due to their low abundance,short length,and sequence similarities.In this study,we report on a highly sensitive,one-step RNA O-circle amplification(ROA)assay for rapid and accurate miRNA detection.The ROA assay commences with the hybridization of a circular probe with the test RNA,followed by a linear rolling circle amplification(RCA)using dUTP.This amplification process is facilitated by U-nick reactions,which lead to an exponential amplification for readout.Under optimized conditions,assays can be completed within an hour,producing an amplification yield up to the microgram level,with a detection limit as low as 0.15 fmol(6 pM).Notably,the ROA assay requires only one step,and the results can be easily read visually,making it user-friendly.This ROA assay has proven effective in detecting various miRNAs and phage ssRNA.Overall,the ROA assay offers a user-friendly,rapid,and accurate solution for miRNA detection.
