Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

Table 1 Properties of different classes of genetic marker in terms of their qualitative suitability for use in molecular systematics studies of helminths

Class of marker	Genetic marker	Nucleotide substitution saturation^a	Length of references in database^b	Easy alignment of sequences across wide phylogenetic range^b	Easy to design universal primers^b
Nuclear rRNA	18S rRNA	No	Mostly partial	No	Yes
Nuclear rRNA	28S rRNA	No	Mostly partial	No	Yes
Nuclear spacer	ITS1	Yes	Mostly partial	No	No
Nuclear spacer	ITS2	Yes	Mostly partial	No	No
Mt protein-coding genes	COI	No	Complete	Yes	No
	COII	No	Complete	Yes	No
	cytB	No	Complete	Yes	No
	NAD1	No	Complete	Yes	No
Mt rRNA	12S rRNA	No	Complete	Yes	Yes
Mt rRNA	16S rRNA	No	Complete	Yes	Yes

CI, Confidence interval; Iss, simple index of substitution saturation; Iss.c, critical ISS; Mt, mitochondrial; SD, standard deviation; for other abbreviations, see Abbreviation List
^aSaturation was determined based on the sequence alignment used for each group of helminths. A ‘yes’ indicates saturation, with Iss > Iss.c
^bIndicates the same properties used for molecular identification

ISSN: 1756-3305