I have sequenced tropomyosin gene using universal primers (Friesen et al. 1999) from two catfish species (Clarias macrocephalus and C. gariepinus). Eight sequences from each species were aligned. I have found that two species varied in single nucleotides and also in sequence length. I am interested in conserved sequence within and between species. Are they conserved enough to be used for further species identification if I inferred only 8 samples from 4 sampling locations? You advice is highly appreciated.
If am not mistaken the tropomyosin gene is fragment into exon and intron. The intron could help to identify species but I would say it really depends on your sequence dataset... Please add some data file. Also, you may consider mitochondrial based DNA for species identification (cox1 gene) as it is a good indicator for species identification in many species, including catfish.
Please see http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017812
note that in this paper they based their identification on a rather short sequence, but you may sequence a longer one.
You are right about trypomyosin. Please the file attached. The mismatch segments between two species are consistent across samples. I sequenced COI too, but I also interested in nDNA so that I can further distinguish their reciprocal hybrids. Thank you very much.
Thanks for your response. In the following paper, the authors used PCR-RFLP of tropomyosin for hybrid identification.
Hashimoto, D.T., Mendonça, F.F., Senhorini, J.A., Bortolozzi, J., de Oliveira, C., Foresti, F., and Porto-Foresti, F. 2010. Identification of hybrids between Neotropical fish Leporinus macrocephalus and Leporinus elongatus by PCR-RFLP and multiplex-PCR: Tools for genetic monitoring in aquaculture. Aquaculture 298(3-4): 346–349.
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