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My teachers growing up told me it was impossible to decode the maize genome. But yet its been done.

Why was decoding the genome so significant, and what made it so difficult?

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If I remember correctly : it's huge and has lots of repetitive regions. It's very hard to accurately sequence repeats de novo with high fidelity. –  Thomas Ingalls Dec 24 '11 at 6:47

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The short answer is that corn genome is large and has a huge amount of duplication events. Around 80% of the genome are repeated. It's hard to assemble genomes with large amount of duplications because our sequencing technology, practically, at best can give ~500 base pairs. Figuring out the ordering of duplicated regions relies on scaffold sequences or comparative assembly to rice genome.

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Why was decoding the genome so significant? Because decoding the genome gives us a complete picture of the genetic makeup of an organism.

What made it so difficult? The repetitive sequences as mentioned by other people is a main problem. Imaging you are trying to complete a big puzzle with millions of pieces. Each piece represents a sequencing reads that we get from the experiment. If there are repetitive sequences in the genome, basically the pieces that representing these regions would look very similar (or even entirely identical). Undoubtedly, this would make the puzzle very difficult to finish. To give a scale, the maize genome is ~2.3 billion base pairs and each sequencing reads is <1,000 base pairs.

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