When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. How can physical gaps be closed?

Key Concepts

Whole-Genome Shotgun Sequencing

Whole-genome shotgun sequencing is a method used to sequence an entire genome by randomly breaking the DNA into small fragments, which are then sequenced and assembled into a complete sequence. This approach allows for the rapid generation of genomic data, but it often results in gaps due to the random nature of fragment selection and sequencing errors.

Contigs and Scaffolds

Contigs are contiguous sequences of DNA that are assembled from overlapping fragments, while scaffolds are larger structures that consist of multiple contigs linked together. In genome assembly, scaffolds help provide a framework for the genome by indicating the relative positions of contigs, but gaps may still exist between these structures that need to be addressed for a complete genome assembly.

Gap Closure Techniques

Gap closure techniques involve various strategies to fill in the physical gaps in genomic sequences. These can include using paired-end reads to bridge gaps, employing PCR amplification to target specific regions, or utilizing long-read sequencing technologies that can span larger gaps. Closing gaps is crucial for obtaining a more accurate and complete representation of the genome.