Hi, I have a general question about DNA barcoding of plants (I just need a brief answer, not a lot of detail). I've heard/read that a combination of matK and rbcL sequences are customarily used to provide the highest resolution of classification, but even with these two, it isn't necessarily to species level. So I was wondering: Can both matK and rbcL be BLAST-ed, or do we need another method? And should you do a certain gene first, to get to e.g., family level, and then narrow it down afterwards, or can you just BLAST everything all at once?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I have found a (partial) answer to my own question, by reading a paper involving barcoding of tea samples, which I'm also interesting in doing. It seems that it was enough to confirm the presence of any plant species if even one of the primers yielded sequences with a high enough % identity to references. (Mabye over 99.5%).
Please feel free to correct me if I'm wrong, though.
-
As you have mentioned, plant DNA barcoding to the species level is rather imperfect to put it mildly. Incomplete lineage sorting and hybridization have led to the sharing of chloroplast haplotypes in many taxa. Even if you have complete chloroplast genomes species-level identification with DNA is not possible in many groups due to rampant haplotype sharing.
If you do not have very many sequences to identify and/or if the taxonomic range is small, it is probably preferable to use a cladistic approach to construct a phylogeny with closely related sequences. You could use sequences from your own custom reference library (e.g. species in your study area) or use sequences from a BLAST search. If you have a large number of sequences from a broad range of taxa you might want to use a more high-throughput method like the RDP-naive Bayesian classifier (Wang et al 2007) trained with your own custom database or some other sequence clustering method.
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
06-06-2024, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 06-07-2024, 06:58 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-07-2024, 06:58 AM
|
||
Started by seqadmin, 06-06-2024, 08:18 AM
|
0 responses
23 views
0 likes
|
Last Post
by seqadmin
06-06-2024, 08:18 AM
|
||
Started by seqadmin, 06-06-2024, 08:04 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
06-06-2024, 08:04 AM
|
||
Started by seqadmin, 06-03-2024, 06:55 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
06-03-2024, 06:55 AM
|
Comment