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.
16S.
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.
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 repleta species group O'Grady et al. 2002.
Cytochrome oxidase I (COI).
These primers were suggested by Greg Spicer, based on his work in the virilis species group. We used them to infer phylogeny in the saltans and obscura groups (O'Grady et al. 1998; O'Grady 1999).
Cytochrome oxidase II (COII).
These primers, originally published in Beckenbach et al. (1993), 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.
tLEU: 5' ATGGCAGATTAGTGCAATGG 3'
tLYS: 5' GTTTAAGAGACCAGTACTTG 3'
Information on phylogenetic analysis of previously published mitochonridal genes (cytb, ND5, 16S, and ND1) can also be found in O'Grady (1999).
Other sets of mitochondrial primers, named based on their position in the Drosophila yakuba full 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'
WORKING PRIMER LIST. THESE SEQUENCES NEED TO BE CHECKED AND VERIFIED BEFORE USE. CONTACT ME BEFORE ORDERING!
TM-J-192 AGCTATTGGGTTCAGACCCC
F565 ATTAAAAAGAGGAGCCGC
N2-N-732 GAAGTTTGGTTTAAACCTCC
R984 AAAATGGAGGTAATCCACC
F996 TTTATCTTTAGGTGGATTACCTC
L1091 CTGGGATTAGATACCCCACTAT
MT-F-1402 CAGYTTRATATCATTATTGAC
R1445 GTGGCTGAAGTTTAGGCG
F2077 CTTTACCAGTTCTTGCCG
MT-R-2100 TAAWARTATAGTAATAGCTCC
F2183 CAACATTTATTTTGATTTTTTGG
C1-N-2191 CCCGGTAAAATTAAAATATAAACTTC
C1-J-2195 TGATTTTTTGGTCAYCCWGAAGT
F2273 GGTAAAAAGGAAACTTTCGG
R2511 CCTGTTAATCCTCCTACTGTG
R2659 GTCAATCCAGTAAATAATGG
C1-N-2659 GCTAATCCWGTWARTAATGG
C1-N-2659 GCTAATCCAGTGAATAATGG
R2779 GGGTAATCTGAATAACGTCG
COIIA ATGGCAGATTAGTGCAATGG
COIIA-J-3041 CCATTGCACTAATCTGCCAT
COIIB GTTTAAGAGACCAGTACTTG
COIIB-N-3791 GTTTAAGAGACCAGTACTTG
C2-J-3696 GAAATTTGYGGRGCWAATCATAG
C2-J-3696 GAAATTTGYGGRGCWAATCATAG
F4103 TCTGTATTTGACCCTTCAGC
H4178 GAGGGTGACGGGCGGTGTGT
A8-N-4318 CCATTATGWCCWGAAGGTCC
A8-N-4318 CCATTATGWCCWGAAGGTCC
F4462 TTTGCTCACTTAGTACCTCAAG
MT-F-4585 CGATTAACAGCTAATATAATTGC
R4773 GGTCATGGGCTATAATCAAC
F4930 GATGACGAGATGTTTCACG
MT-R-5025 AATAAATAAAATTATTCCTCATCG
MT-F-5030 GTAACWATTGGWTTACGATGAGG
F5490 TTCWAAAAATCATCATTTTGG
MT-R-5530 AATTGWRATATATAAAAATAATC
R5574 AATAGACCTTATGATTGGAAGTC
C3-J-5778 TGAATGYGGRTTTGAYCC
R5860 CYRATTAAAAAAAATCGTAATG
F5952 GAATGAAATCAAGGTATATTA
N3-N6213 CAGTGATAYRCCTCTYTTTGG
R6562 GATCAAGGTTGGTCAGAA
F6579 TTCTGACCAACCTTGATC
R6882 GAAAGTTGAGTAATACTTCGGG
F6903 CCCGAAGTATTACTCAACTTTC
F7170 TCAACCCTCCTATTAACCG
F7371 CTCAAAATTAGCCCCCAG
R7490 TGTCTCTGCTTTAGTCCATTC
F7707 CAAGAAGAAGAGCTACATCTCC
R7788 GGTGAGATGGATTAGGACTTG
F7809 GTCCTAATCCATCTCACCC
R8299 AGAAGAGGTAAAATTCGGG
F8397 AGTATAGGCTGCTCTAAAGAAAG
R8484 GCTAATATAGCAGCTCCTCC
R8484 GCTAATATAGCAGCTCCTCC
F8502 GTTGGAGGAGCTGCTATATTAG
R8718 GCATATTCATCAGTTGCTCA
R8737 TGAGCAACTGATGAATATGC
R8913 GAAGCTCCTGTATCTGGTTC
F8932 GAACCAGATACAGGAGCTTC
R9158 AGGATGAGGTTATCAACCG
R9593 GTTTCTATAATTCGTACTCATGG
F9656 CCTAAAGCTCCTTCACATACTC
R10050 AATCCTAAAGCTAATGGGTG
F10612 CCAATTAATATTTCAAGATGATGAAA
R10920 TCCTCAAAATGATATTTGTCCTCA
F11338 CACATTCAACCAGAATGATATTT
CB-J-11633 GCYCGACCAGTWGAAGAMCC
R11683 AAATTCTATCTTATGTTTTCAAAAC
N1-N-12158 GATTTTGCWGAAGDGAATCWGA
F12248 AAGCTAATCTAACTTGATAAG
R12595 GTAGCTTTTTTAACTTTATTAGAACG
F12945 GCGACCTCGATGTTGGATTAA
R13398 CGCCTGTTTAACAAAAACAT
F13417 ATGTTTTTGTTAAACAGGCG
L14841 CAACATCTCAGCATGATGAAA
R14922 AAGTTTTATTTTGGCTTA
H15149 CTTTCAGAATGATATTTGTCCTCA
DeSalle92(7) CAAAAATAATGTTCGCCTGT
VF TACATAACACGAGAAGACC
VR GTGATTGCGCTGTTATCC
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