When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. What is the difference between physical and sequence gaps?

Key Concepts

Physical Gaps

Physical gaps refer to regions in a genome assembly where there is a lack of contiguous DNA sequence data. These gaps occur due to limitations in sequencing technology or coverage, resulting in sections of the genome that are not represented in the assembled sequence. They can hinder the complete understanding of the genome's structure and function.

Sequence Gaps

Sequence gaps are specific areas within a genome assembly where the nucleotide sequence is unknown or unresolved. Unlike physical gaps, which may be due to missing data, sequence gaps indicate that the assembly process could not determine the exact sequence of nucleotides in that region. This can occur due to repetitive sequences or complex genomic structures that challenge assembly algorithms.

Contigs and Scaffolds

Contigs are contiguous sequences of DNA that have been assembled from overlapping reads, representing a continuous stretch of the genome. Scaffolds, on the other hand, are larger structures that consist of multiple contigs linked together, often with gaps in between. Understanding the relationship between contigs and scaffolds is essential for interpreting genome assemblies and identifying both physical and sequence gaps.