This chapter presents a comprehensive overview of state-of-the-art technologies for gene and genome assembly, outlining their evolution from early sequencing methods to advanced approaches in synthetic biology. It begins with the fundamental principles of DNA sequencing and the computational frameworks developed for sequence data assembly, emphasizing both short-read and long-read platforms, their underlying algorithms, and applications in genomics and metagenomics. The focus then shifts to gene synthesis, detailing chemical, microarray-based, and enzyme-mediated methods for oligonucleotide production, alongside strategies for assembling these fragments into larger DNA constructs. Core assembly techniques including polymerase cycling assembly, ligase chain reaction, Gibson assembly, Golden Gate cloning, and in vivo homologous recombination are described as key enablers of large-scale DNA construction and fully synthetic genomes. The chapter highlights the interdependence of sequencing and synthesis technologies, illustrating how advances in one domain accelerate innovation in the other. Emerging trends such as high-throughput, automated gene synthesis, and the integration of long-read sequencing platforms are discussed in the context of their transformative impact on synthetic biology, biotechnology, and biosafety.

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Gene and Genome Assembly

  • Slavil Peykov,
  • Boris Kirov

摘要

This chapter presents a comprehensive overview of state-of-the-art technologies for gene and genome assembly, outlining their evolution from early sequencing methods to advanced approaches in synthetic biology. It begins with the fundamental principles of DNA sequencing and the computational frameworks developed for sequence data assembly, emphasizing both short-read and long-read platforms, their underlying algorithms, and applications in genomics and metagenomics. The focus then shifts to gene synthesis, detailing chemical, microarray-based, and enzyme-mediated methods for oligonucleotide production, alongside strategies for assembling these fragments into larger DNA constructs. Core assembly techniques including polymerase cycling assembly, ligase chain reaction, Gibson assembly, Golden Gate cloning, and in vivo homologous recombination are described as key enablers of large-scale DNA construction and fully synthetic genomes. The chapter highlights the interdependence of sequencing and synthesis technologies, illustrating how advances in one domain accelerate innovation in the other. Emerging trends such as high-throughput, automated gene synthesis, and the integration of long-read sequencing platforms are discussed in the context of their transformative impact on synthetic biology, biotechnology, and biosafety.