Table 3 Comparison between a complex genome (angiosperm) and a more simple genome (mammal), and the subsequent problems faced by RAD tag sequencing in complex genomes, adapted from Kejnovsky et al. (2009)
Complex angiosperm genome | Simple mammal genome | Difficulty for RAD tag sequencing | |
|---|---|---|---|
Occurrence of multi-gene families | Large multi-gene families common (37.4% of genes occur in families with >5 members) | Fewer, smaller multi-gene families (in humans 1.4% of genes occur in families with >5 members) | Paralog determination for studies without a reference genome. Paralog discrimination for pairwise SNP comparisons |
Genome size variation | Very large: ∼2000-fold | Relatively small: 5-fold | Larger genomes require more markers for high coverage—making studies more expensive |
Retrotransposable elements | Diverse range, varying in copy number with frequent insertions. Retroelements contribute up to 80% of the genome | Low diversity of retroelement families, with a low frequency of retorelement insertion | Restriction digest sites in different retrotransposons may be hard to analyse, and many reads will be uninformative |
Polyploidy | Frequent occurrence; all species have successive rounds of ancient polyploidization, with many having more recent events too | Absent in mammals, only one controversial report of a polyploid rodent | Discrimination of nearly identical paralogs difficult |
Recombination and translocation | Frequent recombination and chromosome translocations | Lower rates of recombination combined with small number of large translocations | Pairwise comparison between recombined genes difficult |
