I am working on a final project related to DNA Barcoding using the matK gene. The sequencing results I have show a length of 1530 bp. Meanwhile, I read some literature that the ideal DNA Barcoding DNA sequence ranges from 400 - 800 bp. I have permission to ask: Can a DNA sequence with a length of 1530 bp be used for DNA Barcoding analysis? If not, what is the reason?
Please help. Thank you
Yes, you can. The matK gene is around 1500 bp, but it may be difficult to amplify and sequence the entire gene. Shorter sequences or fragments (e.g. 400-800 bp) may be generally sufficient for barcoding (species identification), but you should use the full gene sequence if you have it.
When it comes to marker genes, the bottle neck is not "how long (length) to sequence" but the problem is "how to sequence that long (length)".
If you have basic understanding of sequencing technologies and their benefits and shortfalls, you will understand this better.
So, I recommend to get that information, develop understanding and after that rethink over this question.
Dear Dr. Brenda Febrina, In DNA barcoding analysis, the use of short around 600 base pairs conserved region of the genome to identify species. The marker-related matK gene of chloroplast is 1500 base pairs long, sequencing of longer fragments becomes a very difficult job, but if you have a full-length gene sequence please use that gene for DNA barcoding analysis in plants.
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