Questions: Genome Structure and Organization

Question 1

Approximately what percentage of the human genome encodes proteins?

• A. About 25%
• B. About 10%
• C. About 1.5%
• D. About 50%

Answer: (C)

Only about 1.5% of the human genome consists of protein-coding exon sequences. The remaining 98.5% includes introns, regulatory sequences, repetitive elements (transposons, SINEs, LINEs), and other noncoding sequences. This was one of the surprising findings of the Human Genome Project and highlights that understanding genomes requires looking far beyond protein-coding genes.

Question 2

A larger genome always contains more protein-coding genes than a smaller genome.

• T. True
• F. False

Answer: False

This is the C-value paradox. Genome size varies enormously across organisms (the onion genome is ~16 Gb vs. human ~3.2 Gb) but does not correlate with gene count or organism complexity. Much of the size variation comes from differences in repetitive element content, intron size, and polyploidy — not gene number. Rice has roughly 40,000 protein-coding genes despite a genome one-eighth the size of the human genome (~25,000 genes).

Question 3

Why is repetitive DNA content important to account for when assembling a genome from sequencing reads?

Model answer: Repetitive sequences create ambiguity during assembly because reads from different copies of the same repeat are nearly identical, making it impossible to determine which genomic location each read came from. This leads to collapsed repeats (multiple copies assembled as one), misjoins (reads from different locations incorrectly connected), and gaps in the assembly. Genomes with high repeat content (like maize at ~85% repetitive) are much harder to assemble than compact genomes with few repeats.

This is one of the central challenges in genome assembly. Short-read technologies struggle with repeats longer than the read length. Long-read technologies (PacBio, Oxford Nanopore) help by spanning entire repeat elements, but very long or highly similar repeats remain problematic even with long reads.