Which of the following statements correctly describes the impact of repetitive regions on genome assembly?

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BlackTom AI · Accepted Answer

Examining the statements about repetitive regions in genome assembly requires separating accurate claims from common misconceptions.
Option 1: 'Repetitive regions are always perfectly resolved in genome assemblies, regardless of the sequencing technology or assembly algorithm used.' This is incorrect. In reality, repetitive sequences are a major challenge for assembly, and accuracy depends on read length, coverage, and algorithm; repeats are often collapsed or misassembled rather than perfectly resolved.
Option 2: 'There is only one bioinformatics method available for resolving repetitive regions during genome assembly.' This is false. Numerous approaches exist to handle repeats, including long-read sequencing, optical mapping, scaffolding with Hi-C data, and various assembly algorithms tailored to repeats, making the notion of a single method inaccurate.
Option 3: 'Extra copies of repetitive regions are frequently added to the reconstructed genome during assembly, resulting in an artificially inflated genome size.' While incorrect in general practice, this statement describes a specific error type (over-assembly) that can occur in some cases, but it is not the predominant or defining outcome of repetitive regions across assemblies, and it contradicts the common outcome of underrepresentation or collapse.
Option 4: 'Repetitive regions in the genome are often underrepresented or collapsed in the assembly, leading to a shorter overall assembly length compared to the original genome.' This statement aligns with widely observed issues in genome assembly: repeats can be collapsed or omitted due to ambiguity, read lengths being insufficient to span repeats, and limitations of assembly graphs, which commonly yields a shorter assembled sequence than the true genome.
Overall, the reasoning highlights that repeats pose persistent assembly challenges, with underrepresentation or collapse being the typical consequence, while other options mischaracterize the prevalence or nature of these challenges.

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Which of the following statements correctly describes the impact of repetitive regions on genome assembly?

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