Our project objective is to investigate the genetic diversity of Palestinian date palm, cultivars.
- 6 primers were ordered, these primers were designed specifically for NGS analysis.
- DNA was amplified from all the date palm trees samples. For each sample 6 PCRs were performed, all amplified amplicons were grouped and labeled for the NGS sequence analysis.
- for example the first primer gives 5 different repeats as follows:
#1- 11771
ACTCTTGTGGGACTCCTTTACTAATGTTACATCAATCTCTCTCTCTCTCTCTCTCGTGGATGTGTATACGAGAGTTGTATGATGCATCCATCAAAGTTGGGGTAAAAAAGAAGGAAAGCACATTTAGGCTGTCTCTTATACACATCTCCGACCTAAATGTGCTTTCCTTCTTTTTTACCCCAACTTTGATGGATGCATCATACAACTCTCGTATACACATCCACGAGAGAGAGAGAGAGAGAGATTGATGTAACATTAGTAAAGGAGTCCCACAAGAGTCTGTCTCTTATACACATCTGACG
#2- 2273
ACTCTTGTGGGACTCCTTTACTAATGTTACATCAATCTCTCTCTCTCTCTCTCGTGGATGTGTATACGAGAGTTGTATGATGCATCCATCAAAGTTGGGGTAAAAAAGAAGGAAAGCACATTTAGGCTGTCTCTTATACACATCTCCGAGCCCTAAATGTGCTTTCCTTCTTTTTTACCCCAACTTTGATGGATGCATCATACAACTCTCGTATACACATCCACGAGAGAGAGAGAGAGAGATTGATGTAACATTAGTAAAGGAGTCCCACAAGAGTCTGTCTCTTATACACATCTGACGCT
#3- 426
ACTCTTGTGGGACTCCTTTACTAATGTTACATCAATCTCTCTCTCTCTCTCTCTCTCGTGGATGTGTATACGAGAGTTGTATGATGCATCCATCAAAGTTGGGGTAAAAAAGAAGGAAAGCACATTTAGGCTGTCTCTTATACACATCTCCCCTAAATGTGCTTTCCTTCTTTTTTACCCCAACTTTGATGGATGCATCATACAACTCTCGTATACACATCCACGAGAGAGAGAGAGAGAGAGAGATTGATGTAACATTAGTAAAGGAGTCCCACAAGAGTCTGTCTCTTATACACATCTGA
#4- 272
ACTCTTGTGGGACTCCTTTACTAATGTTACATCAATCTCTCTCTCTCTCTCGTGGATGTGTATACGAGAGTTGTATGATGCATCCATCAAAGTTGGGGTAAAAAAGAAGGAAAGCACATTTAGGCTGTCTCTTATACACATCTCCGAGCCCCCTAAATGTGCTTTCCTTCTTTTTTACCCCAACTTTGATGGATGCATCATACAACTCTCGTATACACATCCACGAGAGAGAGAGAGAGATTGATGTAACATTAGTAAAGGAGTCCCACAAGAGTCTGTCTCTTATACACATCTGACGCTGC
#5- 81
ACTCTTGTGGGACTCCTTTACTAATGTTACATCAATCTCTCTCTCTCTCTCTCTCGTGGATGTGTATACGAGAGTTGTATGATGCATCCATCAAAGTTGGGGTAAAAAGAAGGAAAGCACATTTAGGCTGTCTCTTATACACATCTCCGAGCCTAAATGTGCTTTCCTTCTTTTTACCCCAACTTTGATGGATGCATCATACAACTCTCGTATACACATCCACGAGAGAGAGAGAGAGAGAGATTGATGTAACATTAGTAAAGGAGTCCCACAAGAGTCTGTCTCTTATACACATCTGACGC
These are either:
1. showing the genetic diversity in your data palm (e.g. heterozygosity)
Are date palms diploid, tetraploid, etc? You're getting all possible allele variants from that primer set.
2. artifacts/errors/low quality reads from the sequencing protocol. You can rule out some of those issues by looking at the quality of your reads. You'd need to validate each of the sequences anyway by old-school Sanger reads and/or cloning if you are truly interested in a particular variant.
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