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 assembly, the main practical hurdle is distinguishing where reads originate when they come from the same or very similar sequences in multiple places in the genome.
Option a: Repetitive DNA sequences. This is the core difficulty because reads from repetitive regions can map to many locations, making it hard to determine their true origin and to assemble contigs accurately. Short reads may not span the entire repeat, increasing ambiguity and potentially causing misassemblies or gaps. This is a well-known limiting factor in assembly projects.
Option b: Coding genes. While some genes can be long or have complex exon–intron structures, coding regions are generally well conserved and unique enough to map, so they do not typically cause the greatest assembly trouble compared with repeats. However, they can be challenging if they occur within very repetitive contexts or are highly similar to paralogs, but this is not the primary difficulty described.
Option c: Untranslated regions (UTRs) of coding genes. UTRs can be variable, but they are usually not as repetitive or ambiguous as long repetitive elements. While they can contribute to assembly complexity in certain genomes, they do not usually present the main bottleneck relative to repeats.
Option d: Non-coding genes. Non-coding genes, such as RNA genes, can be short or embedded within introns, and there can be annotation challenges, but in terms of de novo assembly difficulty, repetitive content remains a bigger hurdle. Therefore, non-coding genes are less universally problematic than pervasive repeats.
Overall, the predominant obstacle across many genomes for assembling short reads arises from repetitive DNA sequences, which disrupt unique placement of reads and contig construction, more so than the other listed region types.

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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