Table 1.

Comparison of the four commonly used genome-partitioning approaches.

	Genome skimming	RNA-seq	RAD-seq	Hyb-seq
Demand for plant materials	Fresh, silica-gel dried plant tissues and specimen	Fresh plant tissues	Fresh, silica-gel dried plant tissues	Fresh, silica-gel dried plant tissues and specimen
Demand for DNA template quality	Low	High	Medium	Low
Applicable to specimen	Yes	No	No	Yes
Material for sequencing	Total genomic DNA	cDNA	Restriction fragments	Captured loci using probes
Genome data obtained	Complete plastid genome, nrDNA, partial mitochondrial genome, coding and non-coding genes	Randomly sequenced loci of vast majority of nuclear genome; coding genes	Loci with single nucleotide polymorphism (SNP) mainly from nuclear genome; coding and non-coding genes	Targeted nuclear, plastid and/or mitochondrial loci; coding and non-coding genes
Targeted loci sequenced	Yes	No	No	Yes
Identification of orthologs	Easy	Relatively easy	Difficult	Easy
Missing data among species	No	Yes	Yes	No
Taxonomic levels for phylogenetic relationships	All levels from shallow to deep	Deep levels, above intra-generic	Shallow levels, below inter-generic	All levels from shallow to deep, above intraspecific