What makes certain genomes harder to sequence? Are there any trends among taxonomic groups?

Question

[DNAlias]

Like for example, I've heard that bird genomes are difficult to sequence because of their high degree of heterozygosity. Are there other clades known for having highly heterozygous genomes? I also know that mammalian genomes can be harder than other animals due to their large size. Are there any other trends like these?

[microfuge]

NCBI taxonomy can be potentially used to get such trends. Something like for each clade get the fraction of species with an available genome. Will try to give it a try.

Answer 1

[Mensur Dlakic]

Repetitive sequences, especially long repeats, are by far the biggest challenge. Polyploidy in some plants is a problem. Sample contamination and sequencing errors contribute as well.