Background:The single-molecular sequencing(SMS)is under rapid development and generating increasingly long and accurate sequences.De novo assembly of genomes from SMS sequences is a critical step for many genomic stud...Background:The single-molecular sequencing(SMS)is under rapid development and generating increasingly long and accurate sequences.De novo assembly of genomes from SMS sequences is a critical step for many genomic studies.To scale well with the developing trends of SMS,many de novo assemblers for SMS have been released.These assembly workflows can be categorized into two different kinds:the correction-and-assembly strategy and the assembly-and-correction strategy,both of which are gaining more and more attentions.Results:In this article we make a discussion on the characteristics of errors in SMS sequences・We then review the currently widely applied de novo assemblers for SMS sequences.We also describe computational methods relevant to de novo assembly,including the alignment methods and the error correction methods.Benchmarks are provided to analyze their performance on different datasets and to provide use guides on applying the computation methods.Conclusion:We make a detailed review on the latest development of de novo assembly and some relevant algorithms for SMS,including their rationales,solutions and results.Besides,we provide use guides on the algorithms based on their benchmark results.Finally we conclude the review by giving some developing trends of third generation sequencing(TGS).展开更多
Dear Editor,The completeness and accuracy of genome assemblies are crucial for ensuring the reliability of downstream analyses,including functional and evolutionary studies.With the advent of third-generation sequenci...Dear Editor,The completeness and accuracy of genome assemblies are crucial for ensuring the reliability of downstream analyses,including functional and evolutionary studies.With the advent of third-generation sequencing,the assembly of telomere-totelomere(T2T)genomes has become possible.展开更多
Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms ...Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms of species evolution,exploring gene functions,and identifying disease-related variations.However,some of the repetitive DNA sequences remain“dark materials”in the genome as they are difficult to reveal by the second-generation sequencing approaches.In recent years,breakthroughs in third-generation sequencing technologies have significantly improved the accuracy and continuity of genome assemblies,therefore,being able to resolve the“last piece of the puzzle”in the genome.展开更多
The application of heterosis is a promising approach for greatly increasing yield in soybean(Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we re...The application of heterosis is a promising approach for greatly increasing yield in soybean(Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male-sterile mutant ms-1,which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome13, based on SLAF_BSA sequencing followed by genotyping of an F_(2) population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein-coding genes, including an ortholog of the kinesin-like protein gene NACK2, named Gm Ms1. The Gm Ms1 knockout plants generated via CRISPR/Casmediated gene editing displayed a complete malesterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that Gm Ms1 could be used to create male-sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male-sterile line system to utilize heterosis in soybean.展开更多
Recent studies have decoded the human Y chromosome sequencing with predominant precision and coverage,offering promising prospects in human genetics and clinical translation.Such an achievement is facilitated by third...Recent studies have decoded the human Y chromosome sequencing with predominant precision and coverage,offering promising prospects in human genetics and clinical translation.Such an achievement is facilitated by third-generation sequencing technologies including Oxford Nanopore Technology and Pacific Biosciences,which can overcome the limitations of next-generation sequencing.In the context of digestive diseases,these advancements hold significant potential as they can help address the‘missing heritability’problem and detect various genomic variants in genetic association analyses,beyond single nucleotide polymorphisms,hoping to reveal‘major’genes for complex diseases.Besides,the completion of the Y chromosome enables research into sex-specific genetic effects on diseases and this knowledge can lead to sex-specific therapeutic targets and a better understanding of molecular mechanisms behind gender disparities.In summary,the recent decoding of the Y chromosome,coupled with third-generation sequencing,offers new opportunities to address heritability gaps,discover major disease genes and investigate sex-specific effects in digestive diseases,providing valuable insights for clinicians in delivering precise healthcare services.展开更多
文摘Background:The single-molecular sequencing(SMS)is under rapid development and generating increasingly long and accurate sequences.De novo assembly of genomes from SMS sequences is a critical step for many genomic studies.To scale well with the developing trends of SMS,many de novo assemblers for SMS have been released.These assembly workflows can be categorized into two different kinds:the correction-and-assembly strategy and the assembly-and-correction strategy,both of which are gaining more and more attentions.Results:In this article we make a discussion on the characteristics of errors in SMS sequences・We then review the currently widely applied de novo assemblers for SMS sequences.We also describe computational methods relevant to de novo assembly,including the alignment methods and the error correction methods.Benchmarks are provided to analyze their performance on different datasets and to provide use guides on applying the computation methods.Conclusion:We make a detailed review on the latest development of de novo assembly and some relevant algorithms for SMS,including their rationales,solutions and results.Besides,we provide use guides on the algorithms based on their benchmark results.Finally we conclude the review by giving some developing trends of third generation sequencing(TGS).
基金supported by the National Natural Science Foundation of China(NSFC)(no.32300475)the Science and Technology Talent Special Project of Guangxi(Gui Ke AD23026320)+1 种基金funding from the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources(SKLCUSA-b202307)the Starting Research Grant for High-level Talents from Guangxi University to L.X.
文摘Dear Editor,The completeness and accuracy of genome assemblies are crucial for ensuring the reliability of downstream analyses,including functional and evolutionary studies.With the advent of third-generation sequencing,the assembly of telomere-totelomere(T2T)genomes has become possible.
基金supported by the National Natural Science Foundation of China(32090034)Zhejiang Provincial Natural Science Foundation of China(2022XHSJJ001)+3 种基金Hangzhou City Leading Innovation and Entrepreneurship Team(TD2020004)“Pioneer”and“Leading Goose”Research and Development Program of Zhejiang(2024SSYS0033)Westlake Education FoundationWestlake Laboratory of Life Sciences and Biomedicine.
文摘Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms of species evolution,exploring gene functions,and identifying disease-related variations.However,some of the repetitive DNA sequences remain“dark materials”in the genome as they are difficult to reveal by the second-generation sequencing approaches.In recent years,breakthroughs in third-generation sequencing technologies have significantly improved the accuracy and continuity of genome assemblies,therefore,being able to resolve the“last piece of the puzzle”in the genome.
基金supported by the National Key Research and Development Program of China(2016YFD0100201)the National Natural Science Foundation of China(31771819)+1 种基金the National Natural Science Foundation of Anhui Province,China(1908085QC105)the Research Fundsfor Academic and Technological Leaders and Reserve Candidates in Anhui Province(RC312005)。
文摘The application of heterosis is a promising approach for greatly increasing yield in soybean(Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male-sterile mutant ms-1,which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome13, based on SLAF_BSA sequencing followed by genotyping of an F_(2) population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein-coding genes, including an ortholog of the kinesin-like protein gene NACK2, named Gm Ms1. The Gm Ms1 knockout plants generated via CRISPR/Casmediated gene editing displayed a complete malesterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that Gm Ms1 could be used to create male-sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male-sterile line system to utilize heterosis in soybean.
文摘Recent studies have decoded the human Y chromosome sequencing with predominant precision and coverage,offering promising prospects in human genetics and clinical translation.Such an achievement is facilitated by third-generation sequencing technologies including Oxford Nanopore Technology and Pacific Biosciences,which can overcome the limitations of next-generation sequencing.In the context of digestive diseases,these advancements hold significant potential as they can help address the‘missing heritability’problem and detect various genomic variants in genetic association analyses,beyond single nucleotide polymorphisms,hoping to reveal‘major’genes for complex diseases.Besides,the completion of the Y chromosome enables research into sex-specific genetic effects on diseases and this knowledge can lead to sex-specific therapeutic targets and a better understanding of molecular mechanisms behind gender disparities.In summary,the recent decoding of the Y chromosome,coupled with third-generation sequencing,offers new opportunities to address heritability gaps,discover major disease genes and investigate sex-specific effects in digestive diseases,providing valuable insights for clinicians in delivering precise healthcare services.
