Next Generation Sequencing involves many short sequencing reads being assembled into large contiguous sequences using computer algorithms. Which of the following types of genomic regions make this process most difficult?

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In Next Generation Sequencing, the challenge is not only about sequencing length but about how reads map back to the genome and how contigs are assembled from those mappings.
Option a: Non-coding genes. While non-coding regions can be regulatory and sometimes repetitive, the primary difficulty in assembly often lies elsewhere. Non-coding genes themselves are not inherently problematic if their sequences are unique enough, so this option overstates the difficulty posed by non-coding regions alone.
Option b: Repetitive DNA sequences. This is the core issue in genome assembly: repetitive elements like transposons, satellite repeats, and segmental duplications create many nearly identical copies. Short reads can map to multiple genomic locations, causing ambiguity in placement, breaks in contigs, and incorrect assemblies. This leads to fragmented assemblies and gaps where repeats exceed read length or are highly similar.
Option c: Coding genes. Coding regions tend to be more conserved and often lie in unique sequences, making them comparatively easier to assemble and annotate. Although some gene families have paralogs, overall coding regions are not the primary source of assembly ambiguity.
Option d: Untranslated regions (UTRs) of coding genes. UTRs can be variable and sometimes repetitive, but they are generally shorter and not as repetitive as broad classes of repetitive DNA. While they can contribute to assembly challenges, they do not represent the dominant difficulty compared with long, highly repetitive elements.
Thus, the main factor that makes assembling short reads into long contigs particularly hard is the presence of repetitive DNA sequences, which create multiple equally plausible mapping locations and disrupt unambiguous assembly.

Next Generation Sequencing involves many short sequencing reads being assembled into large contiguous sequences using computer algorithms. Which of the following types of genomic regions make this process most difficult?

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