A good general reference for mitochondrial primers in insects is Simon et al. (1994). Bonacum et al. (2001) also reported on eight sets of mitochondrial primers. Below, we include information based on our recent publications. Most oligo names are either based on the numerical position of the primers in the Drosophila yakuba genome or are a reflection of the region in which they are located (e.g., tRNA Leu is located in the transfer RNA gene for Leucine).
Cytochrome oxidase I (COI)
These primers were suggested by Greg Spicer, based on his work in theDrosophila virilis species group. We used them to infer phylogeny in thesaltans and obscura groups (O'Grady et al. 1998; O'Grady 1999). We also used this region to examine relationships among craneflies in the genusDicranomyia (Nitta and O'Grady, 2008). Primers 2183 and 3041 generate a ~850bp fragment that, when cleanly amplified, can be sequenced through. The 2640 primer is used in conjunction with 3041 if the longer fragment either fails to amplify or does not sequence cleanly.
2183: 5' CAACATTTATTTTGATTTTTTGG 3'
2640: 5' GCWGTMTTTGCTATTATAGCAGG 3'
3041: 5' TYCATTGCACTAATCTGCCATATTAG 3'
Cytochrome oxidase II (COII)
These primers, originally published in Liu and Beckenbach (1992), have been very useful for species (Oliveira et al. 2003), species group (O'Grady et al. 1998; O'Grady 1999; O'Grady and Zilversmit 2004), subgenus (O'Grady and Kidwell 2002), and genus (Remsen and O'Grady 2002; Zilversmit et al. 2002) divergences in Drosophilidae. Primers are anchored in transfer RNA genes flanking COII and are able to amplify the entire gene. We have also used this region to infer relationships among endemic Hawaiian craneflies (Limoniidae) in the genus Dicranomyia (Nitta and O'Grady 2008)
tLEU: 5' ATGGCAGATTAGTGCAATGG 3'
(this is the 3037 primer, so named because of its location in the mt genome, this is partially overlapping with and complimentary to the COI primer 3041)
tLYS: 5' GTTTAAGAGACCAGTACTTG 3'
(this is the same as 3771 or 3791 based on its location in the mt genome)
NADH Dehydrogenase 2 (ND2)
We used this region to infer relationships among endemic Hawaiian craneflies (Limoniidae) in the genus Dicranomyia (Nitta and O'Grady 2008). These primers are sometimes referred to as simply 192 and 732 based on their positions in the genome.
This region has been widely used in insect systematics. DeSalle (1992) used 16S to examine relationships across the Drosophilidae. Remsen and O'Grady (2002) and Zilversmit et al. (2002) also used this slowly evolving region of mtDNA to examine divergences among drosophilid genera. It was also useful in inferring relationships among endemic HawaiianDicranomyia.. DeSalle (1992) used a combination of primers to amplify a 905bp fragment. We have used various combinations of these original primers, depending on the taxa in which we were focusing. Most drosophilid studies use the entire 905bp fragment; our cranefly work used a smaller piece of ~500bp.
AT rich region
This region, also referred to as the D-loop has been used in many studies of closely related taxa (Simon et al. 1994). We used it to examine at recent divergences within the Drosophila mayaguana subcluster of the repletaspecies group (O'Grady et al. 2002).
page construction in progress....
Other sets of mitochondrial primers, named based on their position in the Drosophila yakuba mitochondrial genome, include the following:
N2-J-1006 5' TAGGTGGACTACCTCCATTTTYAGG 3'
C1-N-1560 5' TGTTCCTACTATTCCGGCTCA 3'
C1-J-1718 5' GGAGGATTTGGAAATTGATTAGTTCC 3'
C1-N-2191 5' CCCGGTAAAATTAAAATATAAACTTC 3'
C1-J-2183 5' CAACATTTATTTTGATTTTTTGG 3'
C1-N-2659 5' GCTAATCCAGTGAATAATGG 3'
C2-J-3696 5' GAAATTTGYGGRGCWAATCATAG 3'
A8-N-4102 5' AARTTTGTTATCATTTTC 3'
C2-J-3696 5' GAAATTTGYGGRGCWAATCATAG 3'
A8-N-4478 5' GTTGTGTATGATTAATTCAACC 3'
C3-J-5014 5' TTATTTATTKTWTCWGAAGT 3'
C3-N-5460 5' TCAACAAAGTGTCAGTATCA 3'
C3-J-5778 5' TGAATGYGGRTTTGAYCC 3'
N5-N-6708 5' GGTTCWATATGATTTATACC 3'
This is a working list of mtDNA primers that we are currently using in our lab. Some have been published before and others are modifications of existing primers. Names refer to the location in the genome and the direction, forward or reverse, of the primer. Please email me before ordering these as I may have additional information about their utility.