21 research outputs found
Universal barcoding regions, rbcL, matK and trnH-psbA do not discriminate Cinnamomum species in Sri Lanka.
The genus Cinnamomum consists of about 250 species spread globally. Out of these, C. verum (C. zeylanicum), also known as true cinnamon or Ceylon cinnamon, has gained worldwide attention due to its culinary uses and medicinal values. Sri Lanka is the largest true cinnamon producer in the world and accounts for about 80-90% of global production. Other than the cultivated species, Sri Lankan natural vegetation is home to seven endemic wild species of the genus Cinnamomum. While these are underutilized, proper identification and characterization are essential steps in any sustainable conservation and utilization strategies. Currently, species identification is purely based on morphological traits, and intraspecific diversity has made it more challenging. In this study, all the eight Cinnamomum species found in Sri Lanka, C. capparu-coronde, C. citriodorum C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum, C. sinharajaense, and C. verum were collected in triplicates and identified using typical morphological traits. DNA extracted with the same collection was assessed with universal barcoding regions, rbcL, matK, and trnH-psbA. While no intraspecific sequence differences were observed in C. citriodorum, C. rivulorum, and C. verum, the others had polymorphic sites in one, two, or all regions assessed. Interestingly, two individuals of C. sinharajaense had identical barcodes to the cultivated species C. verum, while the other one had one variable cite in matK region and three cites in trnH-psbA reigon. Further, one C. dubium and one C. capparu-coronde accession each had identical, rbcL, and trnH-psbA sequences while those had only a single nucleotide variation observed in matK region. Overall, the phylogeny of Cinnamomum species found in Sri Lanka could not be completely resolved with DNA barcoding regions studied
Agarose gel electrophoresis of methylation specific PCR.
<p>(A), (B) and (C): samples 1 to 8. (D), (E) and (F): samples 9 to19. Top panel, non methylated PCR (Non Met PCR). Middle panel, methylated PCR (Met PCR). Bottom panel, methylated triplet primed PCR (mTP-PCR). L: l kb DNA molecular weight marker (Promega), N: Negative control (without genomic DNA).</p
Electropherograms of samples 1–8 obtained from 3’ direct triplet primed PCR followed by capillary electrophoresis.
<p>(A)- (H): samples 1 to 8. Peaks in the eletropherogram indicate the number of CGG repeats in each individual.</p
The Bayesian phylogenomic tree constructed for <i>Cinnamomum</i> species based on complete chloroplast sequences.
Posterior probability values are given next to the nodes and Ocotea porosa was set as the outgroup.</p
Seed-based assembly statistics for nine <i>Cinnamomum</i> samples.
Seed-based assembly statistics for nine Cinnamomum samples.</p
Distance matrix obtained for the ITS alignment of <i>Cinnamomum</i> samples.
Distance matrix obtained for the ITS alignment of Cinnamomum samples.</p
Nucleotide diversity of the mitochondrial genes <i>atp6</i> and <i>cox1</i> among 10 <i>Cinnamomum</i> species.
Accession numbers in the first column represent atp6 and cox1 respectively. (XLSX)</p
Distance matrix obtained for the chloroplast genome alignment of <i>Cinnamomum</i> samples.
Distance matrix obtained for the chloroplast genome alignment of Cinnamomum samples.</p
Sequence variation in two parts of the <i>ycf1</i> gene among <i>Cinnamomum</i> species.
Sequence variation in two parts of the ycf1 gene among Cinnamomum species.</p